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  • 1
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    Cancer. BRCA2 enters the fray (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, John H -- Elledge, Stephen J -- New York, N.Y. -- Science. 2002 Sep 13;297(5588):1822-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12228708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; BRCA1 Protein/metabolism ; BRCA2 Protein/*chemistry/*metabolism ; Binding Sites ; Breast Neoplasms/genetics ; Crystallography, X-Ray ; DNA/*metabolism ; DNA Damage ; *DNA Repair ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/metabolism ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Predisposition to Disease ; Humans ; Mice ; Ovarian Neoplasms/genetics ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rad51 Recombinase ; Rats ; Recombination, Genetic ; Replication Protein A
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Visualization and functional analysis of RNA-dependent RNA polymerase lattices (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-22
    Description: Positive-strand RNA viruses such as poliovirus replicate their genomes on intracellular membranes of their eukaryotic hosts. Electron microscopy has revealed that purified poliovirus RNA-dependent RNA polymerase forms planar and tubular oligomeric arrays. The structural integrity of these arrays correlates with cooperative RNA binding and RNA elongation and is sensitive to mutations that disrupt intermolecular contacts predicted by the polymerase structure. Membranous vesicles isolated from poliovirus-infected cells contain structures consistent with the presence of two-dimensional polymerase arrays on their surfaces during infection. Therefore, host cytoplasmic membranes may function as physical foundations for two-dimensional polymerase arrays, conferring the advantages of surface catalysis to viral RNA replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lyle, John M -- Bullitt, Esther -- Bienz, Kurt -- Kirkegaard, Karla -- AI-42119/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2002 Jun 21;296(5576):2218-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12077417" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Inclusion Bodies, Viral/metabolism/ultrastructure ; Microscopy, Electron ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Poliovirus/*enzymology/physiology ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA Replicase/*chemistry/isolation & purification/*metabolism/ultrastructure ; RNA, Viral/biosynthesis/*metabolism ; Viral Core Proteins/metabolism ; Virus Replication
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  • 3
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    Crystal structure of the GpIbalpha-thrombin complex essential for platelet aggregation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-12
    Description: Direct interaction between platelet receptor glycoprotein Ibalpha (GpIbalpha) and thrombin is required for platelet aggregation and activation at sites of vascular injury. Abnormal GpIbalpha-thrombin binding is associated with many pathological conditions,including occlusive arterial thrombosis and bleeding disorders. The crystal structure of the GpIbalpha-thrombin complex at 2.6 angstrom resolution reveals simultaneous interactions of GpIbalpha with exosite I of one thrombin molecule,and with exosite II of a second thrombin molecule. In the crystal lattice,the periodic arrangement of GpIbalpha-thrombin complexes mirrors a scaffold that could serve as a driving force for tight platelet adhesion. The details of these interactions reconcile GpIbalpha-thrombin binding modes that are presently controversial,highlighting two distinct interfaces that are potential targets for development of novel antithrombotic drugs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dumas, John J -- Kumar, Ravindra -- Seehra, Jasbir -- Somers, William S -- Mosyak, Lidia -- New York, N.Y. -- Science. 2003 Jul 11;301(5630):222-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Screening Sciences, Wyeth, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12855811" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Blood Platelets/chemistry/physiology ; Crystallization ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Platelet Adhesiveness ; *Platelet Aggregation ; Platelet Glycoprotein GPIb-IX Complex/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thrombin/*chemistry/*metabolism
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  • 4
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    Cylindrical channels from concave helices (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Calladine, C R -- Pratap, V -- Chandran, V -- Mizuguchi, K -- Luisi, B F -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):661-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12561825" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Escherichia coli Proteins/*chemistry ; Glycine/chemistry ; Ion Channels/*chemistry ; *Models, Molecular ; Protein Conformation ; Protein Structure, Secondary
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  • 5
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    Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-06
    Description: We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naber, Nariman -- Minehardt, Todd J -- Rice, Sarah -- Chen, Xiaoru -- Grammer, Jean -- Matuska, Marija -- Vale, Ronald D -- Kollman, Peter A -- Car, Roberto -- Yount, Ralph G -- Cooke, Roger -- Pate, Edward -- AR39643/AR/NIAMS NIH HHS/ -- AR42895/AR/NIAMS NIH HHS/ -- DK05915/DK/NIDDK NIH HHS/ -- GM29072/GM/NIGMS NIH HHS/ -- RR1081/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 May 2;300(5620):798-801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, San Francisco, CA 94143, USA. naber@itsa.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730601" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*metabolism ; Adenosine Diphosphate/analogs & derivatives/metabolism ; Adenosine Triphosphate/analogs & derivatives/metabolism ; Animals ; Binding Sites ; Computer Simulation ; Crystallography, X-Ray ; *Drosophila Proteins ; Drosophila melanogaster ; Electron Spin Resonance Spectroscopy ; Humans ; Hydrogen Bonding ; Hydrolysis ; Kinesin/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*metabolism ; Molecular Probes/metabolism ; Protein Conformation ; Spin Labels
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  • 6
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    Structural biology. Complex II is complex too (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hederstedt, Lars -- New York, N.Y. -- Science. 2003 Jan 31;299(5607):671-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden. lars.hederstedt@cob.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12560540" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Anaerobiosis ; Binding Sites ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex II ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Heme/chemistry/metabolism ; Models, Molecular ; Multienzyme Complexes/antagonists & inhibitors/*chemistry/*metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists & inhibitors/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/antagonists & inhibitors/*chemistry/*metabolism ; Succinic Acid/metabolism ; Ubiquinone/chemistry/metabolism
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  • 7
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    Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-05-10
    Description: Multidrug efflux pumps cause serious problems in cancer chemotherapy and treatment of bacterial infections. Yet high-resolution structures of ligand transporter complexes have previously been unavailable. We obtained x-ray crystallographic structures of the trimeric AcrB pump from Escherichia coli with four structurally diverse ligands. The structures show that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilizing the binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Edward W -- McDermott, Gerry -- Zgurskaya, Helen I -- Nikaido, Hiroshi -- Koshland, Daniel E Jr -- AI 09644/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2003 May 9;300(5621):976-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12738864" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Infective Agents/chemistry/metabolism ; Anti-Infective Agents, Local/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/isolation & purification/*metabolism ; Cell Membrane/chemistry ; Chemistry, Physical ; Ciprofloxacin/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Dequalinium/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/isolation & purification/*metabolism ; Ethidium/chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Membrane Proteins/*chemistry/isolation & purification/*metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins ; Physicochemical Phenomena ; Protein Binding ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Rhodamines/chemistry/metabolism ; Static Electricity
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  • 8
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    Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: The T cell receptor (TCR) inherently has dual specificity. T cells must recognize self-antigens in the thymus during maturation and then discriminate between foreign pathogens in the periphery. A molecular basis for this cross-reactivity is elucidated by the crystal structure of the alloreactive 2C TCR bound to self peptide-major histocompatibility complex (pMHC) antigen H-2Kb-dEV8 refined against anisotropic 3.0 angstrom resolution x-ray data. The interface between peptide and TCR exhibits extremely poor shape complementarity, and the TCR beta chain complementarity-determining region 3 (CDR3) has minimal interaction with the dEV8 peptide. Large conformational changes in three of the TCR CDR loops are induced upon binding, providing a mechanism of structural plasticity to accommodate a variety of different peptide antigens. Extensive TCR interaction with the pMHC alpha helices suggests a generalized orientation that is mediated by the Valpha domain of the TCR and rationalizes how TCRs can effectively "scan" different peptides bound within a large, low-affinity MHC structural framework for those that provide the slight additional kinetic stabilization required for signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, K C -- Degano, M -- Pease, L R -- Huang, M -- Peterson, P A -- Teyton, L -- Wilson, I A -- AI42266/AI/NIAID NIH HHS/ -- AI42267/AI/NIAID NIH HHS/ -- R01 CA58896/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1998 Feb 20;279(5354):1166-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9469799" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallization ; Crystallography, X-Ray ; H-2 Antigens/*chemistry/*immunology/metabolism ; Ligands ; Mice ; Mice, Transgenic ; Models, Molecular ; Mutation ; Oligopeptides/*chemistry/immunology/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/*immunology/metabolism ; Recombinant Proteins
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  • 9
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    A preorganized active site in the crystal structure of the Tetrahymena ribozyme (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-12-05
    Description: Group I introns possess a single active site that catalyzes the two sequential reactions of self-splicing. An RNA comprising the two domains of the Tetrahymena thermophila group I intron catalytic core retains activity, and the 5.0 angstrom crystal structure of this 247-nucleotide ribozyme is now described. Close packing of the two domains forms a shallow cleft capable of binding the short helix that contains the 5' splice site. The helix that provides the binding site for the guanosine substrate deviates significantly from A-form geometry, providing a tight binding pocket. The binding pockets for both the 5' splice site helix and guanosine are formed and oriented in the absence of these substrates. Thus, this large ribozyme is largely preorganized for catalysis, much like a globular protein enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Golden, B L -- Gooding, A R -- Podell, E R -- Cech, T R -- New York, N.Y. -- Science. 1998 Oct 9;282(5387):259-64.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA. bgolden@petunia.colorado.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9841391" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; Base Sequence ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Guanosine/metabolism ; Introns ; Magnesium/metabolism ; Manganese/metabolism ; *Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phosphates/metabolism ; RNA Splicing ; RNA, Catalytic/*chemistry/metabolism ; Tetrahymena thermophila/*genetics
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  • 10
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    Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-10
    Description: The 2.5 angstrom resolution x-ray crystal structure of the Escherichia coli RNA polymerase (RNAP) alpha subunit amino-terminal domain (alphaNTD), which is necessary and sufficient to dimerize and assemble the other RNAP subunits into a transcriptionally active enzyme and contains all of the sequence elements conserved among eukaryotic alpha homologs, has been determined. The alphaNTD monomer comprises two distinct, flexibly linked domains, only one of which participates in the dimer interface. In the alphaNTD dimer, a pair of helices from one monomer interact with the cognate helices of the other to form an extensive hydrophobic core. All of the determinants for interactions with the other RNAP subunits lie on one face of the alphaNTD dimer. Sequence alignments, combined with secondary-structure predictions, support proposals that a heterodimer of the eukaryotic RNAP subunits related to Saccharomyces cerevisiae Rpb3 and Rpb11 plays the role of the alphaNTD dimer in prokaryotic RNAP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, G -- Darst, S A -- GM19441-01/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 10;281(5374):262-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9657722" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; DNA-Directed RNA Polymerases/*chemistry ; Dimerization ; Escherichia coli/*enzymology ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA Polymerase II/chemistry ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment
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  • 11
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    Biological hydrogen production: not so elementary (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adams, M W -- Stiefel, E I -- New York, N.Y. -- Science. 1998 Dec 4;282(5395):1842-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. adams@bmb.uga.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9874636" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Carbon Monoxide/chemistry ; Clostridium/*enzymology ; Crystallography, X-Ray ; Cyanides/chemistry ; Humans ; Hydrogen/*metabolism ; Hydrogenase/*chemistry/*metabolism ; Iron/chemistry ; Ligands ; Oxidation-Reduction ; Pyruvic Acid/metabolism
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  • 12
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    A model for the mechanism of human topoisomerase I (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22-base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of the enzyme that contact DNA. The linker region that connects the central core of the enzyme to the carboxyl-terminal domain assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme. The positively charged DNA-proximal surface of the linker makes only a few contacts with the DNA downstream of the cleavage site. In combination with the crystal structures of the reconstituted human topoisomerase I before and after DNA cleavage, this information suggests which amino acid residues are involved in catalyzing phosphodiester bond breakage and religation. The structures also lead to the proposal that the topoisomerization step occurs by a mechanism termed "controlled rotation."〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stewart, L -- Redinbo, M R -- Qiu, X -- Hol, W G -- Champoux, J J -- CA65656/CA/NCI NIH HHS/ -- GM16713/GM/NIGMS NIH HHS/ -- GM49156/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Mar 6;279(5356):1534-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Structure Center and Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195-7742, USA. emerald_biostructures@rocketmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9488652" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Topoisomerases, Type I/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; *Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Tyrosine/chemistry/metabolism
