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  • 1
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    A light-actuated nanovalve derived from a channel protein (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-30
    Description: Toward the realization of nanoscale device control, we report a molecular valve embedded in a membrane that can be opened by illumination with long-wavelength ultraviolet (366 nanometers) light and then resealed by visible irradiation. The valve consists of a channel protein, the mechanosensitive channel of large conductance (MscL) from Escherichia coli, modified by attachment of synthetic compounds that undergo light-induced charge separation to reversibly open and close a 3-nanometer pore. The system is compatible with a classical encapsulation system, the liposome, and external photochemical control over transport through the channel is achieved.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kocer, Armagan -- Walko, Martin -- Meijberg, Wim -- Feringa, Ben L -- New York, N.Y. -- Science. 2005 Jul 29;309(5735):755-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BiOMaDe Technology Foundation, Nijenborgh 4, 9747 AG Groningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16051792" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Cysteine/chemistry ; Escherichia coli Proteins/*chemistry ; Fluoresceins/chemistry ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Ion Channels/*chemistry ; *Light ; Lipid Bilayers ; Liposomes ; *Nanostructures ; Nanotechnology ; Osmolar Concentration ; Patch-Clamp Techniques ; Photolysis ; Protein Structure, Secondary ; *Ultraviolet Rays
    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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    Functional genomic analysis of the Wnt-wingless signaling pathway (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-09
    Description: The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DasGupta, Ramanuj -- Kaykas, Ajamete -- Moon, Randall T -- Perrimon, Norbert -- New York, N.Y. -- Science. 2005 May 6;308(5723):826-33. Epub 2005 Apr 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Howard Hughes Medical Institute (HHMI), Harvard Medical School, New Research Building, No. 339, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. rdasgupt@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15817814" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Line ; Cloning, Molecular ; Computational Biology ; Cytoskeletal Proteins/metabolism ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster/*genetics/metabolism ; Embryo, Nonmammalian/metabolism ; Embryonic Development ; Epistasis, Genetic ; *Gene Expression Regulation ; Genes, Insect ; Genes, Reporter ; *Genomics ; Mutation ; Phenotype ; Phosphorylation ; Protein Kinases/metabolism ; Proteins/metabolism ; Proto-Oncogene Proteins/genetics/*metabolism ; *RNA Interference ; *Signal Transduction ; Trans-Activators/metabolism ; Transcription Factors/chemistry/genetics/metabolism ; Transfection ; Wnt Proteins ; Wnt1 Protein ; Wnt3 Protein ; Zebrafish ; Zebrafish Proteins ; beta Catenin ; rab5 GTP-Binding Proteins/genetics/metabolism
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  • 3
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    Crystal structure of the malaria vaccine candidate apical membrane antigen 1 (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-02-26
    Description: Apical membrane antigen 1 from Plasmodium is a leading malaria vaccine candidate. The protein is essential for host-cell invasion, but its molecular function is unknown. The crystal structure of the three domains comprising the ectoplasmic region of the antigen from P. vivax, solved at 1.8 angstrom resolution, shows that domains I and II belong to the PAN motif, which defines a superfamily of protein folds implicated in receptor binding. We also mapped the epitope of an invasion-inhibitory monoclonal antibody specific for the P. falciparum ortholog and modeled this to the structure. The location of the epitope and current knowledge on structure-function correlations for PAN domains together suggest a receptor-binding role during invasion in which domain II plays a critical part. These results are likely to aid vaccine and drug design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pizarro, Juan Carlos -- Vulliez-Le Normand, Brigitte -- Chesne-Seck, Marie-Laure -- Collins, Christine R -- Withers-Martinez, Chrislaine -- Hackett, Fiona -- Blackman, Michael J -- Faber, Bart W -- Remarque, Edmond J -- Kocken, Clemens H M -- Thomas, Alan W -- Bentley, Graham A -- MC_U117532063/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):408-11. Epub 2005 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unite d'Immunologie Structurale, Centre National de la Recherche Scientifique, URA 2185, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15731407" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Antibodies, Monoclonal/immunology ; Antigens, Protozoan/*chemistry/immunology ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Epitope Mapping ; Epitopes ; Heparin/metabolism ; Malaria Vaccines ; Membrane Proteins/*chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Plasmodium falciparum/chemistry/immunology ; Plasmodium vivax/chemistry/*immunology ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protozoan Proteins/*chemistry/immunology ; Recombinant Proteins/chemistry ; Sequence Alignment
    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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  • 4
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    Complement factor H variant increases the risk of age-related macular degeneration (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-03-12
