4mxd - Revision history

OCA at 14:44, 8 November 2023

OCA — Wed, 08 Nov 2023 14:44:39 GMT

←Older revision		Revision as of 14:44, 8 November 2023
Line 1:		Line 1:

	==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==		==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==
-	<StructureSection load='4mxd' size='340' side='right'caption='[[4mxd]]' scene=''>	+	<StructureSection load='4mxd' size='340' side='right'caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' 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=4MXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mxd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXD 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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [https://pdbe.org/4mxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [https://www.ebi.ac.uk/pdbsum/4mxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxd ProSAT]</span></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]] 1.45Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [https://pdbe.org/4mxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [https://www.ebi.ac.uk/pdbsum/4mxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MENH_ECOLI MENH_ECOLI] Catalyzes a proton abstraction reaction that results in 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and the formation of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). Is also able to catalyze the hydrolysis of the thioester bond in palmitoyl-CoA in vitro.<ref>PMID:15808744</ref> <ref>PMID:18284213</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to be a specific general base by an open-closed conformational change in the catalysis of 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical alpha/beta-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of a half of the alpha-helical cap domain, which causes extensive structural changes in the alpha/beta-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche-conformation to form the functional triad. NMR analysis shows that the inactive, open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couple formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the triad off its nucelophilicity, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.
		+
		+	Molecular Basis of the General Base Catalysis of an alpha/beta-Hydrolase Catalytic Triad.,Sun Y, Yin S, Feng Y, Li J, Zhou J, Liu C, Zhu G, Guo Z J Biol Chem. 2014 Apr 15. PMID:24737327<ref>PMID:24737327</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4mxd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Feng Y]]		[[Category: Feng Y]]

OCA at 10:48, 31 August 2022

OCA — Wed, 31 Aug 2022 10:48:22 GMT

←Older revision		Revision as of 10:48, 31 August 2022
Line 1:		Line 1:

	==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==		==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==
-	<StructureSection load='4mxd' size='340' side='right'caption='[[4mxd]]~~, [[Resolution\|resolution]] 1.45Å~~' scene=''>	+	<StructureSection load='4mxd' size='340' side='right'caption='[[4mxd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[4mxd]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXD FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [https://pdbe.org/4mxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [https://www.ebi.ac.uk/pdbsum/4mxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxd ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4myd\|4myd]], [[4mys\|4mys]]</div></td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate_synthase 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.20 4.2.99.20] </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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [https://pdbe.org/4mxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [https://www.ebi.ac.uk/pdbsum/4mxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxd ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/MENH_ECOLI MENH_ECOLI]] Catalyzes a proton abstraction reaction that results in 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and the formation of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). Is also able to catalyze the hydrolysis of the thioester bond in palmitoyl-CoA in vitro.<ref>PMID:15808744</ref> <ref>PMID:18284213</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to be a specific general base by an open-closed conformational change in the catalysis of 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical alpha/beta-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of a half of the alpha-helical cap domain, which causes extensive structural changes in the alpha/beta-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche-conformation to form the functional triad. NMR analysis shows that the inactive, open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couple formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the triad off its nucelophilicity, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.
-
-	Molecular Basis of the General Base Catalysis of an alpha/beta-Hydrolase Catalytic Triad.,Sun Y, Yin S, Feng Y, Li J, Zhou J, Liu C, Zhu G, Guo Z J Biol Chem. 2014 Apr 15. PMID:24737327<ref>PMID:24737327</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4mxd" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Feng, Y]]	+	[[Category: Feng Y]]
-	[[Category: Guo, Z]]	+	[[Category: Guo Z]]
-	[[Category: Li, J]]	+	[[Category: Li J]]
-	[[Category: Liu, C]]	+	[[Category: Liu C]]
-	[[Category: Sun, Y]]	+	[[Category: Sun Y]]
-	[[Category: Yin, S]]	+	[[Category: Yin S]]
-	[[Category: Zhou, J]]	+	[[Category: Zhou J]]
-	[[Category: Zhu, G]]	+	[[Category: Zhu G]]
-	~~[[Category: 2-succinyl-6-hydroxy-2]]~~	+
-	~~[[Category: 4-cyclohexadiene-1-carboxylate synthase]]~~	+
-	~~[[Category: Alpha/beta hydrolase fold]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Open conformation~~]]	+

OCA at 05:04, 25 August 2022

OCA — Thu, 25 Aug 2022 05:04:14 GMT

←Older revision		Revision as of 05:04, 25 August 2022
Line 1:		Line 1:

	==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==		==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==
-	<StructureSection load='4mxd' size='340' side='right' caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='4mxd' size='340' side='right'caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mxd]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MXD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mxd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4myd\|4myd]], [[4mys\|4mys]]</td>~~</tr>~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4myd\|4myd]], [[4mys\|4mys]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2263, JW2258, menH, yfbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate_synthase 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.20 4.2.99.20] </span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate_synthase 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.20 4.2.99.20] </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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [https://pdbe.org/4mxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [https://www.ebi.ac.uk/pdbsum/4mxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxd 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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [~~http~~://pdbe.org/4mxd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mxd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MENH_ECOLI MENH_ECOLI]] Catalyzes a proton abstraction reaction that results in 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and the formation of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). Is also able to catalyze the hydrolysis of the thioester bond in palmitoyl-CoA in vitro.<ref>PMID:15808744</ref> <ref>PMID:18284213</ref>	+	[[https://www.uniprot.org/uniprot/MENH_ECOLI MENH_ECOLI]] Catalyzes a proton abstraction reaction that results in 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and the formation of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). Is also able to catalyze the hydrolysis of the thioester bond in palmitoyl-CoA in vitro.<ref>PMID:15808744</ref> <ref>PMID:18284213</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]		[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]
-	[[Category: ~~Ecoli~~]]	+	[[Category: Large Structures]]
	[[Category: Feng, Y]]		[[Category: Feng, Y]]
	[[Category: Guo, Z]]		[[Category: Guo, Z]]

OCA at 08:40, 5 August 2016

OCA — Fri, 05 Aug 2016 08:40:04 GMT

←Older revision		Revision as of 08:40, 5 August 2016
Line 1:		Line 1:
		+
	==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==		==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==
	<StructureSection load='4mxd' size='340' side='right' caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='4mxd' size='340' side='right' caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2263, JW2258, menH, yfbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2263, JW2258, menH, yfbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate_synthase 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.20 4.2.99.20] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate_synthase 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.20 4.2.99.20] </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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [http://www.ebi.ac.uk/pdbsum/4mxd PDBsum]</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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [http://pdbe.org/4mxd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [http://www.ebi.ac.uk/pdbsum/4mxd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4mxd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:51, 25 December 2014

OCA — Thu, 25 Dec 2014 00:51:33 GMT

←Older revision		Revision as of 00:51, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='4mxd' size='340' side='right' caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='4mxd' size='340' side='right' caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mxd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. <br>	+	<table><tr><td colspan='2'>[[4mxd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MXD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4myd\|4myd]], [[4mys\|4mys]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4myd\|4myd]], [[4mys\|4mys]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.~~1.2~~] </span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2263, JW2258, menH, yfbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [http://www.ebi.ac.uk/pdbsum/4mxd PDBsum]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate_synthase 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.20 4.2.99.20] </span></td></tr>
-	<table>	+	<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=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [http://www.ebi.ac.uk/pdbsum/4mxd PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MENH_ECOLI MENH_ECOLI]] Catalyzes a proton abstraction reaction that results in 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and the formation of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). Is also able to catalyze the hydrolysis of the thioester bond in palmitoyl-CoA in vitro.<ref>PMID:15808744</ref> <ref>PMID:18284213</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 17:
	Molecular Basis of the General Base Catalysis of an alpha/beta-Hydrolase Catalytic Triad.,Sun Y, Yin S, Feng Y, Li J, Zhou J, Liu C, Zhu G, Guo Z J Biol Chem. 2014 Apr 15. PMID:24737327<ref>PMID:24737327</ref>		Molecular Basis of the General Base Catalysis of an alpha/beta-Hydrolase Catalytic Triad.,Sun Y, Yin S, Feng Y, Li J, Zhou J, Liu C, Zhu G, Guo Z J Biol Chem. 2014 Apr 15. PMID:24737327<ref>PMID:24737327</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 21:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]		[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]
-	[[Category: Feng, Y.]]	+	[[Category: Ecoli]]
-	[[Category: Guo, Z.]]	+	[[Category: Feng, Y]]
-	[[Category: Li, J.]]	+	[[Category: Guo, Z]]
-	[[Category: Liu, C.]]	+	[[Category: Li, J]]
-	[[Category: Sun, Y.]]	+	[[Category: Liu, C]]
-	[[Category: Yin, S.]]	+	[[Category: Sun, Y]]
-	[[Category: Zhou, J.]]	+	[[Category: Yin, S]]
-	[[Category: Zhu, G.]]	+	[[Category: Zhou, J]]
		+	[[Category: Zhu, G]]
	[[Category: 2-succinyl-6-hydroxy-2]]		[[Category: 2-succinyl-6-hydroxy-2]]
	[[Category: 4-cyclohexadiene-1-carboxylate synthase]]		[[Category: 4-cyclohexadiene-1-carboxylate synthase]]

OCA at 06:50, 7 May 2014

OCA — Wed, 07 May 2014 06:50:54 GMT

←Older revision		Revision as of 06:50, 7 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4mxd\| PDB=4mxd \| SCENE= }}~~	+	==1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)==
-	===1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)===	+	<StructureSection load='4mxd' size='340' side='right' caption='[[4mxd]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4mxd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4myd\|4myd]], [[4mys\|4mys]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mxd RCSB], [http://www.ebi.ac.uk/pdbsum/4mxd PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to be a specific general base by an open-closed conformational change in the catalysis of 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical alpha/beta-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of a half of the alpha-helical cap domain, which causes extensive structural changes in the alpha/beta-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche-conformation to form the functional triad. NMR analysis shows that the inactive, open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couple formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the triad off its nucelophilicity, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.