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  • 13
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    Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-04-16
    Description: Photoactive yellow protein (PYP) is a member of the xanthopsin family of eubacterial blue-light photoreceptors. On absorption of light, PYP enters a photocycle that ultimately transduces the energy contained in a light signal into an altered biological response. Nanosecond time-resolved x-ray crystallography was used to determine the structure of the short-lived, red-shifted, intermediate state denoted [pR], which develops within 1 nanosecond after photoelectronic excitation of the chromophore of PYP by absorption of light. The resulting structural model demonstrates that the [pR] state possesses the cis conformation of the 4-hydroxyl cinnamic thioester chromophore, and that the process of trans to cis isomerization is accompanied by the specific formation of new hydrogen bonds that replace those broken upon excitation of the chromophore. Regions of flexibility that compose the chromophore-binding pocket serve to lower the activation energy barrier between the dark state, denoted pG, and [pR], and help initiate entrance into the photocycle. Direct structural evidence is provided for the initial processes of transduction of light energy, which ultimately translate into a physiological signal.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perman, B -- Srajer, V -- Ren, Z -- Teng, T -- Pradervand, C -- Ursby, T -- Bourgeois, D -- Schotte, F -- Wulff, M -- Kort, R -- Hellingwerf, K -- Moffat, K -- New York, N.Y. -- Science. 1998 Mar 20;279(5358):1946-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9506946" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/metabolism ; Chromatiaceae/chemistry ; Crystallography, X-Ray ; Energy Metabolism ; Fourier Analysis ; Hydrogen Bonding ; Isomerism ; Kinetics ; *Light ; Models, Molecular ; *Photoreceptors, Microbial ; *Protein Conformation ; Signal Transduction
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  • 14
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    Taking a structured approach to understanding proteins (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1998 Feb 13;279(5353):978-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9490484" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Databases, Factual ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry/classification/genetics ; Software
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    Structure of key cytoskeletal protein tubulin revealed (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-01-31
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1998 Jan 9;279(5348):176-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9446222" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry ; Binding Sites ; Cell Division ; Crystallization ; Crystallography/*methods ; Crystallography, X-Ray ; *Cytoskeletal Proteins ; GTP-Binding Proteins/chemistry ; Guanosine Triphosphate/metabolism ; Microtubules/chemistry ; Models, Molecular ; *Protein Conformation ; Protein Structure, Secondary ; Tubulin/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 16
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    Crystal structure of invasin: a bacterial integrin-binding protein (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: The Yersinia pseudotuberculosis invasin protein promotes bacterial entry by binding to host cell integrins with higher affinity than natural substrates such as fibronectin. The 2.3 angstrom crystal structure of the invasin extracellular region reveals five domains that form a 180 angstrom rod with structural similarities to tandem fibronectin type III domains. The integrin-binding surfaces of invasin and fibronectin include similarly located key residues, but in the context of different folds and surface shapes. The structures of invasin and fibronectin provide an example of convergent evolution, in which invasin presents an optimized surface for integrin binding, in comparison with host substrates.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamburger, Z A -- Brown, M S -- Isberg, R R -- Bjorkman, P J -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):291-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 156-29, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514372" target="_blank"〉PubMed〈/a〉
    Keywords: *Adhesins, Bacterial ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Evolution, Molecular ; Fibronectins/chemistry/metabolism ; Hydrogen Bonding ; Integrins/*metabolism ; Ligands ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Yersinia pseudotuberculosis/*chemistry/metabolism
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  • 17
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    Visualization of dioxygen bound to copper during enzyme catalysis (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-27
    Description: X-ray crystal structures of three species related to the oxidative half of the reaction of the copper-containing quinoprotein amine oxidase from Escherichia coli have been determined. Crystals were freeze-trapped either anaerobically or aerobically after exposure to substrate, and structures were determined to resolutions between 2.1 and 2.4 angstroms. The oxidation state of the quinone cofactor was investigated by single-crystal spectrophotometry. The structures reveal the site of bound dioxygen and the proton transfer pathways involved in oxygen reduction. The quinone cofactor is regenerated from the iminoquinone intermediate by hydrolysis involving Asp383, the catalytic base in the reductive half-reaction. Product aldehyde inhibits the hydrolysis, making release of product the rate-determining step of the reaction in the crystal.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilmot, C M -- Hajdu, J -- McPherson, M J -- Knowles, P F -- Phillips, S E -- New York, N.Y. -- Science. 1999 Nov 26;286(5445):1724-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10576737" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amine Oxidase (Copper-Containing)/*chemistry/*metabolism ; Anaerobiosis ; Aspartic Acid/chemistry/metabolism ; Binding Sites ; Catalysis ; Copper/*metabolism ; Crystallography, X-Ray ; Dihydroxyphenylalanine/*analogs & derivatives/chemistry/metabolism ; Dimerization ; Electrons ; Escherichia coli/enzymology ; Hydrogen Bonding ; Nitric Oxide/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Phenethylamines/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Spectrum Analysis
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  • 18
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    Identification of an RNA-protein bridge spanning the ribosomal subunit interface (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-09-25
    Description: The 7.8 angstrom crystal structure of the 70S ribosome reveals a discrete double-helical bridge (B4) that projects from the 50S subunit, making contact with the 30S subunit. Preliminary modeling studies localized its contact site, near the bottom of the platform, to the binding site for ribosomal protein S15. Directed hydroxyl radical probing from iron(II) tethered to S15 specifically cleaved nucleotides in the 715 loop of domain II of 23S ribosomal RNA, one of the known sites in 23S ribosomal RNA that are footprinted by the 30S subunit. Reconstitution studies show that protection of the 715 loop, but none of the other 30S-dependent protections, is correlated with the presence of S15 in the 30S subunit. The 715 loop is specifically protected by binding free S15 to 50S subunits. Moreover, the previously determined structure of a homologous stem-loop from U2 small nuclear RNA fits closely to the electron density of the bridge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Culver, G M -- Cate, J H -- Yusupova, G Z -- Yusupov, M M -- Noller, H F -- 1F32GM18065-01/GM/NIGMS NIH HHS/ -- GM-17129/GM/NIGMS NIH HHS/ -- GM-59140/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Sep 24;285(5436):2133-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10497132" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/chemistry ; Hydroxyl Radical ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Bacterial/*chemistry/metabolism ; RNA, Ribosomal, 23S/*chemistry/metabolism ; RNA, Small Nuclear/chemistry/metabolism ; Ribosomal Proteins/chemistry/*metabolism ; Ribosomes/*chemistry/metabolism/ultrastructure ; Thermus thermophilus/chemistry
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  • 19
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    Perspectives: protein structure. Class-conscious TCR? (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, I A -- New York, N.Y. -- Science. 1999 Dec 3;286(5446):1867-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. wilson@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10610577" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens/*chemistry/immunology/metabolism ; Binding Sites ; CD4-Positive T-Lymphocytes/immunology/metabolism ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Crystallography, X-Ray ; Histocompatibility Antigens Class I/chemistry/immunology/metabolism ; Histocompatibility Antigens Class II/*chemistry/immunology/metabolism ; Mice ; Models, Molecular ; Peptides/chemistry/immunology/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell, alpha-beta/*chemistry/immunology/metabolism
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  • 20
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    Function is structure (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liljas, A -- New York, N.Y. -- Science. 1999 Sep 24;285(5436):2077-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Center for Chemistry and Chemical Engineering, University of Lund, Lund, Sweden. anders.liljas@mbfys.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10523206" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/biosynthesis/chemistry ; Binding Sites ; Codon ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Nucleic Acid Conformation ; Peptide Elongation Factors/metabolism ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal/chemistry ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/chemistry ; Ribosomes/*chemistry/*physiology/ultrastructure
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  • 21
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    Respiration without O2 (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hederstedt, L -- New York, N.Y. -- Science. 1999 Jun 18;284(5422):1941-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Lund University, Lund, Sweden. Lars.Hederstedt@mikrbiol.lu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10400536" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Bacillus subtilis/enzymology ; Binding Sites ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; *Energy Metabolism ; Escherichia coli/*enzymology ; Evolution, Molecular ; Fumarates/metabolism ; Mitochondria/enzymology ; Oxidation-Reduction ; Oxygen Consumption ; Protein Conformation ; Protein Structure, Secondary ; Succinate Dehydrogenase/*chemistry/*metabolism ; Succinic Acid/metabolism
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  • 22
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    Evolution of shape complementarity and catalytic efficiency from a primordial antibody template (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-22
    Description: The crystal structure of an efficient Diels-Alder antibody catalyst at 1.9 angstrom resolution reveals almost perfect shape complementarity with its transition state analog. Comparison with highly related progesterone and Diels-Alderase antibodies that arose from the same primordial germ line template shows the relatively subtle mutational steps that were able to evolve both structural complementarity and catalytic efficiency.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, J -- Deng, Q -- Chen, J -- Houk, K N -- Bartek, J -- Hilvert, D -- Wilson, I A -- CA27489/CA/NCI NIH HHS/ -- GM38273/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2345-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600746" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Catalytic/*chemistry/genetics/*metabolism ; Binding Sites, Antibody ; Catalysis ; Chemistry, Physical ; Crystallography, X-Ray ; *Evolution, Molecular ; Haptens/chemistry/metabolism ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/chemistry/metabolism ; Ligands ; Models, Molecular ; Mutation ; Physicochemical Phenomena ; Progesterone/immunology ; Protein Conformation ; Solubility ; Temperature ; Templates, Genetic
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  • 23
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    Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: Isoleucyl-transfer RNA (tRNA) synthetase (IleRS) joins Ile to tRNA(Ile) at its synthetic active site and hydrolyzes incorrectly acylated amino acids at its editing active site. The 2.2 angstrom resolution crystal structure of Staphylococcus aureus IleRS complexed with tRNA(Ile) and Mupirocin shows the acceptor strand of the tRNA(Ile) in the continuously stacked, A-form conformation with the 3' terminal nucleotide in the editing active site. To position the 3' terminus in the synthetic active site, the acceptor strand must adopt the hairpinned conformation seen in tRNA(Gln) complexed with its synthetase. The amino acid editing activity of the IleRS may result from the incorrect products shuttling between the synthetic and editing active sites, which is reminiscent of the editing mechanism of DNA polymerases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Silvian, L F -- Wang, J -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1074-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446055" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Adenosine Monophosphate/analogs & derivatives/metabolism ; Amino Acids/metabolism ; Binding Sites ; Crystallography, X-Ray ; DNA-Directed DNA Polymerase/metabolism ; Glutamate-tRNA Ligase/chemistry/metabolism ; Isoleucine/metabolism ; Isoleucine-tRNA Ligase/*chemistry/*metabolism ; Models, Molecular ; Mupirocin/chemistry/*metabolism ; Nucleic Acid Conformation ; Oligopeptides/metabolism ; Protein Conformation ; Protein Structure, Secondary ; RNA, Transfer, Gln/chemistry/metabolism ; RNA, Transfer, Ile/*chemistry/*metabolism ; Staphylococcus aureus/enzymology ; Substrate Specificity
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  • 24
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    Crystallographic evidence for preformed dimers of erythropoietin receptor before ligand activation (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-02-12
    Description: Erythropoietin receptor (EPOR) is thought to be activated by ligand-induced homodimerization. However, structures of agonist and antagonist peptide complexes of EPOR, as well as an EPO-EPOR complex, have shown that the actual dimer configuration is critical for the biological response and signal efficiency. The crystal structure of the extracellular domain of EPOR in its unliganded form at 2.4 angstrom resolution has revealed a dimer in which the individual membrane-spanning and intracellular domains would be too far apart to permit phosphorylation by JAK2. This unliganded EPOR dimer is formed from self-association of the same key binding site residues that interact with EPO-mimetic peptide and EPO ligands. This model for a preformed dimer on the cell surface provides insights into the organization, activation, and plasticity of recognition of hematopoietic cell surface receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Livnah, O -- Stura, E A -- Middleton, S A -- Johnson, D L -- Jolliffe, L K -- Wilson, I A -- GM49497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Feb 12;283(5404):987-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9974392" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Membrane/chemistry ; Crystallography, X-Ray ; Dimerization ; Erythropoietin/metabolism ; Humans ; Hydrogen Bonding ; Janus Kinase 2 ; Ligands ; Models, Molecular ; Peptide Fragments/*chemistry/metabolism ; Peptides, Cyclic/metabolism ; Protein Conformation ; Protein-Tyrosine Kinases/metabolism ; *Proto-Oncogene Proteins ; Receptors, Erythropoietin/*chemistry/metabolism
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  • 25
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    Structure of the VHL-ElonginC-ElonginB complex: implications for VHL tumor suppressor function (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-16
