1e61 - Revision history

OCA at 06:27, 1 May 2024

OCA — Wed, 01 May 2024 06:27:11 GMT

←Older revision		Revision as of 06:27, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E61 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E61 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [https://pdbe.org/1e61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [https://www.ebi.ac.uk/pdbsum/1e61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e61 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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [https://pdbe.org/1e61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [https://www.ebi.ac.uk/pdbsum/1e61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e61 ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</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=1e61 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=1e61 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Much is unknown concerning the role of thiolate ligands of molybdenum in molybdopterin enzymes. It has been suggested that thiolate dissociation from molybdenum is part of the catalytic mechanism of bis-molybdopterin enzymes of the dimethyl sulfoxide reductase (DMSOR) family. For DMSOR from Rhodobacter capsulatus, thiolate dissociation has therefore been investigated crystallographically, by UV/visible spectroscopy, and by enzyme assays. When crystallized from sodium citrate, all four thiolates of DMSOR are within bonding distance of Mo, but after extended exposure to Na(+)-Hepes, a pair of thiolates dissociates, a mixture of structures being indicated after shorter exposures to this buffer. DMSOR is stable in sodium citrate and other buffers but unstable aerobically although not anaerobically in Na(+)-Hepes. Aerobically in Na(+)-Hepes, a first-order reaction (k = 0.032 hr(-)(1) at 37 degrees C) leads to loss of activity in the backward but not the forward (dimethyl sulfoxide reduction) assay and loss of absorption at lambda > approximately 450 nm. This reaction can be reversed by a cycle of reduction and reoxidation ("redox-cycling"). Slower irreversible loss of activity in the forward assay and cofactor dissociation follow. Spectral analogy with a mono-molybdopterin enzyme supports the conclusion that in the Hepes-modified DMSOR form, only two cofactor dithiolene sulfur atoms are coordinated to molybdenum. Loss of activity provides the first clear evidence that sulfur ligand dissociation is an artifact, not part of the catalytic cycle. Clearly, structural data on DMSOR samples extensively exposed to Hepes is not directly relevant to the native enzyme. The nature of the oxygen ligands detected crystallographically is discussed, as is the specificity of Hepes and the mechanism whereby its effects are achieved. DMSOR forms complexes with Na(+)-Hepes and other buffer ions. For DMSOR crystallized from Hepes, electron density in the substrate binding channel suggests that buffers bind in this site. Like the as-prepared enzyme, the modified form (DMSOR(mod)D), known to arise on extended aerobic exposure to dimethyl sulfide, is susceptible to a further degradative reaction, although this is not buffer-dependent. It involves loss of absorption at lambda > approximately 450 nm and, presumably, dissociation of thiolate ligands. Evidence is presented that, as a result of O(2) damage, DMSOR samples not submitted to redox-cycling may be contaminated with DMSOR(mod)D and with material absorbing in the region of 400 nm, analogous to the Hepes-modified enzyme. Since the latter lacks absorption at lambda > approximately 450 nm, its presence may escape detection.
-
-	Reversible dissociation of thiolate ligands from molybdenum in an enzyme of the dimethyl sulfoxide reductase family.,Bray RC, Adams B, Smith AT, Bennett B, Bailey S Biochemistry. 2000 Sep 19;39(37):11258-69. PMID:10985771<ref>PMID:10985771</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1e61" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:13, 26 October 2022

OCA — Wed, 26 Oct 2022 06:13:59 GMT

←Older revision		Revision as of 06:13, 26 October 2022
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	<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E61 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E61 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</div></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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [https://pdbe.org/1e61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [https://www.ebi.ac.uk/pdbsum/1e61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e61 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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [https://pdbe.org/1e61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [https://www.ebi.ac.uk/pdbsum/1e61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e61 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DSTOR_RHOCA DSTOR_RHOCA]] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:2001248</ref> <ref>PMID:8856102</ref>	+	[https://www.uniprot.org/uniprot/DSTOR_RHOCA DSTOR_RHOCA] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:2001248</ref> <ref>PMID:8856102</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 34:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
-	[[Category: Adams, B]]	+	[[Category: Adams B]]
-	[[Category: Bailey, S]]	+	[[Category: Bailey S]]
-	[[Category: Bennett, B]]	+	[[Category: Bennett B]]
-	[[Category: Bray~~, R C~~]]	+	[[Category: Bray RC]]
-	[[Category: Smith~~, A T]]~~	+	[[Category: Smith AT]]
-	~~[[Category: Dmso]]~~	+
-	~~[[Category: Molybdopterin]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Reductase~~]]	+

