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  • Binding Sites  (18)
  • American Association for the Advancement of Science (AAAS)  (18)
  • American Association for the Advancement of Science
  • American Chemical Society
  • Cambridge University Press
  • 2000-2004  (18)
  • 1940-1944
  • 2002  (18)
Collection
Keywords
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  • American Association for the Advancement of Science (AAAS)  (18)
  • American Association for the Advancement of Science
  • American Chemical Society
  • Cambridge University Press
Years
  • 2000-2004  (18)
  • 1940-1944
Year
  • 1
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    A natural product that lowers cholesterol as an antagonist ligand for FXR (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-04
    Description: Extracts of the resin of the guggul tree (Commiphora mukul) lower LDL (low-density lipoprotein) cholesterol levels in humans. The plant sterol guggulsterone [4,17(20)-pregnadiene-3,16-dione] is the active agent in this extract. We show that guggulsterone is a highly efficacious antagonist of the farnesoid X receptor (FXR), a nuclear hormone receptor that is activated by bile acids. Guggulsterone treatment decreases hepatic cholesterol in wild-type mice fed a high-cholesterol diet but is not effective in FXR-null mice. Thus, we propose that inhibition of FXR activation is the basis for the cholesterol-lowering activity of guggulsterone. Other natural products with specific biologic effects may modulate the activity of FXR or other relatively promiscuous nuclear hormone receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Urizar, Nancy L -- Liverman, Amy B -- Dodds, D'Nette T -- Silva, Frank Valentin -- Ordentlich, Peter -- Yan, Yingzhuo -- Gonzalez, Frank J -- Heyman, Richard A -- Mangelsdorf, David J -- Moore, David D -- New York, N.Y. -- Science. 2002 May 31;296(5573):1703-6. Epub 2002 May 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11988537" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Caco-2 Cells ; Carrier Proteins/genetics/metabolism ; Cells, Cultured ; Chenodeoxycholic Acid/pharmacology ; Cholesterol/*metabolism ; Cholesterol, Dietary/administration & dosage ; DNA/metabolism ; DNA-Binding Proteins/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Hepatocytes/metabolism ; Histone Acetyltransferases ; Humans ; *Hydroxysteroid Dehydrogenases ; Hypolipidemic Agents/metabolism/*pharmacology ; Ligands ; Liver/metabolism ; *Membrane Glycoproteins ; Mice ; Nuclear Receptor Coactivator 1 ; Pregnenediones/metabolism/*pharmacology ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors/genetics/metabolism ; Receptors, Steroid/antagonists & inhibitors/metabolism ; Transcription Factors/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Transcriptional Activation/drug effects ; Transfection ; Tumor Cells, Cultured
    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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    Enzyme dynamics during catalysis (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-23
    Description: Internal protein dynamics are intimately connected to enzymatic catalysis. However, enzyme motions linked to substrate turnover remain largely unknown. We have studied dynamics of an enzyme during catalysis at atomic resolution using nuclear magnetic resonance relaxation methods. During catalytic action of the enzyme cyclophilin A, we detect conformational fluctuations of the active site that occur on a time scale of hundreds of microseconds. The rates of conformational dynamics of the enzyme strongly correlate with the microscopic rates of substrate turnover. The present results, together with available structural data, allow a prediction of the reaction trajectory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eisenmesser, Elan Zohar -- Bosco, Daryl A -- Akke, Mikael -- Kern, Dorothee -- GM62117/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Feb 22;295(5559):1520-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11859194" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Cyclophilin A/*chemistry/*metabolism ; Hydrogen Bonding ; Isomerism ; Kinetics ; Mathematics ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation
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  • 3
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    Structure of a cofactor-deficient nitrogenase MoFe protein (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-04-16
    Description: One of the most complex biosynthetic processes in metallobiochemistry is the assembly of nitrogenase, the key enzyme in biological nitrogen fixation. We describe here the crystal structure of an iron-molybdenum cofactor-deficient form of the nitrogenase MoFe protein, into which the cofactor is inserted in the final step of MoFe protein assembly. The MoFe protein folds as a heterotetramer containing two copies each of the homologous alpha and beta subunits. In this structure, one of the three alpha subunit domains exhibits a substantially changed conformation, whereas the rest of the protein remains essentially unchanged. A predominantly positively charged funnel is revealed; this funnel is of sufficient size to accommodate insertion of the negatively charged cofactor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmid, Benedikt -- Ribbe, Markus W -- Einsle, Oliver -- Yoshida, Mika -- Thomas, Leonard M -- Dean, Dennis R -- Rees, Douglas C -- Burgess, Barbara K -- New York, N.Y. -- Science. 2002 Apr 12;296(5566):352-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Mail Code 147-75CH, 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/11951047" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Azotobacter vinelandii/*enzymology ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Molybdoferredoxin/*chemistry/genetics/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Static Electricity ; Surface Properties