    Description: Mutation of the VHL tumor suppressor is associated with the inherited von Hippel-Lindau (VHL) cancer syndrome and the majority of kidney cancers. VHL binds the ElonginC-ElonginB complex and regulates levels of hypoxia-inducible proteins. The structure of the ternary complex at 2.7 angstrom resolution shows two interfaces, one between VHL and ElonginC and another between ElonginC and ElonginB. Tumorigenic mutations frequently occur in a 35-residue domain of VHL responsible for ElonginC binding. A mutational patch on a separate domain of VHL indicates a second macromolecular binding site. The structure extends the similarities to the SCF (Skp1-Cul1-F-box protein) complex that targets proteins for degradation, supporting the hypothesis that VHL may function in an analogous pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stebbins, C E -- Kaelin, W G Jr -- Pavletich, N P -- New York, N.Y. -- Science. 1999 Apr 16;284(5413):455-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Structural Biology, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10205047" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Cycle Proteins/chemistry/metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; *Genes, Tumor Suppressor ; Humans ; Hydrogen Bonding ; *Ligases ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mutation, Missense ; Neoplasms/genetics ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/metabolism ; S-Phase Kinase-Associated Proteins ; Surface Properties ; Transcription Factors/*chemistry/metabolism ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Von Hippel-Lindau Tumor Suppressor Protein ; von Hippel-Lindau Disease/*genetics
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  • 26
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    Space-grown neuraminidase crystals (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeLucas, L J -- New York, N.Y. -- Science. 1999 Jun 4;284(5420):1621.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10383336" target="_blank"〉PubMed〈/a〉
    Keywords: Cryopreservation ; Crystallization ; Crystallography, X-Ray ; Drug Design ; Drug Industry ; Enzyme Inhibitors ; Neuraminidase/antagonists & inhibitors/*chemistry ; *Spacecraft ; United States ; United States National Aeronautics and Space Administration ; *Weightlessness
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  • 27
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    Molecular architecture of the rotary motor in ATP synthase (1999)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 1999-11-27
    Description: Adenosine triphosphate (ATP) synthase contains a rotary motor involved in biological energy conversion. Its membrane-embedded F0 sector has a rotation generator fueled by the proton-motive force, which provides the energy required for the synthesis of ATP by the F1 domain. An electron density map obtained from crystals of a subcomplex of yeast mitochondrial ATP synthase shows a ring of 10 c subunits. Each c subunit forms an alpha-helical hairpin. The interhelical loops of six to seven of the c subunits are in close contact with the gamma and delta subunits of the central stalk. The extensive contact between the c ring and the stalk suggests that they may rotate as an ensemble during catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stock, D -- Leslie, A G -- Walker, J E -- New York, N.Y. -- Science. 1999 Nov 26;286(5445):1700-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10576729" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Mitochondria/enzymology ; Models, Molecular ; Molecular Motor Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proton-Motive Force ; Proton-Translocating ATPases/*chemistry/metabolism ; Protons ; Saccharomyces cerevisiae/enzymology
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  • 28
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    X-ray crystallographic structure of the Norwalk virus capsid (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: Norwalk virus, a noncultivatable human calicivirus, is the major cause of epidemic gastroenteritis in humans. The first x-ray structure of a calicivirus capsid, which consists of 180 copies of a single protein, has been determined by phase extension from a low-resolution electron microscopy structure. The capsid protein has a protruding (P) domain connected by a flexible hinge to a shell (S) domain that has a classical eight-stranded beta-sandwich motif. The structure of the P domain is unlike that of any other viral protein with a subdomain exhibiting a fold similar to that of the second domain in the eukaryotic translation elongation factor-Tu. This subdomain, located at the exterior of the capsid, has the largest sequence variation among Norwalk-like human caliciviruses and is likely to contain the determinants of strain specificity and cell binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prasad, B V -- Hardy, M E -- Dokland, T -- Bella, J -- Rossmann, M G -- Estes, M K -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):287-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Marrs Mclean Department of Biochemistry, Division of Molecular Virology, Baylor College of Medicine, Houston, TX 77030, USA. bprasad@bcm.tmc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514371" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Capsid/*chemistry/metabolism ; *Capsid Proteins ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Dimerization ; Genome, Viral ; Humans ; Hydrogen Bonding ; Image Processing, Computer-Assisted ; Models, Molecular ; Molecular Sequence Data ; Norwalk virus/*chemistry/genetics/physiology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Virus Assembly
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    A structural model of transcription elongation (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-01
    Description: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzheva, N -- Mustaev, A -- Kozlov, M -- Malhotra, A -- Nikiforov, V -- Goldfarb, A -- Darst, S A -- GM30717/GM/NIGMS NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- GM53759/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):619-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Public Health Research Institute, 455 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10915625" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; DNA Primers ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Oligodeoxyribonucleotides/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
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    Crystal structure of a gammadelta T cell receptor ligand T22: a truncated MHC-like fold (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-15
    Description: Murine T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. The crystal structure of T22b at 3.1 angstroms reveals similarities to MHC class I molecules, but one side of the normal peptide-binding groove is severely truncated, which allows direct access to the beta-sheet floor. Potential gammadelta TCR-binding sites can be inferred from functional mapping of T10 and T22 point mutants and allelic variants. Thus, T22 represents an unusual variant of the MHC-like fold and indicates that gammadelta and alphabeta TCRs interact differently with their respective MHC ligands.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wingren, C -- Crowley, M P -- Degano, M -- Chien, Y -- Wilson, I A -- AI33431/AI/NIAID NIH HHS/ -- CA58896/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2000 Jan 14;287(5451):310-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10634787" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Substitution ; Animals ; Binding Sites ; Crystallography, X-Ray ; Glycosylation ; Histocompatibility Antigens Class I/*chemistry ; Hydrogen Bonding ; Ligands ; Mice ; Models, Molecular ; Point Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/immunology/metabolism ; Receptors, Antigen, T-Cell, gamma-delta/immunology/*metabolism ; Surface Properties ; beta 2-Microglobulin/chemistry
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    Structural basis of Smad2 recognition by the Smad anchor for receptor activation (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-30
    Description: The Smad proteins mediate transforming growth factor-beta (TGFbeta) signaling from the transmembrane serine-threonine receptor kinases to the nucleus. The Smad anchor for receptor activation (SARA) recruits Smad2 to the TGFbeta receptors for phosphorylation. The crystal structure of a Smad2 MH2 domain in complex with the Smad-binding domain (SBD) of SARA has been determined at 2.2 angstrom resolution. SARA SBD, in an extended conformation comprising a rigid coil, an alpha helix, and a beta strand, interacts with the beta sheet and the three-helix bundle of Smad2. Recognition between the SARA rigid coil and the Smad2 beta sheet is essential for specificity, whereas interactions between the SARA beta strand and the Smad2 three-helix bundle contribute significantly to binding affinity. Comparison of the structures between Smad2 and a comediator Smad suggests a model for how receptor-regulated Smads are recognized by the type I receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, G -- Chen, Y G -- Ozdamar, B -- Gyuricza, C A -- Chong, P A -- Wrana, J L -- Massague, J -- Shi, Y -- CA85171/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2000 Jan 7;287(5450):92-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10615055" target="_blank"〉PubMed〈/a〉
    Keywords: *Activin Receptors, Type I ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phosphorylation ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/chemistry/genetics/metabolism ; Receptors, Transforming Growth Factor beta/chemistry/genetics/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Transduction ; Smad2 Protein ; Trans-Activators/*chemistry/genetics/*metabolism ; Zinc Fingers
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    Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-06-10
    Description: Cyclic nucleotides are second messengers that are essential in vision, muscle contraction, neurotransmission, exocytosis, cell growth, and differentiation. These molecules are degraded by a family of enzymes known as phosphodiesterases, which serve a critical function by regulating the intracellular concentration of cyclic nucleotides. We have determined the three-dimensional structure of the catalytic domain of phosphodiesterase 4B2B to 1.77 angstrom resolution. The active site has been identified and contains a cluster of two metal atoms. The structure suggests the mechanism of action and basis for specificity and will provide a framework for structure-assisted drug design for members of the phosphodiesterase family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, R X -- Hassell, A M -- Vanderwall, D -- Lambert, M H -- Holmes, W D -- Luther, M A -- Rocque, W J -- Milburn, M V -- Zhao, Y -- Ke, H -- Nolte, R T -- AI33072/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2000 Jun 9;288(5472):1822-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Chemistry, Department of Molecular Sciences, Glaxo Wellcome Research and Development, Research Triangle Park, NC 27709, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10846163" target="_blank"〉PubMed〈/a〉
    Keywords: 3',5'-Cyclic-AMP Phosphodiesterases/*chemistry/*metabolism ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/chemistry/*metabolism ; Cyclic GMP/chemistry/metabolism ; Cyclic Nucleotide Phosphodiesterases, Type 4 ; Hydrogen Bonding ; Hydrolysis ; Metals/metabolism ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Substrate Specificity
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    Twists in catalysis: alternating conformations of Escherichia coli thioredoxin reductase (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-19
    Description: In thioredoxin reductase (TrxR) from Escherichia coli, cycles of reduction and reoxidation of the flavin adenine dinucleotide (FAD) cofactor depend on rate-limiting rearrangements of the FAD and NADPH (reduced form of nicotinamide adenine dinucleotide phosphate) domains. We describe the structure of the flavin-reducing conformation of E. coli TrxR at a resolution of 3.0 angstroms. The orientation of the two domains permits reduction of FAD by NADPH and oxidation of the enzyme dithiol by the protein substrate, thioredoxin. The alternate conformation, described by Kuriyan and co-workers, permits internal transfer of reducing equivalents from reduced FAD to the active-site disulfide. Comparison of these structures demonstrates that switching between the two conformations involves a "ball-and-socket" motion in which the pyridine nucleotide-binding domain rotates by 67 degrees.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lennon, B W -- Williams, C H Jr -- Ludwig, M L -- GM16429/GM/NIGMS NIH HHS/ -- GM18723/GM/NIGMS NIH HHS/ -- GM21444/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 18;289(5482):1190-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Research Division, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10947986" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Crystallography, X-Ray ; Escherichia coli/*enzymology ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Models, Molecular ; NADP/metabolism ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Tertiary ; Thioredoxin-Disulfide Reductase/*chemistry/*metabolism ; Thioredoxins/metabolism
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    Dynamically controlled protein tunneling paths in photosynthetic reaction centers (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-10-06
    Description: Marcus theory has explained how thermal nuclear motions modulate the energy gap between donor and acceptor sites in protein electron transfer reactions. Thermal motions, however, may also modulate electron tunneling between these reactions. Here we identify a new mechanism of nuclear dynamics amplification that plays a central role when interference among the dominant tunneling pathway tubes is destructive. In these cases, tunneling takes place in protein conformations far from equilibrium that minimize destructive interference. As an example, we demonstrate how this dynamical amplification mechanism affects certain reaction rates in the photosynthetic reaction center and therefore may be critical for biological function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Balabin, I A -- Onuchic, J N -- GM48043/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Oct 6;290(5489):114-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11021791" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; Computer Simulation ; Crystallography, X-Ray ; Darkness ; *Electrons ; Hydrogen Bonding ; Light ; Pheophytins/chemistry/metabolism ; Photosynthetic Reaction Center Complex Proteins/*chemistry/*metabolism ; Physicochemical Phenomena ; Protein Conformation ; Quinones/chemistry/metabolism ; Thermodynamics
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    Structural mechanism for STI-571 inhibition of abelson tyrosine kinase (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-09-16
    Description: The inadvertent activation of the Abelson tyrosine kinase (Abl) causes chronic myelogenous leukemia (CML). A small-molecule inhibitor of Abl (STI-571) is effective in the treatment of CML. We report the crystal structure of the catalytic domain of Abl, complexed to a variant of STI-571. Critical to the binding of STI-571 is the adoption by the kinase of an inactive conformation, in which a centrally located "activation loop" is not phosphorylated. The conformation of this loop is distinct from that in active protein kinases, as well as in the inactive form of the closely related Src kinases. These results suggest that compounds that exploit the distinctive inactivation mechanisms of individual protein kinases can achieve both high affinity and high specificity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schindler, T -- Bornmann, W -- Pellicena, P -- Miller, W T -- Clarkson, B -- Kuriyan, J -- GM29362/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1938-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10988075" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents/chemistry/*pharmacology ; Benzamides ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Enzyme Inhibitors/chemistry/*pharmacology ; Humans ; Imatinib Mesylate ; Mice ; Models, Molecular ; Phosphorylation ; *Piperazines ; Protein Conformation ; Proto-Oncogene Proteins c-abl/*antagonists & inhibitors/chemistry/metabolism ; Pyrimidines/chemistry/*pharmacology ; Recombinant Fusion Proteins ; Structure-Activity Relationship
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    A structural framework for deciphering the link between I-Ag7 and autoimmune diabetes (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-25
