5ow0 - Revision history

OCA at 01:26, 28 December 2023

OCA — Thu, 28 Dec 2023 01:26:08 GMT

←Older revision		Revision as of 01:26, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='5ow0' size='340' side='right'caption='[[5ow0]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5ow0' size='340' side='right'caption='[[5ow0]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ow0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Geomg Geomg~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OW0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OW0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ow0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacter_metallireducens_GS-15 Geobacter metallireducens GS-15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OW0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>~~, ~~<scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 1.7Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">etfB-5, Gmet_1525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269799 GEOMG]), etfA-5, Gmet_1526 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269799 GEOMG])</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=5ow0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ow0 OCA], [https://pdbe.org/5ow0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ow0 RCSB], [https://www.ebi.ac.uk/pdbsum/5ow0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ow0 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=5ow0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ow0 OCA], [~~http~~://pdbe.org/5ow0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ow0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ow0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ow0 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q39VG5_GEOMG Q39VG5_GEOMG]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Geomg~~]]	+	[[Category: Geobacter metallireducens GS-15]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chowdhury~~, N P~~]]	+	[[Category: Chowdhury NP]]
-	[[Category: Essen, L O]]	+	[[Category: Essen L-O]]
-	[[Category: Heider, J]]	+	[[Category: Heider J]]
-	[[Category: Kleinsorge, D]]	+	[[Category: Kleinsorge D]]
-	[[Category: Koelzer, S]]	+	[[Category: Koelzer S]]
-	[[Category: Peschke, P]]	+	[[Category: Peschke P]]
-	[[Category: Schuehle, K]]	+	[[Category: Schuehle K]]
-	[[Category: Vogt~~, M S]]~~	+	[[Category: Vogt MS]]
-	~~[[Category: Amp]]~~	+
-	~~[[Category: Anaerobic]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Fad]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Toluene metabolism~~]]	+

OCA at 07:32, 2 September 2020

OCA — Wed, 02 Sep 2020 07:32:28 GMT

←Older revision		Revision as of 07:32, 2 September 2020
Line 1:		Line 1:

-	==Crystal structure of an electron transfer flavoprotein from ~~Geobacillus~~ metallireducens==	+	==Crystal structure of an electron transfer flavoprotein from Geobacter metallireducens==
-	<StructureSection load='5ow0' size='340' side='right' caption='[[5ow0]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5ow0' size='340' side='right'caption='[[5ow0]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ow0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OW0 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OW0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ow0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geomg Geomg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OW0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OW0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5ow0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ow0 OCA], [http://pdbe.org/5ow0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ow0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ow0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ow0 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">etfB-5, Gmet_1525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269799 GEOMG]), etfA-5, Gmet_1526 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269799 GEOMG])</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=5ow0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ow0 OCA], [http://pdbe.org/5ow0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ow0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ow0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ow0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	(R)-Benzylsuccinate is the characteristic initial intermediate of anaerobic toluene metabolism, which is formed by a radical-type addition of toluene to fumarate. Its further degradation proceeds by activation to the coenzyme A (CoA)-thioester and beta-oxidation involving a specific (R)-2-benzylsuccinyl-CoA dehydrogenase (BbsG) affiliated with the family of acyl-CoA dehydrogenases. In this report, we present the biochemical properties of electron transfer flavoproteins (ETFs) from the strictly anaerobic toluene-degrading species Geobacter metallireducens and Desulfobacula toluolica and the facultatively anaerobic bacterium Aromatoleum aromaticum We determined the X-ray structure of the ETF paralogue involved in toluene metabolism of G. metallireducens, revealing strong overall similarities to previously characterized ETF variants but significantly different structural properties in the hinge regions mediating conformational changes. We also show that all strictly anaerobic toluene degraders utilize one of multiple genome-encoded related ETF paralogues, which constitute a distinct clade of similar sequences in the ETF family, for beta-oxidation of benzylsuccinate. In contrast, facultatively anaerobic toluene degraders contain only one ETF species, which is utilized in all beta-oxidation pathways. Our phylogenetic analysis of the known sequences of the ETF family suggests that at least 36 different clades can be differentiated, which are defined either by the taxonomic group of the respective host species (e.g., clade P for Proteobacteria) or by functional specialization (e.g., clade T for anaerobic toluene degradation).IMPORTANCE This study documents the involvement of ETF in anaerobic toluene metabolism as the physiological electron acceptor for benzylsuccinyl-CoA dehydrogenase. While toluene-degrading denitrifying proteobacteria use a common ETF species, which is also used for other beta-oxidation pathways, obligately anaerobic sulfate- or ferric-iron-reducing bacteria use specialized ETF paralogues for toluene degradation. Based on the structure and sequence conservation of these ETFs, they form a new clade that is only remotely related to the previously characterized members of the ETF family. An exhaustive analysis of the available sequences indicated that the protein family consists of several closely related clades of proven or potential electron-bifurcating ETF species and many deeply branching nonbifurcating clades, which either follow the host phylogeny or are affiliated according to functional criteria.
		+
		+	Structural and Functional Characterization of an Electron Transfer Flavoprotein Involved in Toluene Degradation in Strictly Anaerobic Bacteria.,Vogt MS, Schuhle K, Kolzer S, Peschke P, Chowdhury NP, Kleinsorge D, Buckel W, Essen LO, Heider J J Bacteriol. 2019 Oct 4;201(21). pii: JB.00326-19. doi: 10.1128/JB.00326-19., Print 2019 Nov 1. PMID:31405915<ref>PMID:31405915</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ow0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geomg]]
		+	[[Category: Large Structures]]
	[[Category: Chowdhury, N P]]		[[Category: Chowdhury, N P]]
	[[Category: Essen, L O]]		[[Category: Essen, L O]]

