5szy - Revision history

OCA at 12:52, 4 October 2023

OCA — Wed, 04 Oct 2023 12:52:17 GMT

←Older revision		Revision as of 12:52, 4 October 2023
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	==Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases==		==Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases==
-	<StructureSection load='5szy' size='340' side='right' caption='[[5szy]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5szy' size='340' side='right'caption='[[5szy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5szy]] 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=5SZY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5SZY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5szy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SZY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5szu\|5szu]], [[5szv\|5szv]], [[5szz\|5szz]], [[5t02\|5t02]]~~<~~/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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">ERS514298_01532, 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'>[https://proteopedia.org/fgij/fg.htm?mol=5szy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5szy OCA], [https://pdbe.org/5szy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5szy RCSB], [https://www.ebi.ac.uk/pdbsum/5szy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5szy 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=5szy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5szy OCA], [~~http~~://pdbe.org/5szy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5szy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5szy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5szy ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0Y5D4F5_NEIME A0A0Y5D4F5_NEIME]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5szy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5szy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thioesterase 3D structures\|Thioesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Forwood, J K~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Khandokar, Y B~~]]	+	[[Category: Neisseria meningitidis]]
-	[[Category: ~~Srivastava, P~~]]	+	[[Category: Forwood JK]]
-	[[Category: ~~Acyl-coa thioesterase~~]]	+	[[Category: Khandokar YB]]
-	[[Category: ~~Coenzyme some]]~~	+	[[Category: Srivastava P]]
-	~~[[Category: Gdp]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nisseria meningitidi]]~~	+
-	~~[[Category: Thioesterase~~]]	+

OCA at 08:54, 27 December 2017

OCA — Wed, 27 Dec 2017 08:54:54 GMT

←Older revision		Revision as of 08:54, 27 December 2017
Line 3:		Line 3:
	<StructureSection load='5szy' size='340' side='right' caption='[[5szy]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5szy' size='340' side='right' caption='[[5szy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5szy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SZY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5szy]] 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=5SZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SZY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5szu\|5szu]], [[5szv\|5szv]], [[5szz\|5szz]], [[5t02\|5t02]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5szu\|5szu]], [[5szv\|5szv]], [[5szz\|5szz]], [[5t02\|5t02]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERS514298_01532, 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=5szy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5szy OCA], [http://pdbe.org/5szy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5szy RCSB], [http://www.ebi.ac.uk/pdbsum/5szy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5szy 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=5szy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5szy OCA], [http://pdbe.org/5szy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5szy RCSB], [http://www.ebi.ac.uk/pdbsum/5szy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5szy ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:55, 18 October 2017

OCA — Wed, 18 Oct 2017 06:55:13 GMT

←Older revision		Revision as of 06:55, 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=5szy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5szy OCA], [http://pdbe.org/5szy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5szy RCSB], [http://www.ebi.ac.uk/pdbsum/5szy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5szy 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=5szy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5szy OCA], [http://pdbe.org/5szy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5szy RCSB], [http://www.ebi.ac.uk/pdbsum/5szy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5szy 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 5szy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:37, 14 September 2016

OCA — Wed, 14 Sep 2016 15:37:38 GMT

←Older revision		Revision as of 15:37, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5szy ~~is ON HOLD~~	+	==Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases==
-		+	<StructureSection load='5szy' size='340' side='right' caption='[[5szy]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Khandokar, Y~~.B.~~, Srivastava, P~~.~~, Forwood, J~~.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5szy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SZY 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5szu\|5szu]], [[5szv\|5szv]], [[5szz\|5szz]], [[5t02\|5t02]]</td></tr>
-	[[~~Category~~: ~~Khandokar~~, Y.B]]	+	<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=5szy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5szy OCA], [http://pdbe.org/5szy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5szy RCSB], [http://www.ebi.ac.uk/pdbsum/5szy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5szy ProSAT]</span></td></tr>
-	[[Category: Forwood, J.K]]	+	</table>
		+	__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 "5szy" [edit=sysop:move=sysop]

OCA — Fri, 09 Sep 2016 15:28:37 GMT

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

←Older revision

Revision as of 15:28, 9 September 2016

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

OCA — Fri, 09 Sep 2016 15:28:36 GMT

New page: '''Unreleased structure''' The entry 5szy 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 5szy 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: Khandokar, Y.B]]
[[Category: Forwood, J.K]]
[[Category: Srivastava, P]]