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  • Amino Acid Sequence  (8)
  • American Association for the Advancement of Science (AAAS)  (8)
  • EDP Sciences
  • National Academy of Sciences
  • Oxford University Press
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (8)
  • EDP Sciences
  • National Academy of Sciences
  • Oxford University Press
  • Nature Publishing Group (NPG)  (4)
Years
  • 1
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    A proteolytic transmembrane signaling pathway and resistance to beta-lactams in staphylococci (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-10
    Description: beta-Lactamase and penicillin-binding protein 2a mediate staphylococcal resistance to beta-lactam antibiotics, which are otherwise highly clinically effective. Production of these inducible proteins is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which autoactivates, and the repressor, which is inactivated, unblocking gene transcription. Compounds that disrupt this regulatory pathway could restore the activity of beta-lactam antibiotics against drug-resistant strains of staphylococci.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, H Z -- Hackbarth, C J -- Chansky, K M -- Chambers, H F -- AI4005804/AI/NIAID NIH HHS/ -- AI46610/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 9;291(5510):1962-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Infectious Diseases, San Francisco General Hospital, Department of Medicine, University of California at San Francisco, 1001 Potrero Avenue, San Francisco, CA 94110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11239156" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacterial Proteins/chemistry/metabolism ; Carrier Proteins/chemistry/genetics/*metabolism ; Catalysis ; Cell Membrane/metabolism ; Cloning, Molecular ; DNA-Binding Proteins/chemistry/metabolism ; Genes, Regulator ; Metalloendopeptidases/chemistry/metabolism ; Mutagenesis, Site-Directed ; *Penicillin-Binding Proteins ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism ; *Signal Transduction ; Staphylococcus aureus/*drug effects/genetics/*metabolism ; Transformation, Bacterial ; *beta-Lactam Resistance ; beta-Lactamases/*biosynthesis ; beta-Lactams
    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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  • 2
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    DUBA: a deubiquitinase that regulates type I interferon production (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: Production of type I interferon (IFN-I) is a critical host defense triggered by pattern-recognition receptors (PRRs) of the innate immune system. Deubiquitinating enzyme A (DUBA), an ovarian tumor domain-containing deubiquitinating enzyme, was discovered in a small interfering RNA-based screen as a regulator of IFN-I production. Reduction of DUBA augmented the PRR-induced IFN-I response, whereas ectopic expression of DUBA had the converse effect. DUBA bound tumor necrosis factor receptor-associated factor 3 (TRAF3), an adaptor protein essential for the IFN-I response. TRAF3 is an E3 ubiquitin ligase that preferentially assembled lysine-63-linked polyubiquitin chains. DUBA selectively cleaved the lysine-63-linked polyubiquitin chains on TRAF3, resulting in its dissociation from the downstream signaling complex containing TANK-binding kinase 1. A discrete ubiquitin interaction motif within DUBA was required for efficient deubiquitination of TRAF3 and optimal suppression of IFN-I. Our data identify DUBA as a negative regulator of innate immune responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kayagaki, Nobuhiko -- Phung, Qui -- Chan, Salina -- Chaudhari, Ruchir -- Quan, Casey -- O'Rourke, Karen M -- Eby, Michael -- Pietras, Eric -- Cheng, Genhong -- Bazan, J Fernando -- Zhang, Zemin -- Arnott, David -- Dixit, Vishva M -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1628-32. Epub 2007 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991829" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Line ; Endopeptidases/*metabolism ; Humans ; Interferon Type I/*biosynthesis/genetics ; Interferon-alpha/genetics ; Molecular Sequence Data ; NF-kappa B/metabolism ; Protein Structure, Tertiary ; RNA, Small Interfering ; Signal Transduction ; TNF Receptor-Associated Factor 3/metabolism ; Toll-Like Receptor 3/metabolism ; Ubiquitin/metabolism ; Ubiquitination
    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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  • 3