    Print ISSN: 0036-8075
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  • 4
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    Structural basis of gating by the outer membrane transporter FecA (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-02
    Description: Siderophore-mediated acquisition systems facilitate iron uptake. We present the crystallographic structure of the integral outer membrane receptor FecA from Escherichia coli with and without ferric citrate at 2.5 and 2.0 angstrom resolution. FecA is composed of three distinct domains: the barrel, plug, and NH2-terminal extension. Binding of ferric citrate triggers a conformational change of the extracellular loops that close the external pocket of FecA. Ligand-induced allosteric transitions are propagated through the outer membrane by the plug domain, signaling the occupancy of the receptor in the periplasm. These data establish the structural basis of gating for receptors dependent on the cytoplasmic membrane protein TonB. By compiling available data for this family of receptors, we propose a mechanism for the energy-dependent transport of siderophores.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferguson, Andrew D -- Chakraborty, Ranjan -- Smith, Barbara S -- Esser, Lothar -- van der Helm, Dick -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2002 Mar 1;295(5560):1715-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11872840" target="_blank"〉PubMed〈/a〉
    Keywords: Adsorption ; Bacterial Outer Membrane Proteins/chemistry/metabolism ; Bacterial Proteins/metabolism ; Binding Sites ; Biological Transport, Active ; Carrier Proteins/*chemistry/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry/metabolism ; Ferric Compounds/*metabolism ; Hydrogen Bonding ; *Ion Channel Gating ; Ligands ; Membrane Proteins/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Receptors, Cell Surface ; Siderophores/*metabolism ; Static Electricity
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  • 5
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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
    Print ISSN: 0036-8075
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  • 6
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    Regulation of corepressor function by nuclear NADH (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-16
    Description: The corepressor CtBP (carboxyl-terminal binding protein) is involved in transcriptional pathways important for development, cell cycle regulation, and transformation. We demonstrate that CtBP binding to cellular and viral transcriptional repressors is regulated by the nicotinamide adenine dinucleotides NAD+ and NADH, with NADH being two to three orders of magnitude more effective. Levels of free nuclear nicotinamide adenine dinucleotides, determined using two-photon microscopy, correspond to the levels required for half-maximal CtBP binding and are considerably lower than those previously reported. Agents capable of increasing NADH levels stimulate CtBP binding to its partners in vivo and potentiate CtBP-mediated repression. We propose that this ability to detect changes in nuclear NAD+/NADH ratio allows CtBP to serve as a redox sensor for transcription.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Qinghong -- Piston, David W -- Goodman, Richard H -- K01 CA096561/CA/NCI NIH HHS/ -- R01 CA115468/CA/NCI NIH HHS/ -- R01 CA115468-05/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 8;295(5561):1895-7. Epub 2002 Feb 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97201, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11847309" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus E1A Proteins/metabolism ; Alcohol Oxidoreductases ; Amino Acid Sequence ; Animals ; Binding Sites ; Cadherins/genetics ; Cell Nucleus/*metabolism ; Cytoplasm/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; *Gene Expression Regulation ; HeLa Cells ; Homeodomain Proteins/metabolism ; Humans ; Microscopy, Fluorescence ; Molecular Sequence Data ; Mutation ; NAD/*metabolism ; Oxidation-Reduction ; Phosphoproteins/chemistry/genetics/*metabolism ; Promoter Regions, Genetic ; Protein Binding ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/*metabolism ; *Transcription Factors ; Transcription, Genetic ; Transfection
    Print ISSN: 0036-8075
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  • 7
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    Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-11-09