    Description: Susceptibility to murine and human insulin-dependent diabetes mellitus correlates strongly with major histocompatibility complex (MHC) class II I-A or HLA-DQ alleles that lack an aspartic acid at position beta57. I-Ag7 lacks this aspartate and is the only class II allele expressed by the nonobese diabetic mouse. The crystal structure of I-Ag7 was determined at 2.6 angstrom resolution as a complex with a high-affinity peptide from the autoantigen glutamic acid decarboxylase (GAD) 65. I-Ag7 has a substantially wider peptide-binding groove around beta57, which accounts for distinct peptide preferences compared with other MHC class II alleles. Loss of Asp(beta57) leads to an oxyanion hole in I-Ag7 that can be filled by peptide carboxyl residues or, perhaps, through interaction with the T cell receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corper, A L -- Stratmann, T -- Apostolopoulos, V -- Scott, C A -- Garcia, K C -- Kang, A S -- Wilson, I A -- Teyton, L -- CA58896/CA/NCI NIH HHS/ -- DK55037/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 21;288(5465):505-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10775108" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Aspartic Acid/chemistry ; Crystallography, X-Ray ; Diabetes Mellitus, Type 1/*immunology ; Drosophila melanogaster ; *Genes, MHC Class II ; Glutamate Decarboxylase/metabolism ; Histocompatibility Antigens Class II/*chemistry/genetics/metabolism ; Humans ; Hydrogen Bonding ; Mice ; Mice, Inbred NOD ; Models, Molecular ; Molecular Sequence Data ; Peptide Library ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/metabolism ; Recombinant Proteins/chemistry/metabolism
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    Structure of the RNA polymerase domain of E. coli primase (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-31
    Description: All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keck, J L -- Roche, D D -- Lynch, A S -- Berger, J M -- New York, N.Y. -- Science. 2000 Mar 31;287(5462):2482-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, 229 Stanley Hall, no. 3206, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10741967" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; DNA Helicases/chemistry/metabolism ; DNA Primase/*chemistry/*metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; DNA, Single-Stranded/*metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Escherichia coli/*enzymology/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/biosynthesis ; Recombinant Proteins/chemistry/metabolism ; Templates, Genetic
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    Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-26
    Description: Polyadenylate [poly(A)] polymerase (PAP) catalyzes the addition of a polyadenosine tail to almost all eukaryotic messenger RNAs (mRNAs). The crystal structure of the PAP from Saccharomyces cerevisiae (Pap1) has been solved to 2.6 angstroms, both alone and in complex with 3'-deoxyadenosine triphosphate (3'-dATP). Like other nucleic acid polymerases, Pap1 is composed of three domains that encircle the active site. The arrangement of these domains, however, is quite different from that seen in polymerases that use a template to select and position their incoming nucleotides. The first two domains are functionally analogous to polymerase palm and fingers domains. The third domain is attached to the fingers domain and is known to interact with the single-stranded RNA primer. In the nucleotide complex, two molecules of 3'-dATP are bound to Pap1. One occupies the position of the incoming base, prior to its addition to the mRNA chain. The other is believed to occupy the position of the 3' end of the mRNA primer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bard, J -- Zhelkovsky, A M -- Helmling, S -- Earnest, T N -- Moore, C L -- Bohm, A -- R01 GM57218-01A2/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 25;289(5483):1346-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10958780" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Deoxyadenine Nucleotides/*chemistry/*metabolism ; Hydrogen Bonding ; Manganese/metabolism ; Models, Molecular ; Mutation ; Polynucleotide Adenylyltransferase/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/metabolism ; RNA, Messenger/metabolism ; Ribosomal Protein S6 ; Ribosomal Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology
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    Determining the 3D structure of HIV-1 protease (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-06-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kent, S -- Marshall, G R -- Wlodawer, A -- New York, N.Y. -- Science. 2000 Jun 2;288(5471):1590.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10858137" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; HIV Protease/chemical synthesis/*chemistry/metabolism ; Ligands ; Protein Conformation ; Recombinant Proteins/chemistry
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    Crystal structure of the ribonucleoprotein core of the signal recognition particle (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-26
    Description: The signal recognition particle (SRP), a protein-RNA complex conserved in all three kingdoms of life, recognizes and transports specific proteins to cellular membranes for insertion or secretion. We describe here the 1.8 angstrom crystal structure of the universal core of the SRP, revealing protein recognition of a distorted RNA minor groove. Nucleotide analog interference mapping demonstrates the biological importance of observed interactions, and genetic results show that this core is functional in vivo. The structure explains why the conserved residues in the protein and RNA are required for SRP assembly and defines a signal sequence recognition surface composed of both protein and RNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Batey, R T -- Rambo, R P -- Lucast, L -- Rha, B -- Doudna, J A -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1232-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10678824" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Base Pairing ; Binding Sites ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Escherichia coli/chemistry/genetics/metabolism ; *Escherichia coli Proteins ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Magnesium/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Potassium/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Bacterial/*chemistry/genetics/metabolism ; Signal Recognition Particle/*chemistry/metabolism ; Transformation, Bacterial ; Water/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structural genomics offers high-speed look at proteins (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 2000 Mar 17;287(5460):1954-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10755949" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biotechnology ; Computer Simulation ; Crystallography, X-Ray ; *Drug Design ; Humans ; Models, Molecular ; Private Sector ; *Protein Conformation ; Protein Folding ; Proteins/*chemistry/*genetics/physiology ; Proteome ; Public Sector ; Research Support as Topic
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  • 42
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    Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-04-21
    Description: Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1863-76. Epub 2001 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11313498" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Fourier Analysis ; Hydrogen Bonding ; Magnesium/metabolism ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/*chemistry/*metabolism ; RNA Processing, Post-Transcriptional ; RNA, Fungal/biosynthesis/chemistry/metabolism ; RNA, Messenger/biosynthesis/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factors/metabolism ; *Transcription, Genetic
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    Ribosome structure. The ribosome in action (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dahlberg, A E -- New York, N.Y. -- Science. 2001 May 4;292(5518):868-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology and Medicine, Brown University, Providence, RI 02912, USA. albert_dahlberg@brown.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11341282" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Anticodon ; Base Pairing ; Binding Sites ; Codon ; Crystallography, X-Ray ; *Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; Ribosomal Proteins/chemistry/metabolism ; Ribosomes/chemistry/*metabolism/*ultrastructure ; Thermus thermophilus/genetics/metabolism/ultrastructure
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  • 44
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    X-ray crystallography. Transcription enzyme structure solved (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):411-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11330276" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Weight ; Protein Conformation ; RNA/biosynthesis/genetics ; RNA Polymerase II/*chemistry/metabolism ; *Transcription, Genetic ; Yeasts/*enzymology
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  • 45
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    Enzymology. Nickel to the fore (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thauer, R K -- New York, N.Y. -- Science. 2001 Aug 17;293(5533):1264-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany. thauer@mailer.uni-marburg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11509713" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/genetics/metabolism ; Bacteria, Anaerobic/*enzymology ; Binding Sites ; Carbon Monoxide/metabolism ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; Escherichia coli/enzymology/genetics ; Iron/chemistry/metabolism ; Multienzyme Complexes/*chemistry/genetics/metabolism ; Nickel/*chemistry/metabolism ; Oxidation-Reduction ; Peptococcaceae/*enzymology ; Recombinant Proteins/chemistry/metabolism ; Sulfur/chemistry
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  • 46
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    Structural biology. Actin' up (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-07-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De La Cruz, E M -- Pollard, T D -- New York, N.Y. -- Science. 2001 Jul 27;293(5530):616-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11474090" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Depolymerizing Factors ; Actins/*chemistry/*metabolism ; Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphate/chemistry/metabolism ; Biopolymers/chemistry/metabolism ; *Contractile Proteins ; Crystallography, X-Ray ; Hydrolysis ; Microfilament Proteins/metabolism ; Phosphates/metabolism ; Profilins ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Rhodamines/metabolism ; Thymosin/metabolism
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  • 47
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    Structural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-12
    Description: Dendritic cell specific intracellular adhesion molecule-3 (ICAM-3) grabbing nonintegrin (DC-SIGN), a C-type lectin present on the surface of dendritic cells, mediates the initial interaction of dendritic cells with T cells by binding to ICAM-3. DC-SIGN and DC-SIGNR, a related receptor found on the endothelium of liver sinusoids, placental capillaries, and lymph nodes, bind to oligosaccharides that are present on the envelope of human immunodeficiency virus (HIV), an interaction that strongly promotes viral infection of T cells. Crystal structures of carbohydrate-recognition domains of DC-SIGN and of DC-SIGNR bound to oligosaccharide, in combination with binding studies, reveal that these receptors selectively recognize endogenous high-mannose oligosaccharides and may represent a new avenue for developing HIV prophylactics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feinberg, H -- Mitchell, D A -- Drickamer, K -- Weis, W I -- GM50565/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 7;294(5549):2163-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11739956" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylglucosamine/chemistry/metabolism ; Calcium/metabolism ; Carbohydrate Conformation ; Carbohydrate Sequence ; Carrier Proteins/chemistry/metabolism ; *Cell Adhesion Molecules ; Collectins ; Crystallization ; Crystallography, X-Ray ; Glycoproteins/chemistry/metabolism ; HIV Envelope Protein gp120/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Lectins/*chemistry/*metabolism ; *Lectins, C-Type ; Ligands ; Mannose/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oligosaccharides/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Cell Surface/*chemistry/*metabolism
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    Chemistry. Nota bene: know thine enemy (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, O -- New York, N.Y. -- Science. 2001 Nov 9;294(5545):1298.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11701920" target="_blank"〉PubMed〈/a〉
    Keywords: *Antigens, Bacterial ; *Bacillus anthracis ; Bacterial Toxins/chemistry/*metabolism ; Crystallography, X-Ray ; Endocytosis ; Hydrogen-Ion Concentration ; Macrophages/metabolism/microbiology ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Phagocytosis ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/*metabolism ; Receptors, Peptide/chemistry/*metabolism
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  • 49
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    Crystal structure of an initiation factor bound to the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-03
    Description: Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, A P -- Clemons, W M Jr -- Brodersen, D E -- Morgan-Warren, R J -- Hartsch, T -- Wimberly, B T -- Ramakrishnan, V -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):498-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11228145" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallography, X-Ray ; Eukaryotic Initiation Factor-1/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal, 16S/*chemistry/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry
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  • 50
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    Structure of a Bag/Hsc70 complex: convergent functional evolution of Hsp70 nucleotide exchange factors (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-02-27
    Description: Bag (Bcl2-associated athanogene) domains occur in a class of cofactors of the eukaryotic chaperone 70-kilodalton heat shock protein (Hsp70) family. Binding of the Bag domain to the Hsp70 adenosine triphosphatase (ATPase) domain promotes adenosine 5'-triphosphate-dependent release of substrate from Hsp70 in vitro. In a 1.9 angstrom crystal structure of a complex with the ATPase of the 70-kilodalton heat shock cognate protein (Hsc70), the Bag domain forms a three-helix bundle, inducing a conformational switch in the ATPase that is incompatible with nucleotide binding. The same switch is observed in the bacterial Hsp70 homolog DnaK upon binding of the structurally unrelated nucleotide exchange factor GrpE. Thus, functional convergence has allowed proteins with different architectures to trigger a conserved conformational shift in Hsp70 that leads to nucleotide exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sondermann, H -- Scheufler, C -- Schneider, C -- Hohfeld, J -- Hartl, F U -- Moarefi, I -- New York, N.Y. -- Science. 2001 Feb 23;291(5508):1553-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max-Planck-Institut fur Biochemie, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11222862" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/metabolism ; Carrier Proteins/*chemistry/*metabolism ; Cattle ; Crystallography, X-Ray ; DNA-Binding Proteins ; *Escherichia coli Proteins ; Evolution, Molecular ; HSC70 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/*chemistry/*metabolism ; Heat-Shock Proteins/chemistry/metabolism ; Humans ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Isoforms ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Transcription Factors
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    Structural biology. A marvellous machine for making messages (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klug, A -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1844-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11397933" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Gene Expression Regulation, Fungal ; Promoter Regions, Genetic ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA Polymerase II/*chemistry/*metabolism ; RNA, Fungal/biosynthesis/chemistry/metabolism ; RNA, Messenger/biosynthesis/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Transcription Factors/isolation & purification/metabolism ; *Transcription, Genetic
