1n63: Difference between revisions

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 ==Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Carbon monoxide reduced state==
-<StructureSection load='1n63' size='340' side='right' caption='[[1n63]], [[Resolution|resolution]] 1.21&Aring;' scene=''>
+<StructureSection load='1n63' size='340' side='right'caption='[[1n63]], [[Resolution|resolution]] 1.21&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1n63]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Oligotropha_carboxidovorans Oligotropha carboxidovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N63 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1n63]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Afipia_carboxidovorans_OM5 Afipia carboxidovorans OM5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N63 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CUN:CU(I)-S-MO(IV)(=O)OH+CLUSTER'>CUN</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MCN:PTERIN+CYTOSINE+DINUCLEOTIDE'>MCN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.21&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1n5w|1n5w]], [[1n60|1n60]], [[1n61|1n61]], [[1n62|1n62]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CUN:CU(I)-S-MO(IV)(=O)OH+CLUSTER'>CUN</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MCN:PTERIN+CYTOSINE+DINUCLEOTIDE'>MCN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.2 1.2.99.2] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n63 OCA], [https://pdbe.org/1n63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n63 RCSB], [https://www.ebi.ac.uk/pdbsum/1n63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n63 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n63 RCSB], [http://www.ebi.ac.uk/pdbsum/1n63 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DCMS_OLICA DCMS_OLICA]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[http://www.uniprot.org/uniprot/DCMM_OLICA DCMM_OLICA]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[http://www.uniprot.org/uniprot/DCML_OLICA DCML_OLICA]] Catalyzes the oxidation of carbon monoxide to carbon dioxide.
+[https://www.uniprot.org/uniprot/DCMS_AFIC5 DCMS_AFIC5] Catalyzes the oxidation of carbon monoxide to carbon dioxide.<ref>PMID:12475995</ref> <ref>PMID:21275368</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n6/1n63_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n6/1n63_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n63 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The CO dehydrogenase of the eubacterium Oligotropha carboxidovorans is a 277-kDa Mo- and Cu-containing iron-sulfur flavoprotein. Here, the enzyme's active site in the oxidized or reduced state, after inactivation with potassium cyanide or with n-butylisocyanide bound to the active site, has been reinvestigated by multiple wavelength anomalous dispersion measurements at atomic resolution, electron spin resonance spectroscopy, and chemical analyses. We present evidence for a dinuclear heterometal [CuSMoO)OH] cluster in the active site of the oxidized or reduced enzyme, which is prone to cyanolysis. The cluster is coordinated through interactions of the Mo with the dithiolate pyran ring of molybdopterin cytosine dinucleotide and of the Cu with the Sgamma of Cys-388, which is part of the active-site loop VAYRC(388)SFR. The previously reported active-site structure [Dobbek, H., Gremer, L., Meyer, O. &amp; Huber, R. (1999) Proc. Natl. Acad. Sci. USA 96, 8884-8889] of an Mo with three oxygen ligands and an SeH-group bound to the Sgamma atom of Cys-388 could not be confirmed. The structure of CO dehydrogenase with the inhibitor n-butylisocyanide bound has led to a model for the catalytic mechanism of CO oxidation which involves a thiocarbonate-like intermediate state. The dinuclear [CuSMo(O)OH] cluster of CO dehydrogenase establishes a previously uncharacterized class of dinuclear molybdoenzymes containing the pterin cofactor.
-Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution.,Dobbek H, Gremer L, Kiefersauer R, Huber R, Meyer O Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15971-6. PMID:12475995<ref>PMID:12475995</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Carbon monoxide dehydrogenase|Carbon monoxide dehydrogenase]]
+*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Oligotropha carboxidovorans]]
+[[Category: Afipia carboxidovorans OM5]]
-[[Category: Dobbek, H]]
+[[Category: Large Structures]]
-[[Category: Gremer, L]]
+[[Category: Dobbek H]]
-[[Category: Huber, R]]
+[[Category: Gremer L]]
-[[Category: Kiefersauer, R]]
+[[Category: Huber R]]
-[[Category: Meyer, O]]
+[[Category: Kiefersauer R]]
-[[Category: Codh]]
+[[Category: Meyer O]]
-[[Category: Molybdenum]]
-[[Category: Molybdopterin]]
-[[Category: Oxidoreductase]]