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    Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: Acetylation of histone H3 lysine 56 (H3-K56) occurs in S phase, and cells lacking H3-K56 acetylation are sensitive to DNA-damaging agents. However, the histone acetyltransferase (HAT) that catalyzes global H3-K56 acetylation has not been found. Here we show that regulation of Ty1 transposition gene product 109 (Rtt109) is an H3-K56 HAT. Cells lacking Rtt109 or expressing rtt109 mutants with alterations at a conserved aspartate residue lose H3-K56 acetylation and exhibit increased sensitivity toward genotoxic agents, as well as elevated levels of spontaneous chromosome breaks. Thus, Rtt109, which shares no sequence homology with any other known HATs, is a unique HAT that acetylates H3-K56.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Junhong -- Zhou, Hui -- Horazdovsky, Bruce -- Zhang, Kangling -- Xu, Rui-Ming -- Zhang, Zhiguo -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):653-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272723" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Camptothecin/pharmacology ; Catalytic Domain ; Chromosome Breakage ; DNA Damage ; *DNA Replication ; Histone Acetyltransferases/chemistry/genetics/*metabolism ; Histones/*metabolism ; Hydroxyurea/pharmacology ; Lysine/*metabolism ; Methyl Methanesulfonate/pharmacology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutagens/pharmacology ; Mutation ; Recombinant Proteins/metabolism ; S Phase ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid
    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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  • 4
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    Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516815/" 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/PMC3516815/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Zhou, Tongqing -- Zhu, Jiang -- Zhang, Baoshan -- Georgiev, Ivelin -- Wang, Charlene -- Chen, Xuejun -- Longo, Nancy S -- Louder, Mark -- McKee, Krisha -- O'Dell, Sijy -- Perfetto, Stephen -- Schmidt, Stephen D -- Shi, Wei -- Wu, Lan -- Yang, Yongping -- Yang, Zhi-Yong -- Yang, Zhongjia -- Zhang, Zhenhai -- Bonsignori, Mattia -- Crump, John A -- Kapiga, Saidi H -- Sam, Noel E -- Haynes, Barton F -- Simek, Melissa -- Burton, Dennis R -- Koff, Wayne C -- Doria-Rose, Nicole A -- Connors, Mark -- NISC Comparative Sequencing Program -- Mullikin, James C -- Nabel, Gary J -- Roederer, Mario -- Shapiro, Lawrence -- Kwong, Peter D -- Mascola, John R -- 5U19 AI 067854-06/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1593-602. doi: 10.1126/science.1207532. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835983" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/genetics/*immunology/isolation & purification ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/metabolism ; Base Sequence ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; *Evolution, Molecular ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/genetics/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; HIV-1/chemistry/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin J-Chains/genetics ; Immunoglobulin Light Chains/chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 5
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    Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-01-24
    Description: Arabidopsis thaliana De-etiolated-1 (AtDET1) is a highly conserved protein, with orthologs in vertebrate and invertebrate organisms. AtDET1 negatively regulates photomorphogenesis, but its biochemical mechanism and function in other species are unknown. We report that human DET1 (hDET1) promotes ubiquitination and degradation of the proto-oncogenic transcription factor c-Jun by assembling a multisubunit ubiquitin ligase containing DNA Damage Binding Protein-1 (DDB1), cullin 4A (CUL4A), Regulator of Cullins-1 (ROC1), and constitutively photomorphogenic-1. Ablation of any subunit by RNA interference stabilized c-Jun and increased c-Jun-activated transcription. These findings characterize a c-Jun ubiquitin ligase and define a specific function for hDET1 in mammalian cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wertz, Ingrid E -- O'Rourke, Karen M -- Zhang, Zemin -- Dornan, David -- Arnott, David -- Deshaies, Raymond J -- Dixit, Vishva M -- GM065997/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1371-4. Epub 2004 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14739464" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cloning, Molecular ; Cullin Proteins/genetics/*metabolism ; DNA-Binding Proteins/metabolism ; Genes, jun ; Humans ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/metabolism ; Protein Binding ; Proteomics ; Proto-Oncogene Proteins c-jun/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Small Interfering/metabolism ; Transfection ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/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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  • 6
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    Rice prolamine protein body biogenesis: a BiP-mediated process (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-11-12