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    Structural biology. Controlling the caspases (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fesik, S W -- Shi, Y -- New York, N.Y. -- Science. 2001 Nov 16;294(5546):1477-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research, Global Pharmaceutical Research & Development, Abbott Laboratories, Abbott Park, IL 60064, USA. stephen.fesik@abbott.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11711663" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; *Apoptosis ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; *Caspase Inhibitors ; Caspases/chemistry/*metabolism ; Crystallography, X-Ray ; Cysteine Proteinase Inhibitors/chemistry/metabolism ; Dimerization ; Humans ; Hydrogen Bonding ; Intracellular Signaling Peptides and Proteins ; Mitochondria/metabolism ; Mitochondrial Proteins/*chemistry/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; X-Linked Inhibitor of Apoptosis Protein
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  • 53
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    Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-26
    Description: In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chabriere, E -- Vernede, X -- Guigliarelli, B -- Charon, M H -- Hatchikian, E C -- Fontecilla-Camps, J C -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2559-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Cristallographie et Cristallogenese des Proteines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat a l'Energie Atomique, Universite Joseph Fourier, CNRS, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11752578" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Anaerobiosis ; Binding Sites ; Carbon Dioxide/metabolism ; Catalysis ; Chemistry, Physical ; Coenzymes/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Desulfovibrio/*enzymology ; Dimerization ; Electron Spin Resonance Spectroscopy ; *Free Radicals/chemistry/metabolism ; Ketone Oxidoreductases/*chemistry/metabolism ; Molecular Conformation ; Molecular Structure ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Conformation ; Pyruvate Synthase ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*chemistry/metabolism
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    Crystal structure of Arp2/3 complex (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-27
    Description: We determined a crystal structure of bovine Arp2/3 complex, an assembly of seven proteins that initiates actin polymerization in eukaryotic cells, at 2.0 angstrom resolution. Actin-related protein 2 (Arp2) and Arp3 are folded like actin, with distinctive surface features. Subunits ARPC2 p34 and ARPC4 p20 in the core of the complex associate through long carboxyl-terminal alpha helices and have similarly folded amino-terminal alpha/beta domains. ARPC1 p40 is a seven-blade beta propeller with an insertion that may associate with the side of an actin filament. ARPC3 p21 and ARPC5 p16 are globular alpha-helical subunits. We predict that WASp/Scar proteins activate Arp2/3 complex by bringing Arp2 into proximity with Arp3 for nucleation of a branch on the side of a preexisting actin filament.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Robinson, R C -- Turbedsky, K -- Kaiser, D A -- Marchand, J B -- Higgs, H N -- Choe, S -- Pollard, T D -- GM-26132/GM/NIGMS NIH HHS/ -- GM-26338/GM/NIGMS NIH HHS/ -- GM-56653/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Nov 23;294(5547):1679-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11721045" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*chemistry/*metabolism ; Actin-Related Protein 2 ; Actin-Related Protein 3 ; Actins/*chemistry/*metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Cattle ; Crystallography, X-Ray ; *Cytoskeletal Proteins ; Macromolecular Substances ; Models, Biological ; Models, Molecular ; Muscle, Skeletal ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Static Electricity ; Thymus Gland
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-08
    Description: Multidrug resistance (MDR) is a serious medical problem and presents a major challenge to the treatment of disease and the development of novel therapeutics. ABC transporters that are associated with multidrug resistance (MDR-ABC transporters) translocate hydrophobic drugs and lipids from the inner to the outer leaflet of the cell membrane. To better elucidate the structural basis for the "flip-flop" mechanism of substrate movement across the lipid bilayer, we have determined the structure of the lipid flippase MsbA from Escherichia coli by x-ray crystallography to a resolution of 4.5 angstroms. MsbA is organized as a homodimer with each subunit containing six transmembrane alpha-helices and a nucleotide-binding domain. The asymmetric distribution of charged residues lining a central chamber suggests a general mechanism for the translocation of substrate by MsbA and other MDR-ABC transporters. The structure of MsbA can serve as a model for the MDR-ABC transporters that confer multidrug resistance to cancer cells and infectious microorganisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, G -- Roth, C B -- GM61905-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1793-800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, MB-9, The Scripps Research Institute, La Jolla, CA 92037, USA. gchang@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546864" target="_blank"〉PubMed〈/a〉
    Keywords: *ATP-Binding Cassette Transporters ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Dimerization ; *Drug Resistance, Microbial ; *Drug Resistance, Multiple ; Escherichia coli/*enzymology ; Lipid A/metabolism ; Membrane Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Static Electricity ; Structure-Activity Relationship
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    Synchrotron radiation. Swiss source shows small is powerful (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiss, G -- New York, N.Y. -- Science. 2001 Oct 19;294(5542):494.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11641472" target="_blank"〉PubMed〈/a〉
    Keywords: Costs and Cost Analysis ; Crystallography, X-Ray ; Gene Expression ; Genetic Techniques ; Nucleosomes ; Switzerland ; *Synchrotrons/economics ; X-Rays
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    Recognition of cognate transfer RNA by the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-08
    Description: Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogle, J M -- Brodersen, D E -- Clemons , W M Jr -- Tarry, M J -- Carter, A P -- Ramakrishnan, V -- F31 GM019384/GM/NIGMS NIH HHS/ -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 May 4;292(5518):897-902.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11340196" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/metabolism/pharmacology ; Anticodon/chemistry/metabolism ; Base Pairing ; Binding Sites ; Codon/chemistry/metabolism ; Crystallography, X-Ray ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Paromomycin/metabolism/pharmacology ; Peptide Chain Elongation, Translational ; Peptide Elongation Factor Tu/metabolism ; Protein Biosynthesis ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Ribosomal, 16S/chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomes/chemistry/*metabolism/ultrastructure ; Thermodynamics ; Thermus thermophilus/chemistry/metabolism/*ultrastructure
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    Antibody catalysis of the oxidation of water (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-08
    Description: Recently we reported that antibodies can generate hydrogen peroxide (H2O2) from singlet molecular oxygen (1O2*). We now show that this process is catalytic, and we identify the electron source for a quasi-unlimited generation of H2O2. Antibodies produce up to 500 mole equivalents of H2O2 from 1O2*, without a reduction in rate, and we have excluded metals or Cl- as the electron source. On the basis of isotope incorporation experiments and kinetic data, we propose that antibodies use H2O as an electron source, facilitating its addition to 1O2* to form H2O3 as the first intermediate in a reaction cascade that eventually leads to H2O2. X-ray crystallographic studies with xenon point to putative conserved oxygen binding sites within the antibody fold where this chemistry could be initiated. Our findings suggest a protective function of immunoglobulins against 1O2* and raise the question of whether the need to detoxify 1O2* has played a decisive role in the evolution of the immunoglobulin fold.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wentworth , P Jr -- Jones, L H -- Wentworth, A D -- Zhu, X -- Larsen, N A -- Wilson, I A -- Xu, X -- Goddard , W A 3rd -- Janda, K D -- Eschenmoser, A -- Lerner, R A -- CA27489/CA/NCI NIH HHS/ -- GM43858/GM/NIGMS NIH HHS/ -- HD 36385/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 7;293(5536):1806-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11546867" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Catalytic/chemistry/*metabolism ; Binding Sites ; Catalysis ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Hydrogen Peroxide/*metabolism ; Kinetics ; Models, Molecular ; Oxidants/chemistry/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Protein Conformation ; Singlet Oxygen ; Spectrometry, Mass, Electrospray Ionization ; Thermodynamics ; Tryptophan/metabolism ; Ultraviolet Rays ; Water/*chemistry/*metabolism ; Xenon/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Global efforts in structural genomics (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-06
    Description: A worldwide initiative in structural genomics aims to capitalize on the recent successes of the genome projects. Substantial new investments in structural genomics in the past 2 years indicate the high level of support for these international efforts. Already, enormous progress has been made on high-throughput methodologies and technologies that will speed up macromolecular structure determinations. Recent international meetings have resulted in the formation of an International Structural Genomics Organization to formulate policy and foster cooperation between the public and private efforts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, R C -- Yokoyama, S -- Wilson, I A -- P50 GM62411/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Oct 5;294(5540):89-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Joint Center for Structural Genomics, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11588249" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Computational Biology ; Congresses as Topic ; Costs and Cost Analysis ; Crystallography, X-Ray ; Databases, Factual ; *Genomics ; Guidelines as Topic ; Humans ; Information Management ; Information Services ; International Cooperation ; Internet ; Nuclear Magnetic Resonance, Biomolecular ; Patents as Topic ; Private Sector ; *Protein Conformation ; Protein Folding ; Proteins/*chemistry ; *Proteome ; Public Sector ; Publishing ; Technology Transfer
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structure. An anthropomorphic integrin (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-10-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Humphries, M J -- Mould, A P -- New York, N.Y. -- Science. 2001 Oct 12;294(5541):316-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, University of Manchester, M13 9PT, UK. martin.humphries@man.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11598288" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/metabolism ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Drug Design ; Humans ; Ligands ; Metals/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Receptors, Vitronectin/*chemistry/metabolism
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    Cell biology. How bacterial flagella flip their switch (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, D -- New York, N.Y. -- Science. 2001 Mar 16;291(5511):2065-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11256392" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/chemistry ; *Bacterial Physiological Phenomena ; Computer Simulation ; Crystallization ; Crystallography, X-Ray ; Flagella/*chemistry/physiology ; Flagellin/*chemistry ; Molecular Motor Proteins/*chemistry/physiology ; Movement ; Protein Folding ; Protein Structure, Secondary
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    Enzymology. Coenzymes and radicals (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-12-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frey, P A -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2489-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53705, USA. frey@biochem.wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11752561" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Catalytic Domain ; Chemistry, Physical ; Coenzyme A/chemistry/metabolism ; Coenzymes/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Electrons ; Ferredoxins/chemistry/metabolism ; Ferricyanides/chemistry/metabolism ; *Free Radicals/chemistry/metabolism ; Ketone Oxidoreductases/*chemistry/metabolism ; Molecular Structure ; Oxidation-Reduction ; Physicochemical Phenomena ; Protons ; Pyruvate Synthase ; Pyruvic Acid/chemistry/metabolism ; Thiamine Pyrophosphate/analogs & derivatives/*chemistry/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structure of an extracellular gp130 cytokine receptor signaling complex (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-17
    Description: The activation of gp130, a shared signal-transducing receptor for a family of cytokines, is initiated by recognition of ligand followed by oligomerization into a higher order signaling complex. Kaposi's sarcoma-associated herpesvirus encodes a functional homolog of human interleukin-6 (IL-6) that activates human gp130. In the 2.4 angstrom crystal structure of the extracellular signaling assembly between viral IL-6 and human gp130, two complexes are cross-linked into a tetramer through direct interactions between the immunoglobulin domain of gp130 and site III of viral IL-6, which is necessary for receptor activation. Unlike human IL-6 (which uses many hydrophilic residues), the viral cytokine largely uses hydrophobic amino acids to contact gp130, which enhances the complementarity of the viral IL-6-gp130 binding interfaces. The cross-reactivity of gp130 is apparently due to a chemical plasticity evident in the amphipathic gp130 cytokine-binding sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chow , D -- He , X -- Snow, A L -- Rose-John, S -- Garcia, K C -- R01-AI-48540-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 16;291(5511):2150-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11251120" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD/*chemistry/*metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytokine Receptor gp130 ; Epitopes ; Humans ; Hydrogen Bonding ; Interleukin-6/*chemistry/immunology/*metabolism ; Membrane Glycoproteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Mimicry ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Viral Proteins/*chemistry/immunology/*metabolism
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    BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-14
    Description: Mutations in the BRCA2 (breast cancer susceptibility gene 2) tumor suppressor lead to chromosomal instability due to defects in the repair of double-strand DNA breaks (DSBs) by homologous recombination, but BRCA2's role in this process has been unclear. Here, we present the 3.1 angstrom crystal structure of a approximately 90-kilodalton BRCA2 domain bound to DSS1, which reveals three oligonucleotide-binding (OB) folds and a helix-turn-helix (HTH) motif. We also (i) demonstrate that this BRCA2 domain binds single-stranded DNA, (ii) present its 3.5 angstrom structure bound to oligo(dT)9, (iii) provide data that implicate the HTH motif in dsDNA binding, and (iv) show that BRCA2 stimulates RAD51-mediated recombination in vitro. These findings establish that BRCA2 functions directly in homologous recombination and provide a structural and biochemical basis for understanding the loss of recombination-mediated DSB repair in BRCA2-associated cancers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Haijuan -- Jeffrey, Philip D -- Miller, Julie -- Kinnucan, Elspeth -- Sun, Yutong -- Thoma, Nicolas H -- Zheng, Ning -- Chen, Phang-Lang -- Lee, Wen-Hwa -- Pavletich, Nikola P -- New York, N.Y. -- Science. 2002 Sep 13;297(5588):1837-48.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Sloan-Kettering Division, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12228710" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; BRCA2 Protein/*chemistry/genetics/*metabolism ; Binding Sites ; Crystallography, X-Ray ; DNA/metabolism ; *DNA Repair ; DNA, Single-Stranded/*metabolism ; DNA-Binding Proteins/metabolism ; Genes, BRCA2 ; Helix-Turn-Helix Motifs ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Mice ; Molecular Sequence Data ; Mutation ; Proteasome Endopeptidase Complex ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/chemistry/*metabolism ; Rad51 Recombinase ; Rats ; *Recombination, Genetic
