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  • Binding Sites  (68)
  • American Association for the Advancement of Science (AAAS)  (68)
  • Elsevier
  • Springer
  • Springer Nature
  • 2020-2024
  • 2005-2009
  • 1995-1999  (68)
  • 1995  (68)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (68)
  • Elsevier
  • Springer
  • Springer Nature
Years
  • 2020-2024
  • 2005-2009
  • 1995-1999  (68)
Year
  • 1
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    Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-28
    Description: DCoH, the dimerization cofactor of hepatocyte nuclear factor-1, stimulates gene expression by associating with specific DNA binding proteins and also catalyzes the dehydration of the biopterin cofactor of phenylalanine hydroxylase. The x-ray crystal structure determined at 3 angstrom resolution reveals that DCoH forms a tetramer containing two saddle-shaped grooves that comprise likely macromolecule binding sites. Two equivalent enzyme active sites flank each saddle, suggesting that there is a spatial connection between the catalytic and binding activities. Structural similarities between the DCoH fold and nucleic acid-binding proteins argue that the saddle motif has evolved to bind diverse ligands or that DCoH unexpectedly may bind nucleic acids.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Endrizzi, J A -- Cronk, J D -- Wang, W -- Crabtree, G R -- Alber, T -- New York, N.Y. -- Science. 1995 Apr 28;268(5210):556-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley 94720-3206, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7725101" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Gene Expression Regulation ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/*chemistry/metabolism
    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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    Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-03-10
    Description: The crystal structure of the tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) from Pyrococcus furiosus, a hyperthermophilic archaeon (formerly archaebacterium) that grows optimally at 100 degrees C, has been determined at 2.3 angstrom resolution by means of multiple isomorphous replacement and multiple crystal form averaging. AOR consists of two identical subunits, each containing an Fe4S4 cluster and a molybdopterin-based tungsten cofactor that is analogous to the molybdenum cofactor found in a large class of oxotransferases. Whereas the general features of the tungsten coordination in this cofactor were consistent with a previously proposed structure, each AOR subunit unexpectedly contained two molybdopterin molecules that coordinate a tungsten by a total of four sulfur ligands, and the pterin system was modified by an intramolecular cyclization that generated a three-ringed structure. In comparison to other proteins, the hyperthermophilic enzyme AOR has a relatively small solvent-exposed surface area, and a relatively large number of both ion pairs and buried atoms. These properties may contribute to the extreme thermostability of this enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chan, M K -- Mukund, S -- Kletzin, A -- Adams, M W -- Rees, D C -- 1F32 GM15006/GM/NIGMS NIH HHS/ -- GM50775/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1995 Mar 10;267(5203):1463-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Pasadena, CA 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7878465" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/metabolism ; Amino Acid Sequence ; Archaea/*enzymology ; Binding Sites ; *Coenzymes ; Computer Graphics ; Crystallography, X-Ray ; Enzyme Stability ; Ferrous Compounds ; Metalloproteins/analysis/chemistry ; Models, Molecular ; Molecular Sequence Data ; Organometallic Compounds/analysis/*chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Structure, Secondary ; Pteridines/analysis/chemistry ; Pterins/analysis/*chemistry ; Surface Properties ; Temperature ; Tungsten/analysis/*chemistry
    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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  • 3
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    Molecular mimicry in protein synthesis? (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-12-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Moore, P B -- New York, N.Y. -- Science. 1995 Dec 1;270(5241):1453-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, New Haven, CT 05620-8107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7491488" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; GTP Phosphohydrolase-Linked Elongation Factors/metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; *Molecular Mimicry ; Peptide Chain Elongation, Translational ; Peptide Elongation Factor G ; Peptide Elongation Factor Tu/*chemistry/metabolism ; Peptide Elongation Factors/*chemistry/metabolism ; *Protein Biosynthesis ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Ribosomes/metabolism
    Print ISSN: 0036-8075
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  • 4
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    Crystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-09
