4rkn - Revision history

OCA at 07:01, 2 March 2023

2023-03-02T07:01:24Z

←Older revision		Revision as of 07:01, 2 March 2023
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	==Wolinella succinogenes octaheme sulfite reductase MccA, form II==		==Wolinella succinogenes octaheme sulfite reductase MccA, form II==
-	<StructureSection load='4rkn' size='340' side='right' caption='[[4rkn]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4rkn' size='340' side='right'caption='[[4rkn]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rkn]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Vibrio_succinogenes Vibrio~~ succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RKN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RKN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rkn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Wolinella_succinogenes_DSM_1740 Wolinella succinogenes DSM 1740]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RKN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DTN:DITHIONITE'>DTN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DTN:DITHIONITE'>DTN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rkm\|4rkm]]</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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [https://pdbe.org/4rkn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [https://www.ebi.ac.uk/pdbsum/4rkn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rkn ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mcca, WS0379 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273121 Vibrio succinogenes])</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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [~~http~~://pdbe.org/4rkn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rkn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rkn ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MCCA_WOLSU MCCA_WOLSU] Respiratory sulfite reductase that catalyzes the reduction of sulfite to sulfide in a single step, consuming six electrons in the process (PubMed:22040142, PubMed:25642962). Required for sulfite respiration under anaerobic growth conditions (PubMed:22040142). Has only marginal activity with nitrite.<ref>PMID:22040142</ref> <ref>PMID:25642962</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ succinogenes]]	+	[[Category: Large Structures]]
-	[[Category: Einsle, O]]	+	[[Category: Wolinella succinogenes DSM 1740]]
-	[[Category: Hermann, B]]	+	[[Category: Einsle O]]
-	[[Category: Kern, M]]	+	[[Category: Hermann B]]
-	[[Category: Pietra, L La]]	+	[[Category: Kern M]]
-	[[Category: Simon, J]]	+	[[Category: La Pietra L]]
-	~~[[Category: Multiheme cytochrome c]]~~	+	[[Category: Simon J]]
-	~~[[Category: Periplasmic]]~~	+
-	~~[[Category: Sulfite reductase]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 09:06, 22 November 2017

2017-11-22T09:06:37Z

←Older revision		Revision as of 09:06, 22 November 2017
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	<StructureSection load='4rkn' size='340' side='right' caption='[[4rkn]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4rkn' size='340' side='right' caption='[[4rkn]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rkn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RKN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rkn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_succinogenes Vibrio succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RKN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DTN:DITHIONITE'>DTN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DTN:DITHIONITE'>DTN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rkm\|4rkm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rkm\|4rkm]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mcca, WS0379 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273121 Vibrio succinogenes])</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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [http://pdbe.org/4rkn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [http://www.ebi.ac.uk/pdbsum/4rkn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rkn 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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [http://pdbe.org/4rkn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [http://www.ebi.ac.uk/pdbsum/4rkn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rkn ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Vibrio succinogenes]]
	[[Category: Einsle, O]]		[[Category: Einsle, O]]
	[[Category: Hermann, B]]		[[Category: Hermann, B]]

OCA at 14:22, 29 March 2017

2017-03-29T14:22:57Z

←Older revision		Revision as of 14:22, 29 March 2017
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		+
	==Wolinella succinogenes octaheme sulfite reductase MccA, form II==		==Wolinella succinogenes octaheme sulfite reductase MccA, form II==
	<StructureSection load='4rkn' size='340' side='right' caption='[[4rkn]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4rkn' size='340' side='right' caption='[[4rkn]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DTN:DITHIONITE'>DTN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DTN:DITHIONITE'>DTN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rkm\|4rkm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rkm\|4rkm]]</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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [http://www.ebi.ac.uk/pdbsum/4rkn 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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [http://pdbe.org/4rkn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [http://www.ebi.ac.uk/pdbsum/4rkn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rkn ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4rkn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:21, 4 March 2015

