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  • Binding Sites  (7)
  • American Association for the Advancement of Science (AAAS)  (7)
  • Oxford University Press
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  • American Association for the Advancement of Science (AAAS)  (7)
  • Oxford University Press
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  • 1
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    Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-18
    Description: The homodimeric nickel-containing CO dehydrogenase from the anaerobic bacterium Carboxydothermus hydrogenoformans catalyzes the oxidation of CO to CO2. A crystal structure of the reduced enzyme has been solved at 1.6 angstrom resolution. This structure represents the prototype for Ni-containing CO dehydrogenases from anaerobic bacteria and archaea. It contains five metal clusters of which clusters B, B', and a subunit-bridging, surface-exposed cluster D are cubane-type [4Fe-4S] clusters. The active-site clusters C and C' are novel, asymmetric [Ni-4Fe-5S] clusters. Their integral Ni ion, which is the likely site of CO oxidation, is coordinated by four sulfur ligands with square planar geometry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dobbek, H -- Svetlitchnyi, V -- Gremer, L -- Huber, R -- Meyer, O -- New York, N.Y. -- Science. 2001 Aug 17;293(5533):1281-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. dobbek@biochem.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11509720" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Oxidoreductases/*chemistry/*metabolism ; Bacteria, Anaerobic/*enzymology ; Binding Sites ; Carbon Dioxide/metabolism ; Carbon Monoxide/*metabolism ; Catalysis ; Chemistry, Physical ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; Hydrogen Bonding ; Iron/*chemistry/metabolism ; Ligands ; Models, Molecular ; Multienzyme Complexes/*chemistry/*metabolism ; Nickel/*chemistry/metabolism ; Oxidation-Reduction ; Peptococcaceae/*enzymology ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; Sulfur/*chemistry/metabolism
    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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    Prototype of a heme chaperone essential for cytochrome c maturation (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-08-26
    Description: Heme, the iron-containing cofactor essential for the activity of many enzymes, is incorporated into its target proteins by unknown mechanisms. Here, an Escherichia coli hemoprotein, CcmE, was shown to bind heme in the bacterial periplasm by way of a single covalent bond to a histidine. The heme was then released and delivered to apocytochrome c. Thus, CcmE can be viewed as a heme chaperone guiding heme to its appropriate biological partner and preventing illegitimate complex formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schulz, H -- Hennecke, H -- Thony-Meyer, L -- New York, N.Y. -- Science. 1998 Aug 21;281(5380):1197-200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mikrobiologisches Institut, Eidgenossische Technische Hochschule, Schmelzbergstrasse 7, CH-8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9712585" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Apoproteins/metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cytochrome c Group/*metabolism ; Cytochromes c ; Escherichia coli/genetics/*metabolism ; Heme/*metabolism ; Histidine/metabolism ; Mass Spectrometry ; Membrane Proteins/chemistry/genetics/*metabolism ; Molecular Chaperones/chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/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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  • 3
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    Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-21
    Description: To achieve X-chromosome dosage compensation, organisms must distinguish X chromosomes from autosomes. We identified multiple, cis-acting regions that recruit the Caenorhabditis elegans dosage compensation complex (DCC) through a search for regions of X that bind the complex when detached from X. The DCC normally assembles along the entire X chromosome, but not all detached regions recruit the complex, despite having genes known to be dosage compensated on the native X. Thus, the DCC binds first to recruitment sites, then spreads to neighboring X regions to accomplish chromosome-wide gene repression. From a large chromosomal domain, we defined a 793-base pair fragment that functions in vivo as an X-recognition element to recruit the DCC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Csankovszki, Gyorgyi -- McDonel, Patrick -- Meyer, Barbara J -- F32-GM065007/GM/NIGMS NIH HHS/ -- R37-GM30702/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Feb 20;303(5661):1182-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14976312" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/*genetics/metabolism ; Caenorhabditis elegans Proteins/*metabolism ; Carrier Proteins/metabolism ; Chromosomes/metabolism ; Cosmids ; DNA-Binding Proteins/metabolism ; Disorders of Sex Development ; *Dosage Compensation, Genetic ; Female ; In Situ Hybridization, Fluorescence ; Male ; Models, Genetic ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Repetitive Sequences, Nucleic Acid ; X Chromosome/*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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  • 4