    Description: Kidney bean purple acid phosphatase (KBPAP) is an Fe(III)-Zn(II) metalloenzyme resembling the mammalian Fe(III)-Fe(II) purple acid phosphatases. The structure of the homodimeric 111-kilodalton KBPAP was determined at a resolution of 2.9 angstroms. The enzyme contains two domains in each subunit. The active site is located in the carboxyl-terminal domain at the carboxy end of two sandwiched beta alpha beta alpha beta motifs. The two metal ions are 3.1 angstroms apart and bridged monodentately by Asp164. The iron is further coordinated by Tyr167, His325, and Asp135, and the zinc by His286, His323, and Asn201. The active-site structure is consistent with previous proposals regarding the mechanism of phosphate ester hydrolysis involving nucleophilic attack on the phosphate group by an Fe(III)-coordinated hydroxide ion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strater, N -- Klabunde, T -- Tucker, P -- Witzel, H -- Krebs, B -- New York, N.Y. -- Science. 1995 Jun 9;268(5216):1489-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Anorganisch-Chemisches Institut, Universitat Munster, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7770774" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Phosphatase/*chemistry/metabolism ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Fabaceae/enzymology ; Ferric Compounds/chemistry/metabolism ; Glycoproteins/*chemistry/metabolism ; Ligands ; Models, Molecular ; Plants, Medicinal ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Zinc/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 5
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    Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-02-03
    Description: The guanine-uracil (G.U) base pair that helps to define the 5'-splice site of group I introns is phylogenetically highly conserved. In such a wobble base pair, G makes two hydrogen bonds with U in a geometry shifted from that of a canonical Watson-Crick pair. The contribution made by individual functional groups of the G.U pair in the context of the Tetrahymena ribozyme was examined by replacement of the G.U pair with synthetic base pairs that maintain a wobble configuration, but that systematically alter functional groups in the major and minor grooves of the duplex. The substitutions demonstrate that the exocyclic amine of G, when presented on the minor groove surface by the wobble base pair conformation, contributes substantially (2 kilocalories.mole-1) to binding by making a tertiary interaction with the ribozyme active site. It contributes additionally to transition state stabilization. The ribozyme active site also makes tertiary contacts with a tripod of 2'-hydroxyls on the minor groove surface of the splice site helix. This suggests that the ribozyme binds the duplex primarily in the minor groove. The alanyl aminoacyl transfer RNA (tRNA) synthetase recognizes the exocyclic amine of an invariant G.U pair and contacts a similar array of 2'-hydroxyls when binding the tRNA(Ala) acceptor stem, providing an unanticipated parallel between protein-RNA and RNA-RNA interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Strobel, S A -- Cech, T R -- New York, N.Y. -- Science. 1995 Feb 3;267(5198):675-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7839142" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Base Sequence ; Binding Sites ; Exons ; Guanine/chemistry/*metabolism ; Guanosine Monophosphate/metabolism ; Hydrogen Bonding ; Introns ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Oligoribonucleotides/*metabolism ; RNA Splicing ; RNA, Catalytic/chemistry/*metabolism ; Tetrahymena/enzymology ; Uracil/chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 6
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    Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-11
    Description: In the molecular scheme of living organisms, adenosine 3',5'-monophosphate (cyclic AMP or cAMP) has been a universal second messenger. In eukaryotic cells, the primary receptors for cAMP are the regulatory subunits of cAMP-dependent protein kinase. The crystal structure of a 1-91 deletion mutant of the type I alpha regulatory subunit was refined to 2.8 A resolution. Each of the two tandem cAMP binding domains provides an extensive network of hydrogen bonds that buries the cyclic phosphate and the ribose between two beta strands that are linked by a short alpha helix. Each adenine base stacks against an aromatic ring that lies outside the beta barrel. This structure provides a molecular basis for understanding how cAMP binds cooperatively to its receptor protein, thus mediating activation of the kinase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, Y -- Dostmann, W R -- Herberg, F W -- Durick, K -- Xuong, N H -- Ten Eyck, L -- Taylor, S S -- Varughese, K I -- GM07313/GM/NIGMS NIH HHS/ -- GM34921/GM/NIGMS NIH HHS/ -- RR01644/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 11;269(5225):807-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0654, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638597" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Amino Acid Sequence ; Binding Sites ; Carrier Proteins/*chemistry/genetics/metabolism ; Computer Graphics ; Crystallization ; Crystallography, X-Ray ; Cyclic AMP/analogs & derivatives/*metabolism ; Cyclic AMP-Dependent Protein Kinases/*chemistry ; Enzyme Activation ; Hydrogen Bonding ; *Intracellular Signaling Peptides and Proteins ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 7
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    Crystal structure of Pseudomonas mevalonii HMG-CoA reductase at 3.0 angstrom resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-06-23
