5m8w - Revision history

OCA at 18:31, 1 November 2023

OCA — Wed, 01 Nov 2023 18:31:16 GMT

←Older revision		Revision as of 18:31, 1 November 2023
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	<StructureSection load='5m8w' size='340' side='right'caption='[[5m8w]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='5m8w' size='340' side='right'caption='[[5m8w]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m8w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sulfurospirillum_multivorans Sulfurospirillum multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M8W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5M8W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurospirillum_multivorans Sulfurospirillum multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M8W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4CH:4-CHLOROPHENOL'>4CH</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BVQ:NORPSEUDO-B12'>BVQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.279Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5m2g\|5m2g]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4CH:4-CHLOROPHENOL'>4CH</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BVQ:NORPSEUDO-B12'>BVQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5m8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m8w OCA], [~~http~~://pdbe.org/5m8w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m8w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m8w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m8w 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=5m8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m8w OCA], [https://pdbe.org/5m8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m8w RCSB], [https://www.ebi.ac.uk/pdbsum/5m8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m8w ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PCEA_SULMU PCEA_SULMU] Catalyzes the reductive dechlorination of tetrachloroethene (PCE) to trichloroethene (TCE) and of trichloroethene to cis-1,2-dichloroethene (DCE) (PubMed:8663199, PubMed:11976751, PubMed:12420164, PubMed:24433392, PubMed:28671181). In addition, trans-1,3-dichloropropene, 1,1,3-trichloropropene and 2,3-dichloropropene are reduced to a mixture of mono-chloropropenes, 1,1-dichloropropene, and 2-chloropropene, respectively (PubMed:11976751). Is also able to convert brominated phenols such as 4-bromophenol (4-BP), 2,4-dibromophenol (2,4-DBP) and 2,4,6-tribromophenol (2,4,6-TBP) (PubMed:28671181). Utilizes formate or pyruvate as electron donors (PubMed:16802174, PubMed:24433392). Titanium(III) citrate could also serve as electron donor (PubMed:11976751). Reduced methyl viologen can act as the artificial electron donor (PubMed:8663199, PubMed:11976751, PubMed:12420164).<ref>PMID:11976751</ref> <ref>PMID:12420164</ref> <ref>PMID:16802174</ref> <ref>PMID:24433392</ref> <ref>PMID:28671181</ref> <ref>PMID:8663199</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Sulfurospirillum multivorans]]		[[Category: Sulfurospirillum multivorans]]
-	[[Category: Bommer, M]]	+	[[Category: Bommer M]]
-	[[Category: Diekert, G]]	+	[[Category: Diekert G]]
-	[[Category: Dobbek, H]]	+	[[Category: Dobbek H]]
-	[[Category: Hagen~~, W R~~]]	+	[[Category: Hagen WR]]
-	[[Category: Kunze, C]]	+	[[Category: Kunze C]]
-	[[Category: Schubert, T]]	+	[[Category: Schubert T]]
-	[[Category: Uksa, M]]	+	[[Category: Uksa M]]
-	~~[[Category: Organohalide respiration anaerobic crystallisation cobalamin]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:11, 19 August 2020

OCA — Wed, 19 Aug 2020 07:11:49 GMT

←Older revision		Revision as of 07:11, 19 August 2020
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	==PCE reductive dehalogenase from S. multivorans in complex with 4-chlorophenol==		==PCE reductive dehalogenase from S. multivorans in complex with 4-chlorophenol==
-	<StructureSection load='5m8w' size='340' side='right' caption='[[5m8w]], [[Resolution\|resolution]] 2.28Å' scene=''>	+	<StructureSection load='5m8w' size='340' side='right'caption='[[5m8w]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m8w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfurospirillum_multivorans Sulfurospirillum multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M8W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M8W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m8w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfurospirillum_multivorans Sulfurospirillum multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M8W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M8W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4CH:4-CHLOROPHENOL'>4CH</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BVQ:NORPSEUDO-B12'>BVQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4CH:4-CHLOROPHENOL'>4CH</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BVQ:NORPSEUDO-B12'>BVQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5m2g\|5m2g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5m2g\|5m2g]]</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=5m8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m8w OCA], [http://pdbe.org/5m8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m8w RCSB], [http://www.ebi.ac.uk/pdbsum/5m8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m8w ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5m8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m8w OCA], [http://pdbe.org/5m8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m8w RCSB], [http://www.ebi.ac.uk/pdbsum/5m8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m8w ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5m8w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5m8w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Sulfurospirillum multivorans]]		[[Category: Sulfurospirillum multivorans]]
	[[Category: Bommer, M]]		[[Category: Bommer, M]]