-	~~==Function==~~	+	Molecular Basis of the General Base Catalysis of an alpha/beta-Hydrolase Catalytic Triad.,Sun Y, Yin S, Feng Y, Li J, Zhou J, Liu C, Zhu G, Guo Z J Biol Chem. 2014 Apr 15. PMID:24737327<ref>PMID:24737327</ref>
-	~~[[http://www.uniprot.org/uniprot/MENH_ECOLI MENH_ECOLI]] Catalyzes a proton abstraction reaction that results in 2,5-elimination~~ of ~~pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and~~ the ~~formation~~ of 2-~~succinyl-6-hydroxy-2~~,~~4-cyclohexadiene-1-carboxylate (SHCHC)~~. ~~Is also able to catalyze the hydrolysis of the thioester bond in palmitoyl-CoA in vitro~~.~~<ref>~~PMID:~~15808744</ref>~~ <ref>PMID:~~18284213~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4mxd]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4MXD OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]		[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]
	[[Category: Feng, Y.]]		[[Category: Feng, Y.]]

OCA at 07:55, 23 April 2014

OCA — Wed, 23 Apr 2014 07:55:47 GMT

←Older revision		Revision as of 07:55, 23 April 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4mxd\| PDB=4mxd \| SCENE= }}
		+	===1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)===

-	~~The entry 4mxd is ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/MENH_ECOLI MENH_ECOLI]] Catalyzes a proton abstraction reaction that results in 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) and the formation of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). Is also able to catalyze the hydrolysis of the thioester bond in palmitoyl-CoA in vitro.<ref>PMID:15808744</ref> <ref>PMID:18284213</ref>

-	~~Authors~~: ~~Sun, Y., Yin, S., Feng, Y., Li, J., Zhou, J~~.~~, Liu, C~~.~~, Zhu, G~~.~~, Guo, Z~~.	+	==About this Structure==
		+	[[4mxd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXD OCA].

-	~~Description~~: 1.~~45 angstronm crystal structure of E~~.~~coli~~ 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase ~~(MenH)~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase]]
		+	[[Category: Feng, Y.]]
		+	[[Category: Guo, Z.]]
		+	[[Category: Li, J.]]
		+	[[Category: Liu, C.]]
		+	[[Category: Sun, Y.]]
		+	[[Category: Yin, S.]]
		+	[[Category: Zhou, J.]]
		+	[[Category: Zhu, G.]]
		+	[[Category: 2-succinyl-6-hydroxy-2]]
		+	[[Category: 4-cyclohexadiene-1-carboxylate synthase]]
		+	[[Category: Alpha/beta hydrolase fold]]
		+	[[Category: Lyase]]
		+	[[Category: Open conformation]]

OCA at 12:53, 20 November 2013

OCA — Wed, 20 Nov 2013 12:53:59 GMT

←Older revision		Revision as of 12:53, 20 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4mxd is ON HOLD	+	The entry 4mxd is ON HOLD until Paper Publication

	Authors: Sun, Y., Yin, S., Feng, Y., Li, J., Zhou, J., Liu, C., Zhu, G., Guo, Z.		Authors: Sun, Y., Yin, S., Feng, Y., Li, J., Zhou, J., Liu, C., Zhu, G., Guo, Z.

	Description: 1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)		Description: 1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)

OCA at 07:29, 16 October 2013

OCA — Wed, 16 Oct 2013 07:29:31 GMT

←Older revision		Revision as of 07:29, 16 October 2013
Line 3:		Line 3:
	The entry 4mxd is ON HOLD		The entry 4mxd is ON HOLD

-	Authors: ~~SUN~~, Y, Yin, S, Feng, Y, Li, J, Zhou, J, Liu, C, Zhu, G, Guo, Z	+	Authors: Sun, Y., Yin, S., Feng, Y., Li, J., Zhou, J., Liu, C., Zhu, G., Guo, Z.

	Description: 1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)		Description: 1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)

OCA: Protected "4mxd" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2013 06:58:37 GMT

Protected "4mxd" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:58, 2 October 2013