    Description: The rate-limiting step in cholesterol biosynthesis in mammals is catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, a four-electron oxidoreductase that converts HMG-CoA to mevalonate. The crystal structure of HMG-CoA reductase from Pseudomonas mevalonii was determined at 3.0 angstrom resolution by multiple isomorphous replacement. The structure reveals a tightly bound dimer that brings together at the subunit interface the conserved residues implicated in substrate binding and catalysis. These dimers are packed about a threefold crystallographic axis, forming a hexamer with 23 point group symmetry. Difference Fourier studies reveal the binding sites for the substrates HMG-CoA and reduced or oxidized nicotinamide adenine dinucleotide [NAD(H)] and demonstrate that the active sites are at the dimer interfaces. The HMG-CoA is bound by a domain with an unusual fold, consisting of a central alpha helix surrounded by a triangular set of walls of beta sheets and alpha helices. The NAD(H) is bound by a domain characterized by an antiparallel beta structure that defines a class of dinucleotide-binding domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lawrence, C M -- Rodwell, V W -- Stauffacher, C V -- AI 127713/AI/NIAID NIH HHS/ -- HL 47113/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1995 Jun 23;268(5218):1758-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7792601" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Fourier Analysis ; Hydroxymethylglutaryl CoA Reductases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; NAD/metabolism ; Protein Folding ; Protein Structure, Secondary ; Pseudomonas/*enzymology
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  • 8
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    Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe-C-O (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-18
    Description: The relative orientations of carbon monoxide (CO) bound to and photodissociated from myoglobin in solution have been determined with time-resolved infrared polarization spectroscopy. The bound CO is oriented 〈 or = 7 degrees from the heme normal, corresponding to nearly linear FE-C-O. Upon dissociation from the Fe, CO becomes trapped in a docking site that orientationally constrains it to lie approximately in the plane of the heme. Because the bound and "docked" CO are oriented in nearly orthogonal directions CO binding from the docking site is suppressed. These solutions results help to establish how myoglobin discriminates against CO, a controversial issue dominated by the misconception that Fe-C-O is bent.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lim, M -- Jackson, T A -- Anfinrud, P A -- DK45306/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1995 Aug 18;269(5226):962-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Harvard University, Cambridge, MA 02138 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7638619" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon Monoxide/*chemistry/metabolism ; Crystallography, X-Ray ; Ligands ; Light ; Myoglobin/*chemistry/metabolism ; Oxygen/chemistry/metabolism ; Photolysis ; Protein Conformation ; Spectrophotometry, Infrared ; Temperature
    Print ISSN: 0036-8075
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  • 9
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    Functions of the proteasome: the lysis at the end of the tunnel (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldberg, A L -- New York, N.Y. -- Science. 1995 Apr 28;268(5210):522-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7725095" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Archaeal Proteins ; Binding Sites ; Crystallography, X-Ray ; Cysteine Endopeptidases/chemistry/*metabolism ; Endopeptidases/chemistry/*metabolism ; Humans ; Hydrolysis ; Multienzyme Complexes/chemistry/*metabolism ; Proteasome Endopeptidase Complex ; Proteins/*metabolism ; Thermoplasma/enzymology ; Ubiquitins/metabolism
    Print ISSN: 0036-8075
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  • 10
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    Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-25
    Description: The high resolution three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystallized and analyzed at atomic resolution. Electron density distribution of the oxidized bovine cytochrome c oxidase at 2.8 A resolution indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a3 and CuA, at the interface of subunits I and II. The O2 binding site contains heme a3 iron and copper atoms (CuB) with an interatomic distance of 4.5 A; there is no detectable bridging ligand between iron and copper atoms in spite of a strong antiferromagnetic coupling between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a3 and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to CuB, suggesting a possible role in intramolecular electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A phenyl group located halfway between a pyrrole plane of the heme a3 and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsukihara, T -- Aoyama, H -- Yamashita, E -- Tomizaki, T -- Yamaguchi, H -- Shinzawa-Itoh, K -- Nakashima, R -- Yaono, R -- Yoshikawa, S -- New York, N.Y. -- Science. 1995 Aug 25;269(5227):1069-74.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Protein Research, Osaka University, Suita, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7652554" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cattle ; Copper/*analysis ; Crystallization ; Crystallography, X-Ray ; Electron Transport ; Electron Transport Complex IV/*chemistry/metabolism ; Fourier Analysis ; Heme/*analogs & derivatives/analysis ; Hydrogen Bonding ; Magnesium/*analysis ; Mitochondria, Heart/enzymology ; Models, Molecular ; Oxidation-Reduction ; Oxygen/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Proton Pumps ; Zinc/*analysis
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