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    The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-21
    Description: The structure of the heterodimeric flavocytochrome c sulfide dehydrogenase from Chromatium vinosum was determined at a resolution of 2.53 angstroms. It contains a glutathione reductase-like flavin-binding subunit and a diheme cytochrome subunit. The diheme cytochrome folds as two domains, each resembling mitochondrial cytochrome c, and has an unusual interpropionic acid linkage joining the two heme groups in the interior of the subunit. The active site of the flavoprotein subunit contains a catalytically important disulfide bridge located above the pyrimidine portion of the flavin ring. A tryptophan, threonine, or tyrosine side chain may provide a partial conduit for electron transfer to one of the heme groups located 10 angstroms from the flavin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Z W -- Koh, M -- Van Driessche, G -- Van Beeumen, J J -- Bartsch, R G -- Meyer, T E -- Cusanovich, M A -- Mathews, F S -- GM-20530/GM/NIGMS NIH HHS/ -- GM-21277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 21;266(5184):430-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939681" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromatium/*enzymology ; Computer Graphics ; Crystallography, X-Ray ; Cytochrome c Group/*chemistry ; Electron Transport ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Models, Molecular ; Oxidoreductases/*chemistry ; Protein Conformation ; Protein Structure, Secondary
    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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    A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-03
    Description: The plant hormone abscisic acid (ABA) mediates various responses such as stomatal closure, the maintenance of seed dormancy, and the inhibition of plant growth. All three responses are affected in the ABA-insensitive mutant abi1 of Arabidopsis thaliana, suggesting that an early step in the signaling of ABA is controlled by the ABI1 locus. The ABI1 gene was cloned by chromosome walking, and a missense mutation was identified in the structural gene of the abi1 mutant. The ABI1 gene encodes a protein with high similarity to protein serine or threonine phosphatases of type 2C with the novel feature of a putative Ca2+ binding site. Thus, the control of the phosphorylation state of cell signaling components by the ABI1 product could mediate pleiotropic hormone responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, K -- Leube, M P -- Grill, E -- New York, N.Y. -- Science. 1994 Jun 3;264(5164):1452-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Plant Sciences, Swiss Federal Institute of Technology, Zurich.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8197457" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/*pharmacology ; Amino Acid Sequence ; Arabidopsis/enzymology/genetics/*metabolism ; *Arabidopsis Proteins ; Binding Sites ; Calcium/metabolism ; Chromosome Walking ; Cloning, Molecular ; Genes, Plant ; Genetic Markers ; Molecular Sequence Data ; Mutation ; Phosphoprotein Phosphatases/chemistry/genetics/*metabolism ; Plants, Genetically Modified ; *Signal Transduction
    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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    The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-26
    Description: Biological formation and consumption of molecular hydrogen (H2) are catalyzed by hydrogenases, of which three phylogenetically unrelated types are known: [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenase. We present a crystal structure of [Fe]-hydrogenase at 1.75 angstrom resolution, showing a mononuclear iron coordinated by the sulfur of cysteine 176, two carbon monoxide (CO) molecules, and the sp2-hybridized nitrogen of a 2-pyridinol compound with back-bonding properties similar to those of cyanide. The three-dimensional arrangement of the ligands is similar to that of thiolate, CO, and cyanide ligated to the low-spin iron in binuclear [NiFe]- and [FeFe]-hydrogenases, although the enzymes have evolved independently and the CO and cyanide ligands are not found in any other metalloenzyme. The related iron ligation pattern of hydrogenases exemplifies convergent evolution and presumably plays an essential role in H2 activation. This finding may stimulate the ongoing synthesis of catalysts that could substitute for platinum in applications such as fuel cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shima, Seigo -- Pilak, Oliver -- Vogt, Sonja -- Schick, Michael -- Stagni, Marco S -- Meyer-Klaucke, Wolfram -- Warkentin, Eberhard -- Thauer, Rudolf K -- Ermler, Ulrich -- New York, N.Y. -- Science. 