2015-03-04T11:21:11Z

←Older revision		Revision as of 11:21, 4 March 2015
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	<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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [http://www.ebi.ac.uk/pdbsum/4rkn 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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [http://www.ebi.ac.uk/pdbsum/4rkn PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The six-electron reduction of sulfite to sulfide is the pivot point of the biogeochemical cycle of the element sulfur. The octahaem cytochrome c MccA (also known as SirA) catalyses this reaction for dissimilatory sulfite utilization by various bacteria. It is distinct from known sulfite reductases because it has a substantially higher catalytic activity and a relatively low reactivity towards nitrite. The mechanistic reasons for the increased efficiency of MccA remain to be elucidated. Here we show that anoxically purified MccA exhibited a 2- to 5.5-fold higher specific sulfite reductase activity than the enzyme isolated under oxic conditions. We determined the three-dimensional structure of MccA to 2.2 A resolution by single-wavelength anomalous dispersion. We find a homotrimer with an unprecedented fold and haem arrangement, as well as a haem bound to a CX15CH motif. The heterobimetallic active-site haem 2 has a Cu(I) ion juxtaposed to a haem c at a Fe-Cu distance of 4.4 A. While the combination of metals is reminiscent of respiratory haem-copper oxidases, the oxidation-labile Cu(I) centre of MccA did not seem to undergo a redox transition during catalysis. Intact MccA tightly bound SO2 at haem 2, a dehydration product of the substrate sulfite that was partially turned over due to photoreduction by X-ray irradiation, yielding the reaction intermediate SO. Our data show the biometal copper in a new context and function and provide a chemical rationale for the comparatively high catalytic activity of MccA.
		+
		+	The octahaem MccA is a haem c-copper sulfite reductase.,Hermann B, Kern M, La Pietra L, Simon J, Einsle O Nature. 2015 Feb 2. doi: 10.1038/nature14109. PMID:25642962<ref>PMID:25642962</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:58, 7 February 2015

2015-02-07T15:58:41Z

←Older revision		Revision as of 15:58, 7 February 2015
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-	'''~~Unreleased structure~~'''	+	==Wolinella succinogenes octaheme sulfite reductase MccA, form II==
-		+	<StructureSection load='4rkn' size='340' side='right' caption='[[4rkn]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~The entry~~ 4rkn is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4rkn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RKN FirstGlance]. <br>
-	~~Authors~~: ~~Hermann, B~~.~~, Kern, M~~.~~, La Pietra, L~~.~~, Simon, J~~.~~, Einsle, O~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DTN:DITHIONITE'>DTN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rkm\|4rkm]]</td></tr>
-	~~Description~~: ~~Wolinella succinogenes octaheme sulfite reductase MccA, form~~ II	+	<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=4rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rkn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rkn RCSB], [http://www.ebi.ac.uk/pdbsum/4rkn PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Simon~~, J]]	+	__TOC__
-	[[Category: ~~La Pietra~~, L]]	+	</StructureSection>
		+	[[Category: Einsle, O]]
	[[Category: Hermann, B]]		[[Category: Hermann, B]]
	[[Category: Kern, M]]		[[Category: Kern, M]]
-	[[Category: ~~Einsle~~, O]]	+	[[Category: Pietra, L La]]
		+	[[Category: Simon, J]]
		+	[[Category: Multiheme cytochrome c]]
		+	[[Category: Periplasmic]]
		+	[[Category: Sulfite reductase]]
		+	[[Category: Unknown function]]

OCA at 16:59, 24 December 2014

2014-12-24T16:59:20Z

←Older revision		Revision as of 16:59, 24 December 2014
Line 6:		Line 6:

	Description: Wolinella succinogenes octaheme sulfite reductase MccA, form II		Description: Wolinella succinogenes octaheme sulfite reductase MccA, form II
		+	[[Category: Unreleased Structures]]
		+	[[Category: Simon, J]]
		+	[[Category: La Pietra, L]]
		+	[[Category: Hermann, B]]
		+	[[Category: Kern, M]]
		+	[[Category: Einsle, O]]

OCA at 11:26, 19 November 2014

2014-11-19T11:26:44Z

←Older revision		Revision as of 11:26, 19 November 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rkn is ON HOLD	+	The entry 4rkn is ON HOLD until Paper Publication

	Authors: Hermann, B., Kern, M., La Pietra, L., Simon, J., Einsle, O.		Authors: Hermann, B., Kern, M., La Pietra, L., Simon, J., Einsle, O.

	Description: Wolinella succinogenes octaheme sulfite reductase MccA, form II		Description: Wolinella succinogenes octaheme sulfite reductase MccA, form II

OCA: Protected "4rkn" [edit=sysop:move=sysop]

2014-10-22T09:45:04Z

Protected "4rkn" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:45, 22 October 2014

OCA: New page: '''Unreleased structure''' The entry 4rkn is ON HOLD Authors: Hermann, B., Kern, M., La Pietra, L., Simon, J., Einsle, O. Description: Wolinella succinogenes octaheme sulfite reductase...

2014-10-22T09:45:02Z

New page: '''Unreleased structure''' The entry 4rkn is ON HOLD Authors: Hermann, B., Kern, M., La Pietra, L., Simon, J., Einsle, O. Description: Wolinella succinogenes octaheme sulfite reductase...

New page

'''Unreleased structure'''

The entry 4rkn is ON HOLD

Authors: Hermann, B., Kern, M., La Pietra, L., Simon, J., Einsle, O.

Description: Wolinella succinogenes octaheme sulfite reductase MccA, form II