OCA at 06:31, 11 August 2021

OCA — Wed, 11 Aug 2021 06:31:38 GMT

←Older revision		Revision as of 06:31, 11 August 2021
Line 3:		Line 3:
	<StructureSection load='1e61' size='340' side='right'caption='[[1e61]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1e61' size='340' side='right'caption='[[1e61]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1E61 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E61 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</div></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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [~~http~~://pdbe.org/1e61 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1e61 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1e61 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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [https://pdbe.org/1e61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [https://www.ebi.ac.uk/pdbsum/1e61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e61 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DSTOR_RHOCA DSTOR_RHOCA]] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:2001248</ref> <ref>PMID:8856102</ref>	+	[[https://www.uniprot.org/uniprot/DSTOR_RHOCA DSTOR_RHOCA]] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:2001248</ref> <ref>PMID:8856102</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:49, 16 October 2019

OCA — Wed, 16 Oct 2019 08:49:35 GMT

←Older revision		Revision as of 08:49, 16 October 2019
Line 1:		Line 1:

	==OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - Structure II BUFFER==		==OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - Structure II BUFFER==
-	<StructureSection load='1e61' size='340' side='right' caption='[[1e61]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1e61' size='340' side='right'caption='[[1e61]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E61 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E61 FirstGlance]. <br>
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
	[[Category: Adams, B]]		[[Category: Adams, B]]

OCA at 07:49, 13 December 2017

OCA — Wed, 13 Dec 2017 07:49:39 GMT

←Older revision		Revision as of 07:49, 13 December 2017
Line 1:		Line 1:
-	==OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - ~~STRUCTURE~~ II BUFFER==	+
		+	==OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - Structure II BUFFER==
	<StructureSection load='1e61' size='340' side='right' caption='[[1e61]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1e61' size='340' side='right' caption='[[1e61]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://pdbe.org/1e61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://pdbe.org/1e61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e61 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/1e61_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e6/1e61_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>

OCA at 04:07, 10 February 2016

OCA — Wed, 10 Feb 2016 04:07:44 GMT

←Older revision		Revision as of 04:07, 10 February 2016
Line 17:		Line 17:
	<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=1e61 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:13, 11 September 2015

OCA — Fri, 11 Sep 2015 05:13:47 GMT

←Older revision		Revision as of 05:13, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://pdbe.org/1e61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~DMSA_RHOCA DMSA_RHOCA~~]] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:~~8856102~~</ref> <ref>PMID:~~2001248~~</ref>	+	[[http://www.uniprot.org/uniprot/DSTOR_RHOCA DSTOR_RHOCA]] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:2001248</ref> <ref>PMID:8856102</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 1e61" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:41, 25 December 2014

OCA — Thu, 25 Dec 2014 11:41:41 GMT

←Older revision		Revision as of 11:41, 25 December 2014
Line 7:		Line 7:
	<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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DMSA_RHOCA DMSA_RHOCA]] Catalyzes the reduction of dimethyl sulfoxide (DMSO) and trimethylamine N-oxide (TMAO) to dimethyl sulfide (DMS) and trimethylamine, respectively. The terminal DMSO reductase can also use various sulfoxides and N-oxide compounds as terminal electron acceptor in addition to DMSO and TMAO.<ref>PMID:8856102</ref> <ref>PMID:2001248</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:13, 22 December 2014

OCA — Mon, 22 Dec 2014 19:13:28 GMT

←Older revision		Revision as of 19:13, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E61 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E61 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
-	[[Category: Adams, B.]]	+	[[Category: Adams, B]]
-	[[Category: Bailey, S.]]	+	[[Category: Bailey, S]]
-	[[Category: Bennett, B.]]	+	[[Category: Bennett, B]]
-	[[Category: Bray, R C.]]	+	[[Category: Bray, R C]]
-	[[Category: Smith, A T.]]	+	[[Category: Smith, A T]]
	[[Category: Dmso]]		[[Category: Dmso]]
	[[Category: Molybdopterin]]		[[Category: Molybdopterin]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Reductase]]		[[Category: Reductase]]