2008 Jul 25;321(5888):572-5. doi: 10.1126/science.1158978.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Terrestrische Mikrobiologie and Laboratorium fur Mikrobiologie, Fachbereich Biologie, Philipps-Universitat Marburg, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany. shima@mpi-marburg.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653896" target="_blank"〉PubMed〈/a〉
    Keywords: Apoenzymes/chemistry ; Binding Sites ; Carbon Monoxide/chemistry ; Catalytic Domain ; Coenzymes/chemistry ; Crystallography, X-Ray ; Cyanides/chemistry/metabolism ; Dimerization ; Evolution, Molecular ; Holoenzymes/chemistry ; Hydrogen/chemistry/*metabolism ; Hydrogenase/*chemistry/isolation & purification/metabolism ; Iron/chemistry ; Ligands ; Methane/biosynthesis ; Methanococcales/*enzymology ; Models, Molecular ; Oxidation-Reduction ; Protein Structure, Secondary ; Protein Structure, Tertiary
    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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    Identification of functional elements and regulatory circuits by Drosophila modENCODE (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-24
    Description: To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" 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/PMC3192495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉modENCODE Consortium -- Roy, Sushmita -- Ernst, Jason -- Kharchenko, Peter V -- Kheradpour, Pouya -- Negre, Nicolas -- Eaton, Matthew L -- Landolin, Jane M -- Bristow, Christopher A -- Ma, Lijia -- Lin, Michael F -- Washietl, Stefan -- Arshinoff, Bradley I -- Ay, Ferhat -- Meyer, Patrick E -- Robine, Nicolas -- Washington, Nicole L -- Di Stefano, Luisa -- Berezikov, Eugene -- Brown, Christopher D -- Candeias, Rogerio -- Carlson, Joseph W -- Carr, Adrian -- Jungreis, Irwin -- Marbach, Daniel -- Sealfon, Rachel -- Tolstorukov, Michael Y -- Will, Sebastian -- Alekseyenko, Artyom A -- Artieri, Carlo -- Booth, Benjamin W -- Brooks, Angela N -- Dai, Qi -- Davis, Carrie A -- Duff, Michael O -- Feng, Xin -- Gorchakov, Andrey A -- Gu, Tingting -- Henikoff, Jorja G -- Kapranov, Philipp -- Li, Renhua -- MacAlpine, Heather K -- Malone, John -- Minoda, Aki -- Nordman, Jared -- Okamura, Katsutomo -- Perry, Marc -- Powell, Sara K -- Riddle, Nicole C -- Sakai, Akiko -- Samsonova, Anastasia -- Sandler, Jeremy E -- Schwartz, Yuri B -- Sher, Noa -- Spokony, Rebecca -- Sturgill, David -- van Baren, Marijke -- Wan, Kenneth H -- Yang, Li -- Yu, Charles -- Feingold, Elise -- Good, Peter -- Guyer, Mark -- Lowdon, Rebecca -- Ahmad, Kami -- Andrews, Justen -- Berger, Bonnie -- Brenner, Steven E -- Brent, Michael R -- Cherbas, Lucy -- Elgin, Sarah C R -- Gingeras, Thomas R -- Grossman, Robert -- Hoskins, Roger A -- Kaufman, Thomas C -- Kent, William -- Kuroda, Mitzi I -- Orr-Weaver, Terry -- Perrimon, Norbert -- Pirrotta, Vincenzo -- Posakony, James W -- Ren, Bing -- Russell, Steven -- Cherbas, Peter -- Graveley, Brenton R -- Lewis, Suzanna -- Micklem, Gos -- Oliver, Brian -- Park, Peter J -- Celniker, Susan E -- Henikoff, Steven -- Karpen, Gary H -- Lai, Eric C -- MacAlpine, David M -- Stein, Lincoln D -- White, Kevin P -- Kellis, Manolis -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC2HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U01HG004261/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- U01HG004271/HG/NHGRI NIH HHS/ -- U01HG004274/HG/NHGRI NIH HHS/ -- U01HG004279/HG/NHGRI NIH HHS/ -- U41HG004269/HG/NHGRI NIH HHS/ -- ZIA DK015600-14/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177974" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Chromatin/genetics/metabolism ; Computational Biology/methods ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/growth & development/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genes, Insect ; *Genome, Insect ; Genomics/methods ; Histones/metabolism ; *Molecular Sequence Annotation ; Nucleosomes/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Small Untranslated/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic
    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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