    Description: Age-related macular degeneration (AMD) is a leading cause of visual impairment and blindness in the elderly whose etiology remains largely unknown. Previous studies identified chromosome 1q32 as harboring a susceptibility locus for AMD. We used single-nucleotide polymorphisms to interrogate this region and identified a strongly associated haplotype in two independent data sets. DNA resequencing of the complement factor H gene within this haplotype revealed a common coding variant, Y402H, that significantly increases the risk for AMD with odds ratios between 2.45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haines, Jonathan L -- Hauser, Michael A -- Schmidt, Silke -- Scott, William K -- Olson, Lana M -- Gallins, Paul -- Spencer, Kylee L -- Kwan, Shu Ying -- Noureddine, Maher -- Gilbert, John R -- Schnetz-Boutaud, Nathalie -- Agarwal, Anita -- Postel, Eric A -- Pericak-Vance, Margaret A -- AG11268/AG/NIA NIH HHS/ -- EY015216/EY/NEI NIH HHS/ -- EY12118/EY/NEI NIH HHS/ -- M01 RR-00095/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):419-21. Epub 2005 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15761120" target="_blank"〉PubMed〈/a〉
    Keywords: Aged ; Alleles ; Binding Sites ; C-Reactive Protein/metabolism ; Case-Control Studies ; Chromosomes, Human, Pair 1/genetics ; Complement Activation ; Complement Factor H/analysis/*genetics/physiology ; Gene Frequency ; Genetic Predisposition to Disease ; *Genetic Variation ; Genotype ; Haplotypes ; Heparin/metabolism ; Humans ; Linkage Disequilibrium ; Macular Degeneration/*genetics ; Odds Ratio ; *Polymorphism, Single Nucleotide ; Risk Factors ; Sequence Analysis, DNA ; Smoking
    Print ISSN: 0036-8075
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  • 5
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    Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-10-01
    Description: Chlorinated natural products include vancomycin and cryptophycin A. Their biosynthesis involves regioselective chlorination by flavin-dependent halogenases. We report the structural characterization of tryptophan 7-halogenase (PrnA), which regioselectively chlorinates tryptophan. Tryptophan and flavin adenine dinucleotide (FAD) are separated by a 10 angstrom-long tunnel and bound by distinct enzyme modules. The FAD module is conserved in halogenases and is related to flavin-dependent monooxygenases. On the basis of biochemical studies, crystal structures, and by analogy with monooxygenases, we predict that FADH2 reacts with O2 to make peroxyflavin, which is decomposed by Cl-. The resulting HOCl is guided through the tunnel to tryptophan, where it is activated to participate in electrophilic aromatic substitution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315827/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315827/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Changjiang -- Flecks, Silvana -- Unversucht, Susanne -- Haupt, Caroline -- van Pee, Karl-Heinz -- Naismith, James H -- BB/C000080/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/14426/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Sep 30;309(5744):2216-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Biomolecular Sciences, EaStchem, University of St. Andrews, St. Andrews KY16 9ST, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16195462" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chlorides/*metabolism ; Crystallography, X-Ray ; Dimerization ; Flavin-Adenine Dinucleotide/analogs & derivatives/metabolism ; Hydrogen Bonding ; Hypochlorous Acid/metabolism ; Indoles/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*chemistry/isolation & purification/metabolism ; Oxygen/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Pseudomonas fluorescens/*enzymology ; Tryptophan/analogs & derivatives/metabolism
    Print ISSN: 0036-8075
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  • 6
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    Structural roles for human translation factor eIF3 in initiation of protein synthesis (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-03
    Description: Protein synthesis in mammalian cells requires initiation factor eIF3, a approximately 750-kilodalton complex that controls assembly of 40S ribosomal subunits on messenger RNAs (mRNAs) bearing either a 5'-cap or an internal ribosome entry site (IRES). Cryo-electron microscopy reconstructions show that eIF3, a five-lobed particle, interacts with the hepatitis C virus (HCV) IRES RNA and the 5'-cap binding complex eIF4F via the same domain. Detailed modeling of eIF3 and eIF4F onto the 40S ribosomal subunit reveals that eIF3 uses eIF4F or the HCV IRES in structurally similar ways to position the mRNA strand near the exit site of 40S, promoting initiation complex assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siridechadilok, Bunpote -- Fraser, Christopher S -- Hall, Richard J -- Doudna, Jennifer A -- Nogales, Eva -- New York, N.Y. -- Science. 2005 Dec 2;310(5753):1513-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16322461" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Eukaryotic Initiation Factor-3/chemistry/*physiology/ultrastructure ; Eukaryotic Initiation Factor-4F/metabolism ; HeLa Cells ; Hepacivirus/genetics ; Humans ; Models, Molecular ; Protein Binding ; Protein Biosynthesis/*physiology ; Protein Conformation ; RNA, Messenger/metabolism ; RNA, Viral/metabolism ; Ribosomes/metabolism ; Structure-Activity Relationship
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  • 7