    Description: Electron tomography of vitrified cells is a noninvasive three-dimensional imaging technique that opens up new vistas for exploring the supramolecular organization of the cytoplasm. We applied this technique to Dictyostelium cells, focusing on the actin cytoskeleton. In actin networks reconstructed without prior removal of membranes or extraction of soluble proteins, the cross-linking of individual microfilaments, their branching angles, and membrane attachment sites can be analyzed. At a resolution of 5 to 6 nanometers, single macromolecules with distinct shapes, such as the 26S proteasome, can be identified in an unperturbed cellular environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Medalia, Ohad -- Weber, Igor -- Frangakis, Achilleas S -- Nicastro, Daniela -- Gerisch, Gunther -- Baumeister, Wolfgang -- New York, N.Y. -- Science. 2002 Nov 8;298(5596):1209-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12424373" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/chemistry/metabolism/*ultrastructure ; Actins/ultrastructure ; Animals ; Binding Sites ; Cell Membrane/metabolism/ultrastructure ; Cell Movement ; Dictyostelium/chemistry/physiology/*ultrastructure ; Endoplasmic Reticulum, Rough/ultrastructure ; Freezing ; *Image Processing, Computer-Assisted ; Macromolecular Substances ; Microfilament Proteins/*ultrastructure ; Organelles/*ultrastructure ; Peptide Hydrolases/ultrastructure ; *Proteasome Endopeptidase Complex ; Proteome ; Protozoan Proteins/ultrastructure ; Ribosomes/ultrastructure ; Tomography/*methods
    Print ISSN: 0036-8075
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  • 8
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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
    Print ISSN: 0036-8075
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  • 9
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    Synthesis beyond the molecule (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-30
    Description: Weak, noncovalent interactions between molecules control many biological functions. In chemistry, noncovalent interactions are now exploited for the synthesis in solution of large supramolecular aggregates. The aim of these syntheses is not only the creation of a particular structure, but also the introduction of specific chemical functions in these supramolecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reinhoudt, D N -- Crego-Calama, M -- New York, N.Y. -- Science. 2002 Mar 29;295(5564):2403-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Supramolecular Chemistry and Technology, University of Twente, Post Office Box 217, 7500 AE Enschede, Netherlands. d.n.reinhoudt@ct.utwente.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11923525" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; *Chemistry/methods ; Chemistry, Physical ; Evolution, Chemical ; Molecular Conformation ; Molecular Structure ; Nanotechnology ; Oligonucleotides/chemistry ; Origin of Life ; Peptides/chemistry ; Physicochemical Phenomena ; Polymers/*chemical synthesis/*chemistry ; Stereoisomerism ; Templates, Genetic
    Print ISSN: 0036-8075
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  • 10
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    Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-21
    Description: Acetyl-coenzyme A (CoA) synthetase (Acs) is an enzyme central to metabolism in prokaryotes and eukaryotes. Acs synthesizes acetyl CoA from acetate, adenosine triphosphate, and CoA through an acetyl-adenosine monophosphate (AMP) intermediate. Immunoblotting and mass spectrometry analysis showed that Salmonella enterica Acs enzyme activity is posttranslationally regulated by acetylation of lysine-609. Acetylation blocks synthesis of the adenylate intermediate but does not affect the thioester-forming activity of the enzyme. Activation of the acetylated enzyme requires the nicotinamide adenine dinucleotide-dependent protein deacetylase activity of the CobB Sir2 protein from S. enterica. We propose that acetylation modulates the activity of all the AMP-forming family of enzymes, including nonribosomal peptide synthetases, luciferase, and aryl- and acyl-CoA synthetases. These findings extend our knowledge of the roles of Sir2 proteins in gene silencing, chromosome stability, and cell aging and imply that lysine acetylation is a common regulatory mechanism in eukaryotes and prokaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Starai, V J -- Celic, I -- Cole, R N -- Boeke, J D -- Escalante-Semerena, J C -- 1S10-RR14702/RR/NCRR NIH HHS/ -- GM62203/GM/NIGMS NIH HHS/ -- GM62385/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 20;298(5602):2390-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin, Madison, WI 53706-1567, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12493915" target="_blank"〉PubMed〈/a〉
    Keywords: Acetate-CoA Ligase/chemistry/genetics/*metabolism ; Acetylation ; Acyl Coenzyme A/metabolism ; Adenosine Monophosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/*metabolism ; Binding Sites ; Coenzyme A/metabolism ; Conserved Sequence ; Enzyme Activation ; Gene Expression Regulation, Bacterial ; Immunoblotting ; Lysine/*metabolism ; Mass Spectrometry ; NAD/metabolism ; Peptide Mapping ; Salmonella enterica/*enzymology/genetics ; Sirtuins/*metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
    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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