5odh - Revision history

OCA at 16:45, 13 December 2023

OCA — Wed, 13 Dec 2023 16:45:46 GMT

←Older revision		Revision as of 16:45, 13 December 2023
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	<StructureSection load='5odh' size='340' side='right'caption='[[5odh]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5odh' size='340' side='right'caption='[[5odh]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5odh]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Methanothermococcus_thermolithotrophicus_dsm_2095~~ Methanothermococcus thermolithotrophicus ~~dsm~~ 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ODH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ODH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5odh]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermococcus_thermolithotrophicus_DSM_2095 Methanothermococcus thermolithotrophicus DSM 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ODH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ODH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9S8:Non-cubane+[4Fe-4S]-cluster'>9S8</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.2Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.98.1 1.8.98.1] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9S8:Non-cubane+[4Fe-4S]-cluster'>9S8</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=5odh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5odh OCA], [~~http~~://pdbe.org/5odh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5odh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5odh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5odh 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=5odh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5odh OCA], [https://pdbe.org/5odh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5odh RCSB], [https://www.ebi.ac.uk/pdbsum/5odh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5odh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2D0TCB9_METTL A0A2D0TCB9_METTL] Part of a complex that catalyzes the reversible reduction of CoM-S-S-CoB to the thiol-coenzymes H-S-CoM (coenzyme M) and H-S-CoB (coenzyme B).[RuleBase:RU366072]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Methanothermococcus thermolithotrophicus ~~dsm~~ 2095]]	+	[[Category: Methanothermococcus thermolithotrophicus DSM 2095]]
-	~~[[Category: Oxidoreductase~~]]	+	[[Category: Ermler U]]
-	[[Category: Ermler, U]]	+	[[Category: Koch J]]
-	[[Category: Koch, J]]	+	[[Category: Shima S]]
-	[[Category: Shima, S]]	+	[[Category: Wagner T]]
-	[[Category: Wagner, T]]	+
-	~~[[Category: Anaerobic]]~~	+
-	~~[[Category: Ccg motif]]~~	+
-	~~[[Category: Ferredoxin]]~~	+
-	~~[[Category: Fes cluster]]~~	+
-	~~[[Category: Flavin-based electron bifurcation]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Heterodisulfide reductase]]~~	+
-	~~[[Category: Macromolecular complex]]~~	+
-	~~[[Category: Metabolism]]~~	+
-	~~[[Category: Methanogenesis]]~~	+
-	~~[[Category: Thioredoxin~~]]	+

OCA at 12:21, 26 August 2020

OCA — Wed, 26 Aug 2020 12:21:22 GMT

←Older revision		Revision as of 12:21, 26 August 2020
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	==Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes==		==Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes==
-	<StructureSection load='5odh' size='340' side='right' caption='[[5odh]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5odh' size='340' side='right'caption='[[5odh]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5odh]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermococcus_thermolithotrophicus_dsm_2095 Methanothermococcus thermolithotrophicus dsm 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ODH OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ODH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5odh]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermococcus_thermolithotrophicus_dsm_2095 Methanothermococcus thermolithotrophicus dsm 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ODH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ODH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9S8:Non-cubane+[4Fe-4S]-cluster'>9S8</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9S8:Non-cubane+[4Fe-4S]-cluster'>9S8</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.98.1 1.8.98.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.98.1 1.8.98.1] </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=5odh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5odh OCA], [http://pdbe.org/5odh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5odh RCSB], [http://www.ebi.ac.uk/pdbsum/5odh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5odh 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=5odh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5odh OCA], [http://pdbe.org/5odh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5odh RCSB], [http://www.ebi.ac.uk/pdbsum/5odh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5odh ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Methanothermococcus thermolithotrophicus dsm 2095]]		[[Category: Methanothermococcus thermolithotrophicus dsm 2095]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

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

OCA — Wed, 30 Aug 2017 03:57:45 GMT

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

←Older revision

Revision as of 03:57, 30 August 2017

OCA: New page: ==Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes== == Structural highlights ==
<table><tr><td colspan='2'>[[5odh]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermococcus_thermolithotrophicus_dsm_2095 Methanothermococcus thermolithotrophicus dsm 2095]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ODH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ODH FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9S8:Non-cubane+[4Fe-4S]-cluster'>9S8</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.98.1 1.8.98.1] </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=5odh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5odh OCA], [http://pdbe.org/5odh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5odh RCSB], [http://www.ebi.ac.uk/pdbsum/5odh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5odh ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In methanogenic archaea, the carbon dioxide (CO2) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferredoxin and the heterodisulfide of coenzymes M and B. Here, we present the structure of the native heterododecameric HdrABC-MvhAGD complex at 2.15-angstrom resolution. HdrB contains two noncubane [4Fe-4S] clusters composed of fused [3Fe-4S]-[2Fe-2S] units sharing 1 iron (Fe) and 1 sulfur (S), which were coordinated at the CCG motifs. Soaking experiments showed that the heterodisulfide is clamped between the two noncubane [4Fe-4S] clusters and homolytically cleaved, forming coenzyme M and B bound to each iron. Coenzymes are consecutively released upon one-by-one electron transfer. The HdrABC-MvhAGD atomic model serves as a structural template for numerous HdrABC homologs involved in diverse microbial metabolic pathways.

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.,Wagner T, Koch J, Ermler U, Shima S Science. 2017 Aug 18;357(6352):699-703. doi: 10.1126/science.aan0425. PMID:28818947<ref>PMID:28818947</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5odh" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Methanothermococcus thermolithotrophicus dsm 2095]]
[[Category: Oxidoreductase]]
[[Category: Ermler, U]]
[[Category: Koch, J]]
[[Category: Shima, S]]
[[Category: Wagner, T]]
[[Category: Anaerobic]]
[[Category: Ccg motif]]
[[Category: Ferredoxin]]
[[Category: Fes cluster]]
[[Category: Flavin-based electron bifurcation]]
[[Category: Flavoprotein]]
[[Category: Heterodisulfide reductase]]
[[Category: Macromolecular complex]]
[[Category: Metabolism]]
[[Category: Methanogenesis]]
[[Category: Thioredoxin]]