5v3a - Revision history

OCA at 08:55, 27 December 2017

OCA — Wed, 27 Dec 2017 08:55:22 GMT

←Older revision		Revision as of 08:55, 27 December 2017
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	<StructureSection load='5v3a' size='340' side='right' caption='[[5v3a]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5v3a' size='340' side='right' caption='[[5v3a]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v3a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v3a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"diplokokkus_intracellularis_meningitidis"_(sic)_weichselbaum_1887 "diplokokkus intracellularis meningitidis" (sic) weichselbaum 1887]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V3A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">A6L27_07605, ERS514410_00397, ERS514534_01643, ERS514708_01580, ERS514851_00814 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=487 "Diplokokkus intracellularis meningitidis" (sic) Weichselbaum 1887])</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=5v3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v3a OCA], [http://pdbe.org/5v3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v3a RCSB], [http://www.ebi.ac.uk/pdbsum/5v3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v3a 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=5v3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v3a OCA], [http://pdbe.org/5v3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v3a RCSB], [http://www.ebi.ac.uk/pdbsum/5v3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v3a ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:56, 18 October 2017

OCA — Wed, 18 Oct 2017 06:56:33 GMT

←Older revision		Revision as of 06:56, 18 October 2017
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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=5v3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v3a OCA], [http://pdbe.org/5v3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v3a RCSB], [http://www.ebi.ac.uk/pdbsum/5v3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v3a 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=5v3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v3a OCA], [http://pdbe.org/5v3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v3a RCSB], [http://www.ebi.ac.uk/pdbsum/5v3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v3a ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. While many of these enzyme families are well characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Neisseria meningitidis. Structural analysis with X-ray crystallographic diffraction data to 2.0 A revealed that each protein subunit harbors a hot dog fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn-24 and Asp-39 as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg-93 as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase.
		+
		+	Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase.,Khandokar YB, Srivastava P, Cowieson N, Sarker S, Aragao D, Das S, Smith KM, Raidal SR, Forwood JK J Biol Chem. 2017 Oct 2. pii: jbc.M117.800227. doi: 10.1074/jbc.M117.800227. PMID:28972175<ref>PMID:28972175</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5v3a" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:50, 24 May 2017

OCA — Wed, 24 May 2017 13:50:55 GMT

←Older revision		Revision as of 13:50, 24 May 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5v3a ~~is ON HOLD~~	+	==Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases==
-		+	<StructureSection load='5v3a' size='340' side='right' caption='[[5v3a]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Khandokar, Y~~.B.~~, Srivastava, P~~.~~, Forwood, J~~.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5v3a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V3A FirstGlance]. <br>
-	~~Description~~: ~~Novel Structural Insights into~~ GDP-~~Mediated Regulation of Acyl~~-~~CoA Thioesterases~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5v3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v3a OCA], [http://pdbe.org/5v3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v3a RCSB], [http://www.ebi.ac.uk/pdbsum/5v3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v3a ProSAT]</span></td></tr>
-	[[Category: Forwood, J.K]]	+	</table>
-	[[Category: Khandokar, Y.B]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Forwood, J K]]
		+	[[Category: Khandokar, Y B]]
	[[Category: Srivastava, P]]		[[Category: Srivastava, P]]
		+	[[Category: Acyl-coa thioesterase]]
		+	[[Category: Coenzyme some]]
		+	[[Category: Gdp]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nisseria meningitidi]]
		+	[[Category: Thioesterase]]

OCA: Protected "5v3a" [edit=sysop:move=sysop]

OCA — Wed, 15 Mar 2017 19:42:08 GMT

Protected "5v3a" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:42, 15 March 2017

OCA: New page: '''Unreleased structure''' The entry 5v3a is ON HOLD Authors: Khandokar, Y.B., Srivastava, P., Forwood, J.K. Description: Novel Structural Insights into GDP-Mediated Regulation of Acyl...

OCA — Wed, 15 Mar 2017 19:42:07 GMT

New page: '''Unreleased structure''' The entry 5v3a is ON HOLD Authors: Khandokar, Y.B., Srivastava, P., Forwood, J.K. Description: Novel Structural Insights into GDP-Mediated Regulation of Acyl...

New page

'''Unreleased structure'''

The entry 5v3a is ON HOLD

Authors: Khandokar, Y.B., Srivastava, P., Forwood, J.K.

Description: Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases
[[Category: Unreleased Structures]]
[[Category: Forwood, J.K]]
[[Category: Khandokar, Y.B]]
[[Category: Srivastava, P]]