5k3x - Revision history

OCA at 09:51, 27 September 2023

2023-09-27T09:51:31Z

←Older revision		Revision as of 09:51, 27 September 2023
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	==Crystal Structure of the sulfite dehydrogenase, SorT R78K mutant from Sinorhizobium meliloti==		==Crystal Structure of the sulfite dehydrogenase, SorT R78K mutant from Sinorhizobium meliloti==
-	<StructureSection load='5k3x' size='340' side='right' caption='[[5k3x]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5k3x' size='340' side='right'caption='[[5k3x]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3x]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ensifer_meliloti Ensifer~~ meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti_1021 Sinorhizobium meliloti 1021]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K3X FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'~~>~~GOL</scene>, <scene name='pdbligand=MSS:(MOLYBDOPTERIN~~-S,~~S)-OXO-MOLYBDENUM'>MSS</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]] 1.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SMc04049 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~266834 Ensifer meliloti])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSS:(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM'>MSS</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Sulfite_oxidase Sulfite oxidase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.8.3.1 1.8.3.1]~~ </~~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=5k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3x OCA], [https://pdbe.org/5k3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k3x RCSB], [https://www.ebi.ac.uk/pdbsum/5k3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3x 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=5k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3x OCA], [~~http~~://pdbe.org/5k3x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k3x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k3x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3x ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q92M24_RHIME Q92M24_RHIME]] The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase.[SAAS:SAAS00086612]	+	[https://www.uniprot.org/uniprot/Q92M24_RHIME Q92M24_RHIME] The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase.[SAAS:SAAS00086612]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ensifer meliloti~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Sulfite oxidase~~]]	+	[[Category: Sinorhizobium meliloti 1021]]
-	[[Category: Lee, M]]	+	[[Category: Lee M]]
-	[[Category: Maher, M]]	+	[[Category: Maher M]]
-	[[Category: McGrath, A]]	+	[[Category: McGrath A]]
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Sulfite dehydrogenase]]~~	+
-	~~[[Category: Suox-fold~~]]	+

OCA at 10:17, 8 November 2017

2017-11-08T10:17:25Z

←Older revision		Revision as of 10:17, 8 November 2017
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	<StructureSection load='5k3x' size='340' side='right' caption='[[5k3x]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5k3x' size='340' side='right' caption='[[5k3x]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k3x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k3x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ensifer_meliloti Ensifer meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSS:(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM'>MSS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSS:(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM'>MSS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMc04049 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266834 Ensifer meliloti])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sulfite_oxidase Sulfite oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.3.1 1.8.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sulfite_oxidase Sulfite oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.3.1 1.8.3.1] </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=5k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3x OCA], [http://pdbe.org/5k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3x RCSB], [http://www.ebi.ac.uk/pdbsum/5k3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3x 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=5k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3x OCA], [http://pdbe.org/5k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3x RCSB], [http://www.ebi.ac.uk/pdbsum/5k3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3x ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ensifer meliloti]]
	[[Category: Sulfite oxidase]]		[[Category: Sulfite oxidase]]
	[[Category: Lee, M]]		[[Category: Lee, M]]

OCA at 06:57, 25 October 2017

2017-10-25T06:57:32Z

←Older revision		Revision as of 06:57, 25 October 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q92M24_RHIME Q92M24_RHIME]] The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase.[SAAS:SAAS00086612]		[[http://www.uniprot.org/uniprot/Q92M24_RHIME Q92M24_RHIME]] The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase.[SAAS:SAAS00086612]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A central conserved arginine, first identified as a clinical mutation leading to sulfite oxidase deficiency, is essential for catalytic competency of sulfite oxidizing molybdoenzymes, but the molecular basis for its effects on turnover and substrate affinity have not been fully elucidated. We have used a bacterial sulfite dehydrogenase, SorT, which lacks an internal heme group, but transfers electrons to an external, electron accepting cytochrome, SorU, to investigate the molecular functions of this arginine residue (Arg78). Assay of the SorT Mo centre catalytic competency in the absence of SorU showed that substitutions in the central arginine (R78Q, R78K and R78M mutations) only moderately altered SorT catalytic properties, except for R78M which caused significant reduction in SorT activity. The substitutions also altered the Mo-centre redox potentials (MoVI/V potential lowered by ca. 60-80mV). However, all Arg78 mutations significantly impaired the ability of SorT to transfer electrons to SorU, where activities were reduced 17 to 46-fold compared to SorTWT, precluding determination of kinetic parameters. This was accompanied by the observation of conformational changes in both the introduced Gln and Lys residues in the crystal structure of the enzymes. Taking into account data collected by others on related SOE mutations we propose that the formation and maintenance of an electron transfer complex between the Mo centre and electron accepting heme groups is the main function of the central arginine, and that the reduced turnover and increases in KMsulfite are caused by the inefficient operation of the oxidative half reaction of the catalytic cycle in enzymes carrying these mutations.
		+
		+	The central active site arginine in sulfite oxidizing enzymes alters kinetic properties by controlling electron transfer and redox interactions.,Hsiao JC, McGrath AP, Kielmann L, Kalimuthu P, Darain F, Bernhardt PV, Harmer J, Lee M, Meyers K, Maher MJ, Kappler U Biochim Biophys Acta. 2017 Oct 3. pii: S0005-2728(17)30147-0. doi:, 10.1016/j.bbabio.2017.10.001. PMID:28986298<ref>PMID:28986298</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5k3x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:44, 24 May 2017

2017-05-24T13:44:52Z

←Older revision		Revision as of 13:44, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k3x is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of the sulfite dehydrogenase, SorT R78K mutant from Sinorhizobium meliloti==
-		+	<StructureSection load='5k3x' size='340' side='right' caption='[[5k3x]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5k3x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K3X FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSS:(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM'>MSS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sulfite_oxidase Sulfite oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.3.1 1.8.3.1] </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=5k3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k3x OCA], [http://pdbe.org/5k3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k3x RCSB], [http://www.ebi.ac.uk/pdbsum/5k3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k3x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q92M24_RHIME Q92M24_RHIME]] The exact function is not known. Can catalyze the reduction of a variety of substrates like dimethyl sulfoxide, trimethylamine N-oxide, phenylmethyl sulfoxide and L-methionine sulfoxide. Cannot reduce cyclic N-oxides. Shows no activity as sulfite oxidase.[SAAS:SAAS00086612]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Sulfite oxidase]]
		+	[[Category: Lee, M]]
		+	[[Category: Maher, M]]
		+	[[Category: McGrath, A]]
		+	[[Category: Electron transfer]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Sulfite dehydrogenase]]
		+	[[Category: Suox-fold]]

OCA at 13:24, 20 June 2016

2016-06-20T13:24:38Z

←Older revision		Revision as of 13:24, 20 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k3x is ON HOLD	+	The entry 5k3x is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5k3x" [edit=sysop:move=sysop]

2016-06-01T14:17:30Z

Protected "5k3x" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:17, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k3x is ON HOLD Authors: Description: Category: Unreleased Structures

2016-06-01T14:17:28Z

New page: '''Unreleased structure''' The entry 5k3x is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k3x is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]