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    Immunology. Insects diversify one molecule to serve two systems (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Du Pasquier, Louis -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1826-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Zoology and Evolutionary Biology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland. dupasquier@dial.eunet.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16166509" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Animals ; Axons/physiology ; Binding Sites ; Biological Evolution ; Cell Adhesion Molecules ; Drosophila Proteins/chemistry/*genetics/*immunology/metabolism ; Drosophila melanogaster/*genetics/*immunology ; Genetic Variation ; Hemocytes/immunology/*metabolism ; Humans ; Immunity, Innate ; Immunoglobulins/chemistry ; Membrane Proteins ; Neurons/metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; Proteins/genetics/physiology ; Receptors, Antigen/immunology/metabolism ; Vertebrates/physiology
    Print ISSN: 0036-8075
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  • 8
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    Structure of SARS coronavirus spike receptor-binding domain complexed with receptor (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-09-17
    Description: The spike protein (S) of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). A defined receptor-binding domain (RBD) on S mediates this interaction. The crystal structure at 2.9 angstrom resolution of the RBD bound with the peptidase domain of human ACE2 shows that the RBD presents a gently concave surface, which cradles the N-terminal lobe of the peptidase. The atomic details at the interface between the two proteins clarify the importance of residue changes that facilitate efficient cross-species infection and human-to-human transmission. The structure of the RBD suggests ways to make truncated disulfide-stabilized RBD variants for use in the design of coronavirus vaccines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Fang -- Li, Wenhui -- Farzan, Michael -- Harrison, Stephen C -- AI061601/AI/NIAID NIH HHS/ -- CA13202/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2005 Sep 16;309(5742):1864-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and 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/16166518" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Viral/immunology ; Binding Sites ; Carboxypeptidases/*chemistry/metabolism ; Cell Line ; Crystallography, X-Ray ; Disease Outbreaks ; Epitopes ; Glycosylation ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/*chemistry/genetics/immunology/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Peptidyl-Dipeptidase A ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Virus/*chemistry/metabolism ; SARS Virus/*chemistry/genetics/physiology ; Severe Acute Respiratory Syndrome/transmission/*virology ; Species Specificity ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins/*chemistry/genetics/immunology/*metabolism ; Viral Vaccines ; Viverridae/virology
    Print ISSN: 0036-8075
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  • 9
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    Structural insights into the activity of enhancer-binding proteins (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-03-26
    Description: Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756573/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756573/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rappas, Mathieu -- Schumacher, Jorg -- Beuron, Fabienne -- Niwa, Hajime -- Bordes, Patricia -- Wigneshweraraj, Sivaramesh -- Keetch, Catherine A -- Robinson, Carol V -- Buck, Martin -- Zhang, Xiaodong -- B17129/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2005 Mar 25;307(5717):1972-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15790859" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA-Binding Proteins/chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; PII Nitrogen Regulatory Proteins ; *Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase Sigma 54 ; Sigma Factor/chemistry/metabolism ; Trans-Activators/*chemistry/*metabolism ; Transcription Factors/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 10
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    Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-08
    Description: The P1 lysozyme Lyz is secreted to the periplasm of Escherichia coli and accumulates in an inactive membrane-tethered form. Genetic and biochemical experiments show that, when released from the bilayer, Lyz is activated by an intramolecular thiol-disulfide isomerization, which requires a cysteine in its N-terminal SAR (signal-arrest-release) domain. Crystal structures confirm the alternative disulfide linkages in the two forms of Lyz and reveal dramatic conformational differences in the catalytic domain. Thus, the exported P1 endolysin is kept inactive by three levels of control-topological, conformational, and covalent-until its release from the membrane is triggered by the P1 holin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Min -- Arulandu, Arockiasamy -- Struck, Douglas K -- Swanson, Stephanie -- Sacchettini, James C -- Young, Ry -- GM27099/GM/NIGMS NIH HHS/ -- GM62410/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):113-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637279" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage P1/*enzymology ; Binding Sites ; Catalytic Domain ; Cell Membrane/enzymology ; Chemistry, Physical ; Crystallography, X-Ray ; Cysteine/chemistry ; Enzyme Activation ; Escherichia coli/enzymology/virology ; Isomerism ; Lipid Bilayers ; Models, Molecular ; Molecular Sequence Data ; Muramidase/*chemistry/genetics/*metabolism ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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