OCA at 10:38, 10 September 2014

OCA — Wed, 10 Sep 2014 10:38:40 GMT

←Older revision		Revision as of 10:38, 10 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1e61.~~png~~\|~~left~~\|200px]]	+	==OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - STRUCTURE II BUFFER==
		+	<StructureSection load='1e61' size='340' side='right' caption='[[1e61]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1e61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E61 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MO:MOLYBDENUM+(IV)OXIDE'>2MO</scene>, <scene name='pdbligand=PGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>PGD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e18\|1e18]], [[1e5v\|1e5v]], [[1e60\|1e60]]</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=1e61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e61 RCSB], [http://www.ebi.ac.uk/pdbsum/1e61 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/e6/1e61_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 ==
		+	Much is unknown concerning the role of thiolate ligands of molybdenum in molybdopterin enzymes. It has been suggested that thiolate dissociation from molybdenum is part of the catalytic mechanism of bis-molybdopterin enzymes of the dimethyl sulfoxide reductase (DMSOR) family. For DMSOR from Rhodobacter capsulatus, thiolate dissociation has therefore been investigated crystallographically, by UV/visible spectroscopy, and by enzyme assays. When crystallized from sodium citrate, all four thiolates of DMSOR are within bonding distance of Mo, but after extended exposure to Na(+)-Hepes, a pair of thiolates dissociates, a mixture of structures being indicated after shorter exposures to this buffer. DMSOR is stable in sodium citrate and other buffers but unstable aerobically although not anaerobically in Na(+)-Hepes. Aerobically in Na(+)-Hepes, a first-order reaction (k = 0.032 hr(-)(1) at 37 degrees C) leads to loss of activity in the backward but not the forward (dimethyl sulfoxide reduction) assay and loss of absorption at lambda > approximately 450 nm. This reaction can be reversed by a cycle of reduction and reoxidation ("redox-cycling"). Slower irreversible loss of activity in the forward assay and cofactor dissociation follow. Spectral analogy with a mono-molybdopterin enzyme supports the conclusion that in the Hepes-modified DMSOR form, only two cofactor dithiolene sulfur atoms are coordinated to molybdenum. Loss of activity provides the first clear evidence that sulfur ligand dissociation is an artifact, not part of the catalytic cycle. Clearly, structural data on DMSOR samples extensively exposed to Hepes is not directly relevant to the native enzyme. The nature of the oxygen ligands detected crystallographically is discussed, as is the specificity of Hepes and the mechanism whereby its effects are achieved. DMSOR forms complexes with Na(+)-Hepes and other buffer ions. For DMSOR crystallized from Hepes, electron density in the substrate binding channel suggests that buffers bind in this site. Like the as-prepared enzyme, the modified form (DMSOR(mod)D), known to arise on extended aerobic exposure to dimethyl sulfide, is susceptible to a further degradative reaction, although this is not buffer-dependent. It involves loss of absorption at lambda > approximately 450 nm and, presumably, dissociation of thiolate ligands. Evidence is presented that, as a result of O(2) damage, DMSOR samples not submitted to redox-cycling may be contaminated with DMSOR(mod)D and with material absorbing in the region of 400 nm, analogous to the Hepes-modified enzyme. Since the latter lacks absorption at lambda > approximately 450 nm, its presence may escape detection.

-	~~{{STRUCTURE_1e61\| PDB=1e61 \| SCENE= }}~~	+	Reversible dissociation of thiolate ligands from molybdenum in an enzyme of the dimethyl sulfoxide reductase family.,Bray RC, Adams B, Smith AT, Bennett B, Bailey S Biochemistry. 2000 Sep 19;39(37):11258-69. PMID:10985771<ref>PMID:10985771</ref>

-	~~===OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - STRUCTURE II BUFFER===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~==About this Structure==~~	+	<references/>
-	~~[[1e61]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1E61 OCA].~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010985771<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rhodobacter capsulatus]]		[[Category: Rhodobacter capsulatus]]
	[[Category: Adams, B.]]		[[Category: Adams, B.]]