7yxm - Revision history

OCA at 07:54, 1 May 2024

OCA — Wed, 01 May 2024 07:54:56 GMT

←Older revision		Revision as of 07:54, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7yxm]] is a 4 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=7YXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YXM FirstGlance]. <br>		<table><tr><td colspan='2'>[[7yxm]] is a 4 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=7YXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7yxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yxm OCA], [https://pdbe.org/7yxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yxm RCSB], [https://www.ebi.ac.uk/pdbsum/7yxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yxm 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=7yxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yxm OCA], [https://pdbe.org/7yxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yxm RCSB], [https://www.ebi.ac.uk/pdbsum/7yxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yxm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q39VG2_GEOMG Q39VG2_GEOMG]]	+	[https://www.uniprot.org/uniprot/Q39VG2_GEOMG Q39VG2_GEOMG]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Anaerobic toluene degradation involves beta-oxidation of the first intermediate (R)-2-benzylsuccinate to succinyl-CoA and benzoyl-CoA. Here, we characterize the last enzyme of this pathway, (S)-2-benzoylsuccinyl-CoA thiolase (BbsAB). Although benzoylsuccinyl-CoA is not available for enzyme assays, the recombinantly produced enzymes from two different species showed the reverse activity, benzoylsuccinyl-CoA formation from benzoyl-CoA and succinyl-CoA. Activity depended on the presence of both subunits, the thiolase family member BbsB and the Zn-finger protein BbsA, which is affiliated to the DUF35 family of unknown function. We determined the structure of BbsAB from Geobacter metallireducens with and without bound CoA at 1.7 and 2.0 A resolution, respectively. CoA binding into the well-known thiolase cavity triggers an induced-fit movement of the highly disordered covering loop, resulting in its rigidification by forming multiple interactions to the outstretched CoA moiety. This event is coupled with an 8 A movement of an adjacent hairpin loop of BbsB and the C-terminal domain of BbsA. Thereby, CoA is placed into a catalytically productive conformation, and a putative second CoA binding site involving BbsA and the partner BbsB' subunit is simultaneously formed that also reaches the active center. Therefore, while maintaining the standard thioester-dependent Claisen-type mechanism, BbsAB represents a new type of thiolase.	+
-		+
-	Finis tolueni: a new type of thiolase with an integrated Zn-finger subunit catalyzes the final step of anaerobic toluene metabolism.,Weidenweber S, Schuhle K, Lippert ML, Mock J, Seubert A, Demmer U, Ermler U, Heider J FEBS J. 2022 Sep;289(18):5599-5616. doi: 10.1111/febs.16443. Epub 2022 Mar 29. PMID:35313080<ref>PMID:35313080</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7yxm" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:30, 28 September 2022

OCA — Wed, 28 Sep 2022 06:30:11 GMT

←Older revision		Revision as of 06:30, 28 September 2022
Line 1:		Line 1:

-	====	+	==Benzoylsuccinyl-CoA thiolase with coenzyme A==
-	<StructureSection load='7yxm' size='340' side='right'caption='[[7yxm]]' scene=''>	+	<StructureSection load='7yxm' size='340' side='right'caption='[[7yxm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7yxm]] is a 4 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=7YXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YXM FirstGlance]. <br>
-	</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=7yxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yxm OCA], [https://pdbe.org/7yxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yxm RCSB], [https://www.ebi.ac.uk/pdbsum/7yxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yxm ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7yxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yxm OCA], [https://pdbe.org/7yxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yxm RCSB], [https://www.ebi.ac.uk/pdbsum/7yxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yxm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q39VG2_GEOMG Q39VG2_GEOMG]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Anaerobic toluene degradation involves beta-oxidation of the first intermediate (R)-2-benzylsuccinate to succinyl-CoA and benzoyl-CoA. Here, we characterize the last enzyme of this pathway, (S)-2-benzoylsuccinyl-CoA thiolase (BbsAB). Although benzoylsuccinyl-CoA is not available for enzyme assays, the recombinantly produced enzymes from two different species showed the reverse activity, benzoylsuccinyl-CoA formation from benzoyl-CoA and succinyl-CoA. Activity depended on the presence of both subunits, the thiolase family member BbsB and the Zn-finger protein BbsA, which is affiliated to the DUF35 family of unknown function. We determined the structure of BbsAB from Geobacter metallireducens with and without bound CoA at 1.7 and 2.0 A resolution, respectively. CoA binding into the well-known thiolase cavity triggers an induced-fit movement of the highly disordered covering loop, resulting in its rigidification by forming multiple interactions to the outstretched CoA moiety. This event is coupled with an 8 A movement of an adjacent hairpin loop of BbsB and the C-terminal domain of BbsA. Thereby, CoA is placed into a catalytically productive conformation, and a putative second CoA binding site involving BbsA and the partner BbsB' subunit is simultaneously formed that also reaches the active center. Therefore, while maintaining the standard thioester-dependent Claisen-type mechanism, BbsAB represents a new type of thiolase.
		+
		+	Finis tolueni: a new type of thiolase with an integrated Zn-finger subunit catalyzes the final step of anaerobic toluene metabolism.,Weidenweber S, Schuhle K, Lippert ML, Mock J, Seubert A, Demmer U, Ermler U, Heider J FEBS J. 2022 Sep;289(18):5599-5616. doi: 10.1111/febs.16443. Epub 2022 Mar 29. PMID:35313080<ref>PMID:35313080</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7yxm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Geobacter metallireducens GS-15]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Ermler U]]
		+	[[Category: Heider J]]
		+	[[Category: Weidenweber S]]

OCA at 10:28, 6 April 2022

OCA — Wed, 06 Apr 2022 10:28:32 GMT

←Older revision		Revision as of 10:28, 6 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7yxm ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7yxm' size='340' side='right'caption='[[7yxm]]' scene=''>
-	~~Authors~~: ~~Ermler, U~~.~~, Heider, J~~.~~, Weidenweber, S~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Benzoylsuccinyl~~-~~CoA thiolase with coenzyme A~~	+	</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=7yxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yxm OCA], [https://pdbe.org/7yxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yxm RCSB], [https://www.ebi.ac.uk/pdbsum/7yxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yxm ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Heider~~, J]]	+	__TOC__
-	[[Category: ~~Weidenweber, S~~]]	+	</StructureSection>
-	[[Category: ~~Ermler, U~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7yxm" [edit=sysop:move=sysop]

OCA — Wed, 23 Feb 2022 06:47:29 GMT

Protected "7yxm" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:47, 23 February 2022

OCA: New page: '''Unreleased structure''' The entry 7yxm is ON HOLD Authors: Ermler, U., Heider, J., Weidenweber, S. Description: Benzoylsuccinyl-CoA thiolase with coenzyme A [[Category: Unreleased S...

OCA — Wed, 23 Feb 2022 06:47:28 GMT

New page: '''Unreleased structure''' The entry 7yxm is ON HOLD Authors: Ermler, U., Heider, J., Weidenweber, S. Description: Benzoylsuccinyl-CoA thiolase with coenzyme A [[Category: Unreleased S...

New page

'''Unreleased structure'''

The entry 7yxm is ON HOLD

Authors: Ermler, U., Heider, J., Weidenweber, S.

Description: Benzoylsuccinyl-CoA thiolase with coenzyme A
[[Category: Unreleased Structures]]
[[Category: Heider, J]]
[[Category: Weidenweber, S]]
[[Category: Ermler, U]]