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  • 1
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    Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-14
    Description: The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded beta-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714533/" 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/PMC2714533/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holden, Lauren G -- Prochnow, Courtney -- Chang, Y Paul -- Bransteitter, Ronda -- Chelico, Linda -- Sen, Udayaditya -- Stevens, Raymond C -- Goodman, Myron F -- Chen, Xiaojiang S -- R01 AI055926/AI/NIAID NIH HHS/ -- R01 AI055926-05/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Nov 6;456(7218):121-4. doi: 10.1038/nature07357. Epub 2008 Oct 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849968" target="_blank"〉PubMed〈/a〉
    Keywords: Antiviral Agents ; *Catalytic Domain ; Crystallography, X-Ray ; Cytidine Deaminase/*chemistry/genetics/isolation & purification/*metabolism ; DNA, Single-Stranded/metabolism ; Escherichia coli ; Humans ; Models, Molecular ; Muscle Proteins/chemistry ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; Structural Homology, Protein ; Structure-Activity Relationship ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-18
    Description: The hemagglutinin (HA) structure at 2.9 angstrom resolution, from a highly pathogenic Vietnamese H5N1 influenza virus, is more related to the 1918 and other human H1 HAs than to a 1997 duck H5 HA. Glycan microarray analysis of this Viet04 HA reveals an avian alpha2-3 sialic acid receptor binding preference. Introduction of mutations that can convert H1 serotype HAs to human alpha2-6 receptor specificity only enhanced or reduced affinity for avian-type receptors. However, mutations that can convert avian H2 and H3 HAs to human receptor specificity, when inserted onto the Viet04 H5 HA framework, permitted binding to a natural human alpha2-6 glycan, which suggests a path for this H5N1 virus to gain a foothold in the human population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, James -- Blixt, Ola -- Tumpey, Terrence M -- Taubenberger, Jeffery K -- Paulson, James C -- Wilson, Ian A -- AI058113/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- GM060938/GM/NIGMS NIH HHS/ -- GM062116/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 21;312(5772):404-10. Epub 2006 Mar 16.〈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. jstevens@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16543414" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antigenic Variation ; Binding Sites ; Birds ; Carbohydrate Conformation ; Cloning, Molecular ; Crystallography, X-Ray ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza ; Virus/*chemistry/genetics/immunology/*metabolism ; Humans ; Influenza A Virus, H5N1 Subtype/*chemistry/genetics/metabolism/*pathogenicity ; Lung/virology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Polysaccharides/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Receptors, Virus/chemistry/*metabolism ; Respiratory Mucosa/virology ; Sialic Acids/chemistry/metabolism ; Species Specificity ; Virulence
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-27
    Description: Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound to the partial inverse agonist carazolol at 2.4 angstrom resolution. The structure provides a high-resolution view of a human G protein-coupled receptor bound to a diffusible ligand. Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair of closely spaced disulfide bridges and a short helical segment within the loop. Cholesterol, a necessary component for crystallization, mediates an intriguing parallel association of receptor molecules in the crystal lattice. Although the location of carazolol in the beta2-adrenergic receptor is very similar to that of retinal in rhodopsin, structural differences in the ligand-binding site and other regions highlight the challenges in using rhodopsin as a template model for this large receptor family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583103/" 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/PMC2583103/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cherezov, Vadim -- Rosenbaum, Daniel M -- Hanson, Michael A -- Rasmussen, Soren G F -- Thian, Foon Sun -- Kobilka, Tong Sun -- Choi, Hee-Jung -- Kuhn, Peter -- Weis, William I -- Kobilka, Brian K -- Stevens, Raymond C -- F32 GM082028/GM/NIGMS NIH HHS/ -- GM075915/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- P50 GM062411/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-04/GM/NIGMS NIH HHS/ -- R01 GM056169/GM/NIGMS NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- R21 GM075811/GM/NIGMS NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-030001/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 23;318(5854):1258-65. Epub 2007 Oct 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962520" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage T4/enzymology ; Binding Sites ; Cell Membrane/chemistry/metabolism ; Cholesterol/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Drug Inverse Agonism ; Humans ; Ligands ; Models, Molecular ; Muramidase/chemistry/metabolism ; Propanolamines/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Adrenergic, beta-2/*chemistry/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Rhodopsin/chemistry/metabolism ; Static Electricity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-27
    Description: The beta2-adrenergic receptor (beta2AR) is a well-studied prototype for heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) that respond to diffusible hormones and neurotransmitters. To overcome the structural flexibility of the beta2AR and to facilitate its crystallization, we engineered a beta2AR fusion protein in which T4 lysozyme (T4L) replaces most of the third intracellular loop of the GPCR ("beta2AR-T4L") and showed that this protein retains near-native pharmacologic properties. Analysis of adrenergic receptor ligand-binding mutants within the context of the reported high-resolution structure of beta2AR-T4L provides insights into inverse-agonist binding and the structural changes required to accommodate catecholamine agonists. Amino acids known to regulate receptor function are linked through packing interactions and a network of hydrogen bonds, suggesting a conformational pathway from the ligand-binding pocket to regions that interact with G proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rosenbaum, Daniel M -- Cherezov, Vadim -- Hanson, Michael A -- Rasmussen, Soren G F -- Thian, Foon Sun -- Kobilka, Tong Sun -- Choi, Hee-Jung -- Yao, Xiao-Jie -- Weis, William I -- Stevens, Raymond C -- Kobilka, Brian K -- F32 GM082028/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM62411/GM/NIGMS NIH HHS/ -- R01 GM056169/GM/NIGMS NIH HHS/ -- R21 GM075811/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 23;318(5854):1266-73. Epub 2007 Oct 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, 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/17962519" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-Agonists/chemistry/metabolism ; Adrenergic beta-Antagonists/chemistry/metabolism ; Amino Acid Sequence ; Bacteriophage T4/enzymology ; Binding Sites ; Cell Line ; Cell Membrane/chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Drug Inverse Agonism ; Humans ; Immunoglobulin Fab Fragments/chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Muramidase/chemistry/metabolism ; Propanolamines/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Adrenergic, beta-2/*chemistry/*metabolism ; Recombinant Fusion Proteins/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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  • 5
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    The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-04
    Description: The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A2A adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586971/" 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/PMC2586971/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaakola, Veli-Pekka -- Griffith, Mark T -- Hanson, Michael A -- Cherezov, Vadim -- Chien, Ellen Y T -- Lane, J Robert -- Ijzerman, Adriaan P -- Stevens, Raymond C -- GM075915/GM/NIGMS NIH HHS/ -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-04/GM/NIGMS NIH HHS/ -- R01 GM089857/GM/NIGMS NIH HHS/ -- U54 GM074961/GM/NIGMS NIH HHS/ -- U54 GM074961-04/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 21;322(5905):1211-7. doi: 10.1126/science.1164772. Epub 2008 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18832607" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine A2 Receptor Antagonists ; Animals ; Binding Sites ; Crystallography, X-Ray ; Humans ; Ligands ; Protein Binding ; Protein Conformation ; Receptor, Adenosine A2A/*chemistry ; Structure-Activity Relationship ; Triazines/chemistry ; Triazoles/chemistry ; Tryptophan/chemistry ; Turkeys
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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