1n62 - Revision history

OCA at 13:27, 13 March 2024

2024-03-13T13:27:32Z

←Older revision		Revision as of 13:27, 13 March 2024
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	<StructureSection load='1n62' size='340' side='right'caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>		<StructureSection load='1n62' size='340' side='right'caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n62]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Oligotropha_carboxidovorans Oligotropha~~ carboxidovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N62 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n62]] 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=1N62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N62 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CUB:CU(I)-S-MO(IV)(=O)O-NBIC+CLUSTER'>CUB</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]] 1.09Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CUB:CU(I)-S-MO(IV)(=O)O-NBIC+CLUSTER'>CUB</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'>[https://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [https://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=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [https://pdbe.org/1n62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [https://www.ebi.ac.uk/pdbsum/1n62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n62 ProSAT]</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=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [https://pdbe.org/1n62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [https://www.ebi.ac.uk/pdbsum/1n62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n62 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~DCMS_OLICO DCMS_OLICO]~~] Catalyzes the oxidation of carbon monoxide to carbon dioxide. ~~[[https~~:/~~/www.uniprot.org/uniprot/DCMM_OLICO DCMM_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[https~~:/~~/www.uniprot.org/uniprot/DCML_OLICO DCML_OLICO]] 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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1n62 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=1n62 ConSurf].
	<div style="clear:both"></div>		<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. & 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1n62" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Afipia carboxidovorans OM5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Oligotropha carboxidovorans]]~~	+	[[Category: Dobbek H]]
-	[[Category: Dobbek, H]]	+	[[Category: Gremer L]]
-	[[Category: Gremer, L]]	+	[[Category: Huber R]]
-	[[Category: Huber, R]]	+	[[Category: Kiefersauer R]]
-	[[Category: Kiefersauer, R]]	+	[[Category: Meyer O]]
-	[[Category: Meyer, O]]	+
-	~~[[Category: Codh]]~~	+
-	~~[[Category: Molybdenum]]~~	+
-	~~[[Category: Molybdopterin]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:32, 5 May 2021

2021-05-05T09:32:45Z

←Older revision		Revision as of 09:32, 5 May 2021
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	<StructureSection load='1n62' size='340' side='right'caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>		<StructureSection load='1n62' size='340' side='right'caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n62]] 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=1N62 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1N62 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n62]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligotropha_carboxidovorans Oligotropha carboxidovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N62 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CUB:CU(I)-S-MO(IV)(=O)O-NBIC+CLUSTER'>CUB</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CUB:CU(I)-S-MO(IV)(=O)O-NBIC+CLUSTER'>CUB</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [https://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [~~http~~://pdbe.org/1n62 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1n62 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1n62 ProSAT]</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=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [https://pdbe.org/1n62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [https://www.ebi.ac.uk/pdbsum/1n62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n62 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DCMS_OLICO DCMS_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[~~http~~://www.uniprot.org/uniprot/DCMM_OLICO DCMM_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[~~http~~://www.uniprot.org/uniprot/DCML_OLICO DCML_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide.	+	[[https://www.uniprot.org/uniprot/DCMS_OLICO DCMS_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[https://www.uniprot.org/uniprot/DCMM_OLICO DCMM_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[https://www.uniprot.org/uniprot/DCML_OLICO DCML_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:56, 31 July 2019

2019-07-31T07:56:53Z

←Older revision		Revision as of 07:56, 31 July 2019
Line 1:		Line 1:

	==Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state==		==Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state==
-	<StructureSection load='1n62' size='340' side='right' caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>	+	<StructureSection load='1n62' size='340' side='right'caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1n62]] 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=1N62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N62 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1n62]] 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=1N62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N62 FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n6/1n62_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n6/1n62_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1n62" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1n62" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbon monoxide dehydrogenase 3D structures\|Carbon monoxide dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Oligotropha carboxidovorans]]		[[Category: Oligotropha carboxidovorans]]
	[[Category: Dobbek, H]]		[[Category: Dobbek, H]]

OCA at 10:19, 25 October 2017

2017-10-25T10:19:13Z

←Older revision		Revision as of 10:19, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state==		==Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state==
	<StructureSection load='1n62' size='340' side='right' caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>		<StructureSection load='1n62' size='340' side='right' caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [http://pdbe.org/1n62 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [http://www.ebi.ac.uk/pdbsum/1n62 PDBsum]</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=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [http://pdbe.org/1n62 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [http://www.ebi.ac.uk/pdbsum/1n62 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n62 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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=1n62 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1n62" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1n62" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Carbon monoxide dehydrogenase\|Carbon monoxide dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:49, 11 September 2015

2015-09-11T08:49:26Z

←Older revision		Revision as of 08:49, 11 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [http://www.ebi.ac.uk/pdbsum/1n62 PDBsum]</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=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [http://pdbe.org/1n62 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [http://www.ebi.ac.uk/pdbsum/1n62 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== 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.	+	[[http://www.uniprot.org/uniprot/DCMS_OLICO DCMS_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[http://www.uniprot.org/uniprot/DCMM_OLICO DCMM_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[http://www.uniprot.org/uniprot/DCML_OLICO DCML_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1n62" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:04, 25 December 2014