OCA at 07:46, 10 October 2018

OCA — Wed, 10 Oct 2018 07:46:30 GMT

←Older revision		Revision as of 07:46, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ow0 ~~is ON HOLD~~	+	==Crystal structure of an electron transfer flavoprotein from Geobacillus metallireducens==
-		+	<StructureSection load='5ow0' size='340' side='right' caption='[[5ow0]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~: ~~Essen, L~~.-O.~~, Vogt, M~~.S., ~~Heider, J~~.~~, Koelzer, S~~., ~~Peschke~~, P., ~~Chowdhury, N~~.P., ~~Schuehle, K~~., ~~Kleinsorge, D~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ow0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OW0 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of an electron transfer flavoprotein from Geobacillus metallireducens~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: ~~Peschke~~, P]]	+	<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=5ow0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ow0 OCA], [http://pdbe.org/5ow0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ow0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ow0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ow0 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chowdhury, N P]]
		+	[[Category: Essen, L O]]
		+	[[Category: Heider, J]]
	[[Category: Kleinsorge, D]]		[[Category: Kleinsorge, D]]
	[[Category: Koelzer, S]]		[[Category: Koelzer, S]]
-	[[Category: ~~Essen~~, ~~L.-O]]~~	+	[[Category: Peschke, P]]
-	~~[[Category: Chowdhury, N.~~P]]	+
	[[Category: Schuehle, K]]		[[Category: Schuehle, K]]
-	[[Category: ~~Heider~~, J]]	+	[[Category: Vogt, M S]]
-	[[Category: ~~Vogt, M.S~~]]	+	[[Category: Amp]]
		+	[[Category: Anaerobic]]
		+	[[Category: Electron transport]]
		+	[[Category: Fad]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Toluene metabolism]]

OCA: Protected "5ow0" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:54:49 GMT

Protected "5ow0" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:54, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ow0 is ON HOLD Authors: Essen, L.-O., Vogt, M.S., Heider, J., Koelzer, S., Peschke, P., Chowdhury, N.P., Schuehle, K., Kleinsorge, D. Description:...

OCA — Wed, 27 Sep 2017 12:54:48 GMT

New page: '''Unreleased structure''' The entry 5ow0 is ON HOLD Authors: Essen, L.-O., Vogt, M.S., Heider, J., Koelzer, S., Peschke, P., Chowdhury, N.P., Schuehle, K., Kleinsorge, D. Description:...

New page

'''Unreleased structure'''

The entry 5ow0 is ON HOLD

Authors: Essen, L.-O., Vogt, M.S., Heider, J., Koelzer, S., Peschke, P., Chowdhury, N.P., Schuehle, K., Kleinsorge, D.

Description: Crystal structure of an electron transfer flavoprotein from Geobacillus metallireducens
[[Category: Unreleased Structures]]
[[Category: Peschke, P]]
[[Category: Kleinsorge, D]]
[[Category: Koelzer, S]]
[[Category: Essen, L.-O]]
[[Category: Chowdhury, N.P]]
[[Category: Schuehle, K]]
[[Category: Heider, J]]
[[Category: Vogt, M.S]]