OCA at 10:06, 10 September 2017

OCA — Sun, 10 Sep 2017 10:06:31 GMT

←Older revision		Revision as of 10:06, 10 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5m8w is ~~ON HOLD until Paper~~ Publication	+	==PCE reductive dehalogenase from S. multivorans in complex with 4-chlorophenol==
		+	<StructureSection load='5m8w' size='340' side='right' caption='[[5m8w]], [[Resolution\|resolution]] 2.28Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5m8w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfurospirillum_multivorans Sulfurospirillum multivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M8W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M8W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4CH:4-CHLOROPHENOL'>4CH</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=BVQ:NORPSEUDO-B12'>BVQ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5m2g\|5m2g]]</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=5m8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m8w OCA], [http://pdbe.org/5m8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m8w RCSB], [http://www.ebi.ac.uk/pdbsum/5m8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m8w ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors. Their reaction mechanism is under debate. Here we report on substrate-enzyme interactions in a tetrachloroethene RDase (PceA) that also converts aryl halides. The shape of PceA's highly apolar active site directs binding of bromophenols at some distance from the cobalt and with the hydroxyl substituent towards the metal. A close cobalt-substrate interaction is not observed by electron paramagnetic resonance spectroscopy. Nonetheless, a halogen substituent para to the hydroxyl group is reductively eliminated and the path of the leaving halide is traced in the structure. Based on these findings, an enzymatic mechanism relying on a long-range electron transfer is concluded, which is without parallel in vitamin B12-dependent biochemistry and represents an effective mode of RDase catalysis.

-	~~Authors: Kunze~~, C., Bommer, M., Hagen~~, W.R.~~, Uksa, M., Dobbek, H., Schubert, T., Diekert, G.	+	Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer.,Kunze C, Bommer M, Hagen WR, Uksa M, Dobbek H, Schubert T, Diekert G Nat Commun. 2017 Jul 3;8:15858. doi: 10.1038/ncomms15858. PMID:28671181<ref>PMID:28671181</ref>

-	~~Description: PCE reductive dehalogenase from~~ S. ~~multivorans in complex with 4~~-~~chlorophenol~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5m8w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Sulfurospirillum multivorans]]
		+	[[Category: Bommer, M]]
		+	[[Category: Diekert, G]]
	[[Category: Dobbek, H]]		[[Category: Dobbek, H]]
		+	[[Category: Hagen, W R]]
	[[Category: Kunze, C]]		[[Category: Kunze, C]]
	[[Category: Schubert, T]]		[[Category: Schubert, T]]
-	[[Category: Hagen, W.R]]
-	[[Category: Bommer, M]]
	[[Category: Uksa, M]]		[[Category: Uksa, M]]
-	[[Category: ~~Diekert, G~~]]	+	[[Category: Organohalide respiration anaerobic crystallisation cobalamin]]
		+	[[Category: Oxidoreductase]]

OCA at 11:07, 9 March 2017

OCA — Thu, 09 Mar 2017 11:07:53 GMT

←Older revision		Revision as of 11:07, 9 March 2017
Line 9:		Line 9:
	[[Category: Dobbek, H]]		[[Category: Dobbek, H]]
	[[Category: Kunze, C]]		[[Category: Kunze, C]]
		+	[[Category: Schubert, T]]
	[[Category: Hagen, W.R]]		[[Category: Hagen, W.R]]
	[[Category: Bommer, M]]		[[Category: Bommer, M]]
-	[[Category: Diekert, G]]
-	[[Category: Schubert, T]]
	[[Category: Uksa, M]]		[[Category: Uksa, M]]
		+	[[Category: Diekert, G]]

OCA: Protected "5m8w" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 16:30:33 GMT

Protected "5m8w" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:30, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5m8w is ON HOLD until Paper Publication Authors: Kunze, C., Bommer, M., Hagen, W.R., Uksa, M., Dobbek, H., Schubert, T., Diekert, G. Description: P...

OCA — Fri, 09 Dec 2016 16:30:32 GMT

New page: '''Unreleased structure''' The entry 5m8w is ON HOLD until Paper Publication Authors: Kunze, C., Bommer, M., Hagen, W.R., Uksa, M., Dobbek, H., Schubert, T., Diekert, G. Description: P...

New page

'''Unreleased structure'''

The entry 5m8w is ON HOLD until Paper Publication

Authors: Kunze, C., Bommer, M., Hagen, W.R., Uksa, M., Dobbek, H., Schubert, T., Diekert, G.

Description: PCE reductive dehalogenase from S. multivorans in complex with 4-chlorophenol
[[Category: Unreleased Structures]]
[[Category: Dobbek, H]]
[[Category: Kunze, C]]
[[Category: Hagen, W.R]]
[[Category: Bommer, M]]
[[Category: Diekert, G]]
[[Category: Schubert, T]]
[[Category: Uksa, M]]