2014-12-25T14:04:46Z

←Older revision		Revision as of 14:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1n62]] 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=1N62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N62 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1n62]] 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=1N62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N62 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CUB:CU(I)-S-MO(IV)(=O)O-NBIC+CLUSTER'>CUB</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><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CUB:CU(I)-S-MO(IV)(=O)O-NBIC+CLUSTER'>CUB</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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [http://www.ebi.ac.uk/pdbsum/1n62 PDBsum]</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=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [http://www.ebi.ac.uk/pdbsum/1n62 PDBsum]</span></td></tr>
-	<table>	+	</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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Oligotropha carboxidovorans]]		[[Category: Oligotropha carboxidovorans]]
-	[[Category: Dobbek, H.]]	+	[[Category: Dobbek, H]]
-	[[Category: Gremer, L.]]	+	[[Category: Gremer, L]]
-	[[Category: Huber, R.]]	+	[[Category: Huber, R]]
-	[[Category: Kiefersauer, R.]]	+	[[Category: Kiefersauer, R]]
-	[[Category: Meyer, O.]]	+	[[Category: Meyer, O]]
	[[Category: Codh]]		[[Category: Codh]]
	[[Category: Molybdenum]]		[[Category: Molybdenum]]
	[[Category: Molybdopterin]]		[[Category: Molybdopterin]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 16:16, 28 September 2014

2014-09-28T16:16:08Z

←Older revision		Revision as of 16:16, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1n62.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state==
		+	<StructureSection load='1n62' size='340' side='right' caption='[[1n62]], [[Resolution\|resolution]] 1.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1n62]] 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=1N62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N62 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CUB:CU(I)-S-MO(IV)(=O)O-NBIC+CLUSTER'>CUB</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><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n5w\|1n5w]], [[1n60\|1n60]], [[1n61\|1n61]], [[1n63\|1n63]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n62 RCSB], [http://www.ebi.ac.uk/pdbsum/1n62 PDBsum]</span></td></tr>
		+	<table>
		+	== 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/n6/1n62_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].
		+	<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. & 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.

-	~~{{STRUCTURE_1n62\| PDB~~=~~1n62 \| SCENE~~= }}	+	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>

-	~~===Crystal Structure~~ of the ~~Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12475995}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1n62]] 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=1N62 OCA].~~	+

	==See Also==		==See Also==
	*[[Carbon monoxide dehydrogenase\|Carbon monoxide dehydrogenase]]		*[[Carbon monoxide dehydrogenase\|Carbon monoxide dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012475995<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Oligotropha carboxidovorans]]		[[Category: Oligotropha carboxidovorans]]
	[[Category: Dobbek, H.]]		[[Category: Dobbek, H.]]

OCA at 17:36, 20 October 2012

2012-10-20T17:36:09Z

←Older revision		Revision as of 17:36, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1n62]] is a 6 chain structure ~~of [[Carbon monoxide dehydrogenase]]~~ 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=1N62 OCA].	+	[[1n62]] 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=1N62 OCA].

	==See Also==		==See Also==

OCA: Protected "1n62" [edit=sysop:move=sysop]

2012-07-27T01:27:06Z

Protected "1n62" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:27, 27 July 2012

OCA at 01:27, 27 July 2012

2012-07-27T01:27:05Z

←Older revision		Revision as of 01:27, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1n62.png\|left\|200px]]		[[Image:1n62.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1n62", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1n62\| PDB=1n62 \| SCENE= }}		{{STRUCTURE_1n62\| PDB=1n62 \| SCENE= }}

	===Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state===		===Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12475995}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12475995 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12475995}}		{{ABSTRACT_PUBMED_12475995}}

	==About this Structure==		==About this Structure==
-	~~1N62~~ is a 6 ~~chains~~ structure of ~~sequences~~ 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=1N62 OCA].	+	[[1n62]] is a 6 chain structure of [[Carbon monoxide dehydrogenase]] 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=1N62 OCA].
		+
		+	==See Also==
		+	*[[Carbon monoxide dehydrogenase\|Carbon monoxide dehydrogenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12475995~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012475995</ref><references group="xtra"/>
	[[Category: Oligotropha carboxidovorans]]		[[Category: Oligotropha carboxidovorans]]
	[[Category: Dobbek, H.]]		[[Category: Dobbek, H.]]
Line 31:		Line 22:
	[[Category: Meyer, O.]]		[[Category: Meyer, O.]]
	[[Category: Codh]]		[[Category: Codh]]
-	[[Category: Copper]]
	[[Category: Molybdenum]]		[[Category: Molybdenum]]
	[[Category: Molybdopterin]]		[[Category: Molybdopterin]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 18:12:37 2009''~~	+