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    Structural insights into group II intron catalysis and branch-site selection (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-23
    Description: Group II self-splicing introns catalyze autoexcision from precursor RNA transcripts by a mechanism strikingly similar to that of the spliceosome, an RNA-protein assembly responsible for splicing together the protein-coding parts of most eukaryotic pre-mRNAs. Splicing in both cases initiates via nucleophilic attack at the 5' splice site by the 2' OH of a conserved intron adenosine residue, creating a branched (lariat) intermediate. Here, we describe the crystal structure at 3.0 A resolution of a 70-nucleotide RNA containing the catalytically essential domains 5 and 6 of the yeast ai5gamma group II self-splicing intron, revealing an unexpected two-nucleotide bulged structure around the branch-point adenosine in domain 6.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Lan -- Doudna, Jennifer A -- New York, N.Y. -- Science. 2002 Mar 15;295(5562):2084-8. Epub 2002 Feb 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry and, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859154" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/metabolism ; Base Pairing ; Binding Sites ; CME-Carbodiimide/*analogs & derivatives ; Catalysis ; Cobalt/metabolism ; Crystallization ; Crystallography, X-Ray ; *Introns ; Magnesium/metabolism ; Manganese/metabolism ; *Nucleic Acid Conformation ; Point Mutation ; RNA Precursors/chemistry/metabolism ; *RNA Splicing ; RNA, Fungal/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Molecular basis of proton motive force generation: structure of formate dehydrogenase-N (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-09
    Description: The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 angstroms through the enzyme. The menaquinone reduction site associated with a possible proton pathway was also characterized. This structure provides critical insights into the proton motive force generation by redox loop, a common mechanism among a wide range of respiratory enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jormakka, Mika -- Tornroth, Susanna -- Byrne, Bernadette -- Iwata, So -- New York, N.Y. -- Science. 2002 Mar 8;295(5561):1863-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biomedical Sciences, Imperial College, London SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11884747" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Catalytic Domain ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Electron Transport ; Escherichia coli/*enzymology ; Formate Dehydrogenases/*chemistry/metabolism ; Formates/metabolism ; Guanine Nucleotides/chemistry/metabolism ; Hydrogen Bonding ; Iron-Sulfur Proteins/chemistry/metabolism ; Membrane Potentials ; Models, Molecular ; Nitrate Reductases/chemistry/metabolism ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; *Proton-Motive Force ; Protons ; Pterins/chemistry/metabolism ; Vitamin K 2/chemistry/metabolism
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    Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-19
    Description: Mycobacterium tuberculosis (Mtb) mounts a stubborn defense against oxidative and nitrosative components of the immune response. Dihydrolipoamide dehydrogenase (Lpd) and dihydrolipoamide succinyltransferase (SucB) are components of alpha-ketoacid dehydrogenase complexes that are central to intermediary metabolism. We find that Lpd and SucB support Mtb's antioxidant defense. The peroxiredoxin alkyl hydroperoxide reductase (AhpC) is linked to Lpd and SucB by an adaptor protein, AhpD. The 2.0 angstrom AhpD crystal structure reveals a thioredoxin-like active site that is responsive to lipoamide. We propose that Lpd, SucB (the only lipoyl protein detected in Mtb), AhpD, and AhpC together constitute a nicotinamide adenine dinucleotide (reduced)-dependent peroxidase and peroxynitrite reductase. AhpD thus represents a class of thioredoxin-like molecules that enables an antioxidant defense.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bryk, R -- Lima, C D -- Erdjument-Bromage, H -- Tempst, P -- Nathan, C -- HL61241/HL/NHLBI NIH HHS/ -- P30 CA08748/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 8;295(5557):1073-7. Epub 2002 Jan 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11799204" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*metabolism ; Amino Acid Sequence ; Antioxidants ; Binding Sites ; Catalysis ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; Dihydrolipoamide Dehydrogenase/*metabolism ; Hydrogen Bonding ; Hydrogen Peroxide/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium tuberculosis/*enzymology/genetics/metabolism ; NAD/metabolism ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Peroxidases/*chemistry/*metabolism ; Peroxiredoxins ; Peroxynitrous Acid/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Thioctic Acid/*analogs & derivatives/metabolism ; Thioredoxins/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-06-20
    Description: Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from the O2 reduction site exchanges its effective accessibility to the matrix aqueous phase for one to the cytosolic phase concomitantly with a significant decrease in the pK of its carboxyl group, on reduction of the metal sites. The movement indicates the aspartate as the proton pumping site. A tyrosine acidified by a covalently linked imidazole nitrogen is a possible proton donor for the O2 reduction by the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoshikawa, S -- Shinzawa-Itoh, K -- Nakashima, R -- Yaono, R -- Yamashita, E -- Inoue, N -- Yao, M -- Fei, M J -- Libeu, C P -- Mizushima, T -- Yamaguchi, H -- Tomizaki, T -- Tsukihara, T -- New York, N.Y. -- Science. 1998 Jun 12;280(5370):1723-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Life Science, Himeji Institute of Technology and CREST, Japan Science and Technology Corporation (JST), Kamigohri Akoh, Hyogo 678-1297, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9624044" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aspartic Acid/chemistry/metabolism ; Azides/metabolism ; Binding Sites ; Carbon Monoxide/metabolism ; Cattle ; Copper/chemistry/metabolism ; Crystallography, X-Ray ; Electron Transport Complex IV/*chemistry/*metabolism ; Heme/analogs & derivatives/chemistry/metabolism ; Hydrogen Bonding ; Hydrogen Peroxide/chemistry/metabolism ; Hydrogen-Ion Concentration ; Ligands ; Metals/metabolism ; Models, Chemical ; Models, Molecular ; Myocardium/*enzymology ; Oxidation-Reduction ; Oxygen/metabolism ; Protein Conformation ; *Proton Pumps ; Tyrosine/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    A structural explanation for the recognition of tyrosine-based endocytotic signals (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-11-13
    Description: Many cell surface proteins are marked for endocytosis by a cytoplasmic sequence motif, tyrosine-X-X-(hydrophobic residue), that is recognized by the mu2 subunit of AP2 adaptors. Crystal structures of the internalization signal binding domain of mu2 complexed with the internalization signal peptides of epidermal growth factor receptor and the trans-Golgi network protein TGN38 have been determined at 2.7 angstrom resolution. The signal peptides adopted an extended conformation rather than the expected tight turn. Specificity was conferred by hydrophobic pockets that bind the tyrosine and leucine in the peptide. In the crystal, the protein forms dimers that could increase the strength and specificity of binding to dimeric receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Owen, D J -- Evans, P R -- New York, N.Y. -- Science. 1998 Nov 13;282(5392):1327-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9812899" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptor Protein Complex 1 ; Adaptor Protein Complex 2 ; *Adaptor Protein Complex 3 ; Adaptor Protein Complex alpha Subunits ; *Adaptor Protein Complex mu Subunits ; Adaptor Proteins, Vesicular Transport ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; *Endocytosis ; *Glycoproteins ; Humans ; Hydrogen Bonding ; Membrane Glycoproteins/*chemistry/metabolism ; Membrane Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Phosphorylation ; Protein Conformation ; Protein Sorting Signals/*chemistry/metabolism ; Protein Structure, Secondary ; Receptor, Epidermal Growth Factor/*chemistry/metabolism ; Tyrosine/chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Ribonuclease P protein structure: evolutionary origins in the translational apparatus (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-05-23
    Description: The crystal structure of Bacillus subtilis ribonuclease P protein is reported at 2.6 angstroms resolution. This protein binds to ribonuclease P RNA to form a ribonucleoprotein holoenzyme with optimal catalytic activity. Mutagenesis and biochemical data indicate that an unusual left-handed betaalphabeta crossover connection and a large central cleft in the protein form conserved RNA binding sites; a metal binding loop may comprise a third RNA binding site. The unusual topology is partly shared with ribosomal protein S5 and the ribosomal translocase elongation factor G, which suggests evolution from a common RNA binding ancestor in the primordial translational apparatus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stams, T -- Niranjanakumari, S -- Fierke, C A -- Christianson, D W -- GM55387/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 May 1;280(5364):752-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9563955" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/enzymology ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Endoribonucleases/*chemistry/metabolism ; *Evolution, Molecular ; Magnesium/metabolism ; Models, Molecular ; Peptide Elongation Factor G ; Peptide Elongation Factors/chemistry ; *Protein Biosynthesis ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA, Bacterial/*chemistry/metabolism ; RNA, Catalytic/*chemistry/metabolism ; Ribonuclease P ; Ribosomal Proteins/chemistry ; Zinc/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Crystal structure and evolution of a transfer RNA splicing enzyme (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-05-02
    Description: The splicing of transfer RNA precursors is similar in Eucarya and Archaea. In both kingdoms an endonuclease recognizes the splice sites and releases the intron, but the mechanism of splice site recognition is different in each kingdom. The crystal structure of the endonuclease from the archaeon Methanococcus jannaschii was determined to a resolution of 2.3 angstroms. The structure indicates that the cleavage reaction is similar to that of ribonuclease A and the arrangement of the active sites is conserved between the archaeal and eucaryal enzymes. These results suggest an evolutionary pathway for splice site recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, H -- Trotta, C R -- Abelson, J -- F32 GM188930-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Apr 10;280(5361):279-84.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, Mail Code 147-75, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9535656" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Cloning, Molecular ; Crystallography, X-Ray ; Dimerization ; Endoribonucleases/*chemistry/genetics/metabolism ; *Evolution, Molecular ; HIV Long Terminal Repeat ; Hydrogen Bonding ; Methanococcus/*enzymology/genetics ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; RNA Precursors/chemistry/metabolism ; *RNA Splicing ; RNA, Archaeal/chemistry/metabolism ; Saccharomyces cerevisiae/enzymology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    High-resolution protein design with backbone freedom (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-11-20
    Description: Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harbury, P B -- Plecs, J J -- Tidor, B -- Alber, T -- Kim, P S -- GM44162/GM/NIGMS NIH HHS/ -- GM48598/GM/NIGMS NIH HHS/ -- GM55758/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Nov 20;282(5393):1462-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9822371" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Circular Dichroism ; Computer Simulation ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutation ; Peptides/chemical synthesis/*chemistry ; *Protein Conformation ; Protein Denaturation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Proteins/chemical synthesis/*chemistry ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-12-04
    Description: A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing. CpI, an enzyme that catalyzes the two-electron reduction of two protons to yield dihydrogen, was found to contain 20 gram atoms of iron per mole of protein, arranged into five distinct [Fe-S] clusters. The probable active-site cluster, previously termed the H-cluster, was found to be an unexpected arrangement of six iron atoms existing as a [4Fe-4S] cubane subcluster covalently bridged by a cysteinate thiol to a [2Fe] subcluster. The iron atoms of the [2Fe] subcluster both exist with an octahedral coordination geometry and are bridged to each other by three non-protein atoms, assigned as two sulfide atoms and one carbonyl or cyanide molecule. This structure provides insights into the mechanism of biological hydrogen activation and has broader implications for [Fe-S] cluster structure and function in biological systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Peters, J W -- Lanzilotta, W N -- Lemon, B J -- Seefeldt, L C -- New York, N.Y. -- Science. 1998 Dec 4;282(5395):1853-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA. petersj@cc.usu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9836629" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Carbon Monoxide/chemistry ; Catalytic Domain ; Clostridium/*enzymology ; Crystallography, X-Ray ; Cyanides/chemistry ; Cysteine/chemistry ; Histidine/chemistry ; Hydrogen/metabolism ; Hydrogenase/*chemistry/metabolism ; Iron/*chemistry ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protons ; Sulfur/chemistry
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    Crystal structure of the ectodomain of human transferrin receptor (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-26
    Description: The transferrin receptor (TfR) undergoes multiple rounds of clathrin-mediated endocytosis and reemergence at the cell surface, importing iron-loaded transferrin (Tf) and recycling apotransferrin after discharge of iron in the endosome. The crystal structure of the dimeric ectodomain of the human TfR, determined here to 3.2 angstroms resolution, reveals a three-domain subunit. One domain closely resembles carboxy- and aminopeptidases, and features of membrane glutamate carboxypeptidase can be deduced from the TfR structure. A model is proposed for Tf binding to the receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawrence, C M -- Ray, S -- Babyonyshev, M -- Galluser, R -- Borhani, D W -- Harrison, S C -- New York, N.Y. -- Science. 1999 Oct 22;286(5440):779-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Children's Hospital Laboratory of Molecular Medicine, 320 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10531064" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; CHO Cells ; Carboxypeptidases/chemistry ; Cell Membrane/chemistry ; Conserved Sequence ; Cricetinae ; Crystallography, X-Ray ; Dimerization ; Ferric Compounds/metabolism ; Glycosylation ; Humans ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Transferrin/*chemistry/metabolism ; Transferrin/metabolism
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    Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-13
    Description: The E6AP ubiquitin-protein ligase (E3) mediates the human papillomavirus-induced degradation of the p53 tumor suppressor in cervical cancer and is mutated in Angelman syndrome, a neurological disorder. The crystal structure of the catalytic hect domain of E6AP reveals a bilobal structure with a broad catalytic cleft at the junction of the two lobes. The cleft consists of conserved residues whose mutation interferes with ubiquitin-thioester bond formation and is the site of Angelman syndrome mutations. The crystal structure of the E6AP hect domain bound to the UbcH7 ubiquitin-conjugating enzyme (E2) reveals the determinants of E2-E3 specificity and provides insights into the transfer of ubiquitin from the E2 to the E3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, L -- Kinnucan, E -- Wang, G -- Beaudenon, S -- Howley, P M -- Huibregtse, J M -- Pavletich, N P -- New York, N.Y. -- Science. 1999 Nov 12;286(5443):1321-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cellular Biochemistry and Biophysics Program, Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10558980" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angelman Syndrome/genetics ; Binding Sites ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; Cysteine/chemistry ; Humans ; Ligases/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Structure, Secondary ; Substrate Specificity ; Ubiquitin-Conjugating Enzymes ; Ubiquitin-Protein Ligases ; Ubiquitins/*metabolism