    Description: Rice prolamines are sequestered within the endoplasmic reticulum (ER) lumen even though they lack a lumenal retention signal. Immunochemical and biochemical data show that BiP, a protein that binds lumenal polypeptides, is localized on the surface of the aggregated prolamine protein bodies (PBs). BiP also forms complexes with nascent chains of prolamines in polyribosomes and with free prolamines with distinct adenosine triphosphate sensitivities. Thus, BiP retains prolamines in the lumen by facilitating their folding and assembly into PBs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, X -- Wu, Y -- Zhang, D Z -- Gillikin, J W -- Boston, R S -- Franceschi, V R -- Okita, T W -- New York, N.Y. -- Science. 1993 Nov 12;262(5136):1054-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Cell Biology, Washington State University, Pullman 99164.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8235623" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/pharmacology ; Amino Acid Sequence ; Endoplasmic Reticulum/metabolism ; Molecular Sequence Data ; Molecular Weight ; Oryza/*metabolism/ultrastructure ; Plant Proteins/chemistry/*metabolism ; Polyribosomes/metabolism ; Prolamins ; Protein Folding ; Puromycin/pharmacology
    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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  • 7
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    Activation of Rho GTPases by DOCK exchange factors is mediated by a nucleotide sensor (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-09-12
    Description: Activation of Rho guanosine triphosphatases (GTPases) to the guanine triphosphate (GTP)-bound state is a critical event in their regulation of the cytoskeleton and cell signaling. Members of the DOCK family of guanine nucleotide exchange factors (GEFs) are important activators of Rho GTPases, but the mechanism of activation by their catalytic DHR2 domain is unknown. Through structural analysis of DOCK9-Cdc42 complexes, we identify a nucleotide sensor within the alpha10 helix of the DHR2 domain that contributes to release of guanine diphosphate (GDP) and then to discharge of the activated GTP-bound Cdc42. Magnesium exclusion, a critical factor in promoting GDP release, is mediated by a conserved valine residue within this sensor, whereas binding of GTP-Mg2+ to the nucleotide-free complex results in magnesium-inducing displacement of the sensor to stimulate discharge of Cdc42-GTP. These studies identify an unusual mechanism of GDP release and define the complete GEF catalytic cycle from GDP dissociation followed by GTP binding and discharge of the activated GTPase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Jing -- Zhang, Ziguo -- Roe, S Mark -- Marshall, Christopher J -- Barford, David -- 10433/Cancer Research UK/United Kingdom -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2009 Sep 11;325(5946):1398-402. doi: 10.1126/science.1174468.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19745154" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Guanine Nucleotide Exchange Factors/*chemistry/*metabolism ; Guanosine Diphosphate/*metabolism ; Guanosine Triphosphate/*metabolism ; Humans ; Magnesium/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; cdc42 GTP-Binding Protein/*chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 8
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    Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-28
    Description: Polycomb repressive complex 2 (PRC2)-mediated histone H3 lysine 27 (H3K27) methylation is vital for Polycomb gene silencing, a classic epigenetic phenomenon that maintains transcriptional silencing throughout cell divisions. We report that PRC2 activity is regulated by the density of its substrate nucleosome arrays. Neighboring nucleosomes activate the PRC2 complex with a fragment of their H3 histones (Ala(31) to Arg(42)). We also identified mutations on PRC2 subunit Su(z)12, which impair its binding and response to the activating peptide and its ability in establishing H3K27 trimethylation levels in vivo. In mouse embryonic stem cells, local chromatin compaction occurs before the formation of trimethylated H3K27 upon transcription cessation of the retinoic acid-regulated gene CYP26a1. We propose that PRC2 can sense the chromatin environment to exert its role in the maintenance of transcriptional states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuan, Wen -- Wu, Tong -- Fu, Hang -- Dai, Chao -- Wu, Hui -- Liu, Nan -- Li, Xiang -- Xu, Mo -- Zhang, Zhuqiang -- Niu, Tianhui -- Han, Zhifu -- Chai, Jijie -- Zhou, Xianghong Jasmine -- Gao, Shaorong -- Zhu, Bing -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Aug 24;337(6097):971-5. doi: 10.1126/science.1225237.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College of Biological Sciences, China Agricultural University, Beijing 100094, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923582" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; CD4-Positive T-Lymphocytes ; Chromatin Immunoprecipitation ; Cytochrome P-450 Enzyme System/genetics ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster ; Embryonic Stem Cells ; Gene Silencing ; Histone-Lysine N-Methyltransferase/chemistry/genetics/*metabolism ; Histones/chemistry/genetics/*metabolism ; Humans ; Lysine/metabolism ; Methylation ; Mice ; Molecular Sequence Data ; Mutagenesis ; Nucleosomes/*metabolism/ultrastructure ; Peptide Fragments/metabolism ; Polycomb Repressive Complex 2 ; Polycomb-Group Proteins ; Repressor Proteins/chemistry/genetics/*metabolism ; *Transcription, Genetic
    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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