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    Structural analysis of the mechanism of adenovirus binding to its human cellular receptor, CAR (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-24
    Description: Binding of virus particles to specific host cell surface receptors is known to be an obligatory step in infection even though the molecular basis for these interactions is not well characterized. The crystal structure of the adenovirus fiber knob domain in complex with domain I of its human cellular receptor, coxsackie and adenovirus receptor (CAR), is presented here. Surface-exposed loops on knob contact one face of CAR, forming a high-affinity complex. Topology mismatches between interacting surfaces create interfacial solvent-filled cavities and channels that may be targets for antiviral drug therapy. The structure identifies key determinants of binding specificity, which may suggest ways to modify the tropism of adenovirus-based gene therapy vectors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bewley, M C -- Springer, K -- Zhang, Y B -- Freimuth, P -- Flanagan, J M -- 1P41 RR12408-01A1/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1999 Nov 19;286(5444):1579-83.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10567268" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviruses, Human/chemistry/*metabolism ; Amino Acid Substitution ; Binding Sites ; Capsid/*chemistry/*metabolism ; *Capsid Proteins ; Coxsackie and Adenovirus Receptor-Like Membrane Protein ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Models, Molecular ; Mutagenesis ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Virus/*chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Thermodynamics
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    Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-09
    Description: Crystal structures of the Asp96 to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined to 1.8 and 2.0 angstroms resolution, respectively. The trapped photoproduct corresponds to the late M state in the transport cycle-that is, after proton transfer to Asp85 and release of a proton to the extracellular membrane surface, but before reprotonation of the deprotonated retinal Schiff base. Its density map describes displacements of side chains near the retinal induced by its photoisomerization to 13-cis,15-anti and an extensive rearrangement of the three-dimensional network of hydrogen-bonded residues and bound water that accounts for the changed pKa values (where Ka is the acid constant) of the Schiff base and Asp85. The structural changes detected suggest the means for conserving energy at the active site and for ensuring the directionality of proton translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luecke, H -- Schobert, B -- Richter, H T -- Cartailler, J P -- Lanyi, J K -- R01-GM29498/GM/NIGMS NIH HHS/ -- R01-GM56445/GM/NIGMS NIH HHS/ -- R01-GM59970/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Oct 8;286(5438):255-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. hudel@uci.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10514362" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cytoplasm/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Ion Transport ; Isomerism ; Light ; Models, Molecular ; Photolysis ; Photons ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Proton Pumps/*chemistry/*metabolism ; Protons ; Retinaldehyde/chemistry/metabolism ; Schiff Bases ; Thermodynamics ; Water
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    Molecular rotary motors (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fillingame, R H -- New York, N.Y. -- Science. 1999 Nov 26;286(5445):1687-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706, USA. rhfillin@facstaff.wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10610565" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Catalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Helix-Loop-Helix Motifs ; Hydrolysis ; Mitochondria/enzymology ; Models, Biological ; *Molecular Motor Proteins/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Proton-Motive Force ; Proton-Translocating ATPases/*chemistry/*metabolism ; Saccharomyces cerevisiae/enzymology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Two-metal-Ion catalysis in adenylyl cyclase (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-31
    Description: Adenylyl cyclase (AC) converts adenosine triphosphate (ATP) to cyclic adenosine monophosphate, a ubiquitous second messenger that regulates many cellular functions. Recent structural studies have revealed much about the structure and function of mammalian AC but have not fully defined its active site or catalytic mechanism. Four crystal structures were determined of the catalytic domains of AC in complex with two different ATP analogs and various divalent metal ions. These structures provide a model for the enzyme-substrate complex and conclusively demonstrate that two metal ions bind in the active site. The similarity of the active site of AC to those of DNA polymerases suggests that the enzymes catalyze phosphoryl transfer by the same two-metal-ion mechanism and likely have evolved from a common ancestor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tesmer, J J -- Sunahara, R K -- Johnson, R A -- Gosselin, G -- Gilman, A G -- Sprang, S R -- DK38828/DK/NIDDK NIH HHS/ -- DK46371/DK/NIDDK NIH HHS/ -- GM34497/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 30;285(5428):756-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10427002" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Adenylyl Cyclase Inhibitors ; Adenylyl Cyclases/chemistry/genetics/*metabolism ; Animals ; Aspartic Acid/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Deoxyadenine Nucleotides/metabolism/pharmacology ; Dideoxynucleotides ; Dimerization ; Enzyme Inhibitors/metabolism ; Hydrogen Bonding ; Ligands ; Magnesium/*metabolism ; Manganese/*metabolism ; Models, Molecular ; Mutation ; Protein Conformation ; Protein Folding ; Rats ; Thionucleotides/metabolism/pharmacology ; Zinc/*metabolism
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    Structural assets of a tumor suppressor (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tonks, N K -- Myers, M P -- New York, N.Y. -- Science. 1999 Dec 10;286(5447):2096-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. tonks@cshl.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10617421" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Membrane/metabolism ; Crystallography, X-Ray ; *Genes, Tumor Suppressor ; Humans ; Hydrogen Bonding ; Membrane Lipids/metabolism ; Models, Biological ; Mutation ; Neoplasms/*etiology/genetics ; PTEN Phosphohydrolase ; Phosphatidylinositol 3-Kinases/chemistry/metabolism ; Phosphatidylinositol Phosphates/metabolism ; Phosphoric Monoester Hydrolases/*chemistry/genetics/*metabolism ; Phosphorylation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; *Tumor Suppressor Proteins
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    The race to the ribosome structure (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1999 Sep 24;285(5436):2048-51.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10523195" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry ; Cryoelectron Microscopy ; Crystallization ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal/chemistry ; RNA, Transfer/chemistry/metabolism ; Ribosomal Proteins/chemistry ; Ribosomes/*chemistry/*ultrastructure
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  • 82
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    Ribosome finally begins to yield its complete structure (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-09-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pennisi, E -- New York, N.Y. -- Science. 1999 Aug 27;285(5432):1343.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10490407" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Haloarcula marismortui/ultrastructure ; Models, Molecular ; Neutrons ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Ribosomal/*chemistry ; Ribosomal Proteins/*chemistry ; Ribosomes/*chemistry/*ultrastructure ; Scattering, Radiation ; Thermus thermophilus/ultrastructure
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  • 83
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    The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-07-03
    Description: The electrostatic influence of the central cavity and pore alpha helices in the potassium ion channel from Streptomyces lividans (KcsA K+ channel) was analyzed by solving the finite difference Poisson equation. The cavity and helices overcome the destabilizing influence of the membrane and stabilize a cation at the membrane center. The electrostatic effect of the pore helices is large compared to that described for water-soluble proteins because of the low dielectric membrane environment. The combined contributions of the ion self-energy and the helix electrostatic field give rise to selectivity for monovalent cations in the water-filled cavity. Thus, the K+ channel uses simple electrostatic principles to solve the fundamental problem of ion destabilization by the cell membrane lipid bilayer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roux, B -- MacKinnon, R -- GM47400/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jul 2;285(5424):100-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉GRTM, Dipartements de Physique et Chimie, Universite de Montreal, Case Postal 6128, succursale Centre-Ville, Montreal, Canada H3C 3J7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10390357" target="_blank"〉PubMed〈/a〉
    Keywords: *Bacterial Proteins ; Cations, Monovalent/*metabolism ; Cell Membrane/*chemistry/metabolism ; Crystallography, X-Ray ; Ion Transport ; Lipid Bilayers ; Models, Molecular ; Potassium/*metabolism ; Potassium Channels/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Static Electricity ; Streptomyces/*chemistry ; Thermodynamics ; Water
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  • 84
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    Structure of a transcribing T7 RNA polymerase initiation complex (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-22
    Description: The structure of a T7 RNA polymerase (T7 RNAP) initiation complex captured transcribing a trinucleotide of RNA from a 17-base pair promoter DNA containing a 5-nucleotide single-strand template extension was determined at a resolution of 2.4 angstroms. Binding of the upstream duplex portion of the promoter occurs in the same manner as that in the open promoter complex, but the single-stranded template is repositioned to place the +4 base at the catalytic active site. Thus, synthesis of RNA in the initiation phase leads to accumulation or "scrunching" of the template in the enclosed active site pocket of T7 RNAP. Only three base pairs of heteroduplex are formed before the RNA peels off the template.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheetham, G M -- Steitz, T A -- GM-22778/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2305-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600732" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacteriophage T7/enzymology ; Catalytic Domain ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Single-Stranded/*chemistry/genetics/metabolism ; DNA-Directed DNA Polymerase/chemistry/metabolism ; DNA-Directed RNA Polymerases/*chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/chemistry/metabolism ; Oligoribonucleotides/chemistry/metabolism ; *Promoter Regions, Genetic ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/biosynthesis/*chemistry/genetics ; Substrate Specificity ; Templates, Genetic ; *Transcription, Genetic ; Viral Proteins
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  • 85
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    Structural basis of chaperone function and pilus biogenesis (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-08-14
    Description: Many Gram-negative pathogens assemble architecturally and functionally diverse adhesive pili on their surfaces by the chaperone-usher pathway. Immunoglobulin-like periplasmic chaperones escort pilus subunits to the usher, a large protein complex that facilitates the translocation and assembly of subunits across the outer membrane. The crystal structure of the PapD-PapK chaperone-subunit complex, determined at 2.4 angstrom resolution, reveals that the chaperone functions by donating its G(1) beta strand to complete the immunoglobulin-like fold of the subunit via a mechanism termed donor strand complementation. The structure of the PapD-PapK complex also suggests that during pilus biogenesis, every subunit completes the immunoglobulin-like fold of its neighboring subunit via a mechanism termed donor strand exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sauer, F G -- Futterer, K -- Pinkner, J S -- Dodson, K W -- Hultgren, S J -- Waksman, G -- R01AI29549/AI/NIAID NIH HHS/ -- R01DK51406/DK/NIDDK NIH HHS/ -- R01GM54033/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1058-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446050" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; Fimbriae Proteins ; Fimbriae, Bacterial/chemistry/*metabolism/ultrastructure ; Models, Molecular ; Molecular Chaperones/*chemistry/*metabolism ; Molecular Sequence Data ; *Periplasmic Proteins ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
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  • 86
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    Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-06-12
    Description: The editing enzyme double-stranded RNA adenosine deaminase includes a DNA binding domain, Zalpha, which is specific for left-handed Z-DNA. The 2.1 angstrom crystal structure of Zalpha complexed to DNA reveals that the substrate is in the left-handed Z conformation. The contacts between Zalpha and Z-DNA are made primarily with the "zigzag" sugar-phosphate backbone, which provides a basis for the specificity for the Z conformation. A single base contact is observed to guanine in the syn conformation, characteristic of Z-DNA. Intriguingly, the helix-turn-helix motif, frequently used to recognize B-DNA, is used by Zalpha to contact Z-DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schwartz, T -- Rould, M A -- Lowenhaupt, K -- Herbert, A -- Rich, A -- New York, N.Y. -- Science. 1999 Jun 11;284(5421):1841-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10364558" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Deaminase/*chemistry/metabolism ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; Helix-Turn-Helix Motifs ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA-Binding Proteins ; Substrate Specificity ; Water/metabolism
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  • 87
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    Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-12-22
    Description: Ribosome recycling factor (RRF), together with elongation factor G (EF-G), catalyzes recycling of ribosomes after one round of protein synthesis. The crystal structure of RRF was determined at 2.55 angstrom resolution. The protein has an unusual fold where domain I is a long three-helix bundle and domain II is a three-layer beta/alpha/beta sandwich. The molecule superimposes almost perfectly with a transfer RNA (tRNA) except that the amino acid-binding 3' end is missing. The mimicry suggests that RRF interacts with the posttermination ribosomal complex in a similar manner to a tRNA, leading to disassembly of the complex. The structural arrangement of this mimicry is entirely different from that of other cases of less pronounced mimicry of tRNA so far described.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Selmer, M -- Al-Karadaghi, S -- Hirokawa, G -- Kaji, A -- Liljas, A -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2349-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, Post Office Box 124, SE-22100 Lund, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600747" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Models, Molecular ; *Molecular Mimicry ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor G/chemistry ; Protein Biosynthesis ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/*metabolism ; RNA, Bacterial/chemistry/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomal Proteins ; Ribosomes/*metabolism ; Sequence Alignment ; Thermotoga maritima/*chemistry/metabolism
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  • 88
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    Structural genomics. Protein data justice for all (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-06-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Service, R F -- New York, N.Y. -- Science. 2000 May 12;288(5468):939-41.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10841704" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology ; Crystallography, X-Ray ; Guidelines as Topic ; Internet ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Conformation ; Proteins/*chemistry/genetics/physiology ; Publishing ; Research Support as Topic
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  • 89
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    Topologically linked protein rings in the bacteriophage HK97 capsid (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-23
    Description: The crystal structure of the double-stranded DNA bacteriophage HK97 mature empty capsid was determined at 3.6 angstrom resolution. The 660 angstrom diameter icosahedral particle contains 420 subunits with a new fold. The final capsid maturation step is an autocatalytic reaction that creates 420 isopeptide bonds between proteins. Each subunit is joined to two of its neighbors by ligation of the side-chain lysine 169 to asparagine 356. This generates 12 pentameric and 60 hexameric rings of covalently joined subunits that loop through each other, creating protein chainmail: topologically linked protein catenanes arranged with icosahedral symmetry. Catenanes have not been previously observed in proteins and provide a stabilization mechanism for the very thin HK97 capsid.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wikoff, W R -- Liljas, L -- Duda, R L -- Tsuruta, H -- Hendrix, R W -- Johnson, J E -- AI40101/AI/NIAID NIH HHS/ -- GM47795/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 22;289(5487):2129-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11000116" target="_blank"〉PubMed〈/a〉
    Keywords: Asparagine/chemistry/metabolism ; Capsid/*chemistry/metabolism ; Chemistry, Physical ; Crystallography, X-Ray ; Hydrogen Bonding ; Lysine/chemistry/metabolism ; Models, Molecular ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Siphoviridae/*chemistry/metabolism
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  • 90
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    Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-10-06
    Description: Memapsin 2 (beta-secretase) is a membrane-associated aspartic protease involved in the production of beta-amyloid peptide in Alzheimer's disease and is a major target for drug design. We determined the crystal structure of the protease domain of human memapsin 2 complexed to an eight-residue inhibitor at 1.9 angstrom resolution. The active site of memapsin 2 is more open and less hydrophobic than that of other human aspartic proteases. The subsite locations from S4 to S2' are well defined. A kink of the inhibitor chain at P2' and the change of chain direction of P3' and P4' may be mimicked to provide inhibitor selectivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hong, L -- Koelsch, G -- Lin, X -- Wu, S -- Terzyan, S -- Ghosh, A K -- Zhang, X C -- Tang, J -- New York, N.Y. -- Science. 2000 Oct 6;290(5489):150-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Protein Studies Program and Crystallography Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11021803" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid Precursor Protein Secretases ; Aspartic Acid Endopeptidases/*chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Endopeptidases ; Humans ; Hydrogen Bonding ; Models, Molecular ; Oligopeptides/*metabolism ; Protease Inhibitors/chemistry/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism
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  • 91
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    Molecular biology. Transposase team puts a headlock on DNA (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-06
    Description: Transposable DNA elements jump from one location in the genome to another. But, the cut-and-paste molecular machinations that support this nomadic lifestyle are still being unraveled. In their Perspective, Williams and Baker at the Massachusetts Institute of Technology discuss new details of transposon relocation revealed through resolution of the structure of a transposase enzyme bound to DNA (Davies et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, T L -- Baker, T A -- New York, N.Y. -- Science. 2000 Jul 7;289(5476):73-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Office 68-517, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. tlwillia@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10928934" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; DNA/*chemistry/*metabolism ; *DNA Transposable Elements ; Ligands ; Manganese/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; Transposases/*chemistry/*metabolism
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  • 92
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    Structural biology. A chloride pump at atomic resolution (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-06-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spudich, J L -- New York, N.Y. -- Science. 2000 May 26;288(5470):1358-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Molecular Genetics, University of Texas-Houston Medical School, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10847850" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/*chemistry/metabolism ; Biological Transport, Active ; Cell Membrane/chemistry/metabolism ; Chlorides/*metabolism ; Crystallography, X-Ray ; Cytoplasm/chemistry/metabolism ; Halobacterium salinarum/chemistry ; Halorhodopsins ; Hydrogen-Ion Concentration ; Ion Pumps/*chemistry/metabolism ; Ion Transport ; Light ; Models, Biological ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Schiff Bases
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 93
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    Structure and function of a human TAFII250 double bromodomain module (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-05-29
    Description: TFIID is a large multiprotein complex that initiates assembly of the transcription machinery. It is unclear how TFIID recognizes promoters in vivo when templates are nucleosome-bound. Here, it is shown that TAFII250, the largest subunit of TFIID, contains two tandem bromodomain modules that bind selectively to multiply acetylated histone H4 peptides. The 2.1 angstrom crystal structure of the double bromodomain reveals two side-by-side, four-helix bundles with a highly polarized surface charge distribution. Each bundle contains an Nepsilon-acetyllysine binding pocket at its center, which results in a structure ideally suited for recognition of diacetylated histone H4 tails. Thus, TFIID may be targeted to specific chromatin-bound promoters and may play a role in chromatin recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jacobson, R H -- Ladurner, A G -- King, D S -- Tjian, R -- New York, N.Y. -- Science. 2000 May 26;288(5470):1422-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10827952" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histone Acetyltransferases ; Histones/metabolism ; Humans ; Lysine/analogs & derivatives/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Nucleosomes/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry/metabolism ; *TATA-Binding Protein Associated Factors ; *Transcription Factor TFIID ; *Transcription, Genetic
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  • 94
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    Perspectives: structural biology. SRP--where the RNA and membrane worlds meet (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walter, P -- Keenan, R -- Schmitz, U -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1212-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California, San Francisco, 94143, USA. walter@cgl.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10712156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cell Membrane/chemistry/*metabolism ; Crystallography, X-Ray ; Endoplasmic Reticulum/chemistry/metabolism ; *Escherichia coli Proteins ; Evolution, Molecular ; Methionine/chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Peptides/metabolism ; Protein Conformation ; Protein Folding ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/*chemistry/metabolism ; RNA, Bacterial/chemistry/metabolism ; Signal Recognition Particle/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 95
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    General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-26
    Description: Many protein enzymes use general acid-base catalysis as a way to increase reaction rates. The amino acid histidine is optimized for this function because it has a pK(a) (where K(a) is the acid dissociation constant) near physiological pH. The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a phosphodiester bond. Reactivity-pH profiles in monovalent or divalent cations, as well as distance to the leaving-group oxygen, implicate cytosine 75 (C75) of the ribozyme as the general acid and ribozyme-bound hydrated metal hydroxide as the general base in the self-cleavage reaction. Moreover, C75 has a pK(a) perturbed to neutrality, making it "histidine-like." Anticooperative interaction is observed between protonated C75 and a metal ion, which serves to modulate the pK(a) of C75. General acid-base catalysis expands the catalytic repertoire of RNA and may provide improved rate acceleration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakano, S -- Chadalavada, D M -- Bevilacqua, P C -- GM58709/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Feb 25;287(5457):1493-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10688799" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Calcium/metabolism ; Catalysis ; Cobalt/metabolism ; Crystallography, X-Ray ; Hepatitis Delta Virus/*chemistry/enzymology ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Kinetics ; Magnesium/metabolism ; Metals/metabolism ; Models, Chemical ; Models, Molecular ; Nucleic Acid Conformation ; Protons ; RNA, Catalytic/chemistry/*metabolism ; RNA, Viral/chemistry/metabolism ; Static Electricity ; Thermodynamics
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
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    Structure. Rhodopsin sees the light (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-19
    Description: Members of the seven transmembrane receptor superfamily bind a remarkable variety of ligands, from neurotransmitters to odorants, and activate a spectacular array of G protein signaling molecules. These G-protein coupled receptors (GPCRs) are important in many cellular functions and so there has been great interest in elucidating how they transmit their signals to the interior of the cell after activation by ligand. As Bourne and Meng explain in their Perspective, the molecular movements of activated GPCRs are becoming clear now that the first crystal structure of a GPCR (rhodopsin, the light-trapping receptor found in the retina of the eye) has been reported (Palczweski et al.).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bourne, H R -- Meng, E C -- New York, N.Y. -- Science. 2000 Aug 4;289(5480):733-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 94143, USA. bourne@cmp.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10950717" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Evolution, Molecular ; Heterotrimeric GTP-Binding Proteins/metabolism ; Ligands ; Lipid Bilayers ; Models, Molecular ; Protein Structure, Secondary ; Receptors, Cell Surface/chemistry/metabolism ; Retinaldehyde/metabolism ; Rhodopsin/*chemistry/metabolism ; Stereoisomerism ; Vision, Ocular
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  • 97
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    Structural biology. Light at the end of the channel (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conaway, J W -- Conaway, R C -- New York, N.Y. -- Science. 2000 Apr 28;288(5466):632-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA. conawayj@omrf.ouhsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10799002" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Models, Molecular ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology ; Templates, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
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    The catalytic pathway of cytochrome p450cam at atomic resolution (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-04
    Description: Members of the cytochrome P450 superfamily catalyze the addition of molecular oxygen to nonactivated hydrocarbons at physiological temperature-a reaction that requires high temperature to proceed in the absence of a catalyst. Structures were obtained for three intermediates in the hydroxylation reaction of camphor by P450cam with trapping techniques and cryocrystallography. The structure of the ferrous dioxygen adduct of P450cam was determined with 0.91 angstrom wavelength x-rays; irradiation with 1.5 angstrom x-rays results in breakdown of the dioxygen molecule to an intermediate that would be consistent with an oxyferryl species. The structures show conformational changes in several important residues and reveal a network of bound water molecules that may provide the protons needed for the reaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schlichting, I -- Berendzen, J -- Chu, K -- Stock, A M -- Maves, S A -- Benson, D E -- Sweet, R M -- Ringe, D -- Petsko, G A -- Sligar, S G -- GM31756/GM/NIGMS NIH HHS/ -- GM33775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 3;287(5458):1615-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, Otto Hahn Strasse 11, 44227 Dortmund, Germany. ilme.schlichting@mpi-dortmund.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10698731" target="_blank"〉PubMed〈/a〉
    Keywords: Camphor/*chemistry/*metabolism ; Camphor 5-Monooxygenase/*chemistry/*metabolism ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Electrons ; Ferric Compounds/chemistry/metabolism ; Ferrous Compounds/chemistry/metabolism ; Hydrogen Bonding ; Hydroxylation ; Ligands ; Models, Molecular ; Molecular Conformation ; Oxygen/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Pseudomonas putida/enzymology ; Water/chemistry/metabolism
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  • 99
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    The complete atomic structure of the large ribosomal subunit at 2.4 A resolution (2000)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2000-08-11
    Description: The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ban, N -- Nissen, P -- Hansen, J -- Moore, P B -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- GM54216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):905-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics & Biochemistry and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937989" target="_blank"〉PubMed〈/a〉
    Keywords: Archaeal Proteins/chemistry/metabolism ; Base Sequence ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; Haloarcula marismortui/*chemistry/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Folding ; RNA, Archaeal/chemistry/metabolism ; RNA, Ribosomal, 23S/*chemistry/metabolism ; RNA, Ribosomal, 5S/*chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/ultrastructure
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  • 100
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    Architecture of RNA polymerase II and implications for the transcription mechanism (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-04-28
    Description: A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, P -- Bushnell, D A -- Fu, J -- Gnatt, A L -- Maier-Davis, B -- Thompson, N E -- Burgess, R R -- Edwards, A M -- David, P R -- Kornberg, R D -- GM49985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Apr 28;288(5466):640-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10784442" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; DNA, Fungal/chemistry/metabolism ; Enzyme Stability ; Escherichia coli/enzymology ; Humans ; *Models, Molecular ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; RNA Polymerase II/*chemistry/genetics/metabolism ; RNA, Fungal/chemistry/metabolism ; RNA, Messenger/chemistry/metabolism ; Thermus/enzymology ; Transcription Factors/chemistry/metabolism ; *Transcription Factors, General ; *Transcription, Genetic ; *Transcriptional Elongation Factors
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