3t89 - Revision history

OCA at 13:20, 14 March 2024

OCA — Thu, 14 Mar 2024 13:20:22 GMT

←Older revision		Revision as of 13:20, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3t89' size='340' side='right'caption='[[3t89]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3t89' size='340' side='right'caption='[[3t89]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T89 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T89 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=MLI:MALONATE+ION'>MLI</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]] 1.949Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</div>~~</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=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>b2262 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </~~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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [https://pdbe.org/3t89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [https://www.ebi.ac.uk/pdbsum/3t89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t89 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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [https://pdbe.org/3t89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [https://www.ebi.ac.uk/pdbsum/3t89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t89 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MENB_ECOLI MENB_ECOLI]] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:1091286</ref> <ref>PMID:20643650</ref>	+	[https://www.uniprot.org/uniprot/MENB_ECOLI MENB_ECOLI] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:1091286</ref> <ref>PMID:20643650</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 A structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate alpha-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase, is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in alpha-proton acidity.	+
-		+
-	Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.,Li HJ, Li X, Liu N, Zhang H, Truglio JJ, Mishra S, Kisker CF, Garcia-Diaz M, Tonge PJ Biochemistry. 2011 Aug 10. PMID:21830810<ref>PMID:21830810</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3t89" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Garcia-Diaz, M]]	+	[[Category: Garcia-Diaz M]]
-	[[Category: Kisker, C]]	+	[[Category: Kisker C]]
-	[[Category: Li, H J]]	+	[[Category: Li H-J]]
-	[[Category: Li, X]]	+	[[Category: Li X]]
-	[[Category: Liu, N]]	+	[[Category: Liu N]]
-	[[Category: Mishra, S]]	+	[[Category: Mishra S]]
-	[[Category: Tonge, P]]	+	[[Category: Tonge P]]
-	[[Category: Truglio, J]]	+	[[Category: Truglio J]]
-	[[Category: Zhang, H]]	+	[[Category: Zhang H]]
-	~~[[Category: Crotonase superfamily]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 16:47, 6 July 2022

OCA — Wed, 06 Jul 2022 16:47:10 GMT

←Older revision		Revision as of 16:47, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis==		==Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis==
-	<StructureSection load='3t89' size='340' side='right' caption='[[3t89]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3t89' size='340' side='right'caption='[[3t89]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3T89 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T89 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=MLI:MALONATE+ION'>MLI</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=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2262 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2262 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [~~http~~://pdbe.org/3t89 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3t89 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3t89 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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [https://pdbe.org/3t89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [https://www.ebi.ac.uk/pdbsum/3t89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t89 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MENB_ECOLI MENB_ECOLI]] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:1091286</ref> <ref>PMID:20643650</ref>	+	[[https://www.uniprot.org/uniprot/MENB_ECOLI MENB_ECOLI]] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:1091286</ref> <ref>PMID:20643650</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 27:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]		[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]
		+	[[Category: Large Structures]]
	[[Category: Garcia-Diaz, M]]		[[Category: Garcia-Diaz, M]]
	[[Category: Kisker, C]]		[[Category: Kisker, C]]

OCA at 19:37, 24 January 2018

OCA — Wed, 24 Jan 2018 19:37:43 GMT

←Older revision		Revision as of 19:37, 24 January 2018
Line 29:		Line 29:
	[[Category: Garcia-Diaz, M]]		[[Category: Garcia-Diaz, M]]
	[[Category: Kisker, C]]		[[Category: Kisker, C]]
-	[[Category: Li, H-J]]	+	[[Category: Li, H J]]
	[[Category: Li, X]]		[[Category: Li, X]]
	[[Category: Liu, N]]		[[Category: Liu, N]]

OCA at 23:13, 5 August 2016

OCA — Fri, 05 Aug 2016 23:13:24 GMT

←Older revision		Revision as of 23:13, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis==		==Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis==
	<StructureSection load='3t89' size='340' side='right' caption='[[3t89]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3t89' size='340' side='right' caption='[[3t89]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T89 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T89 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=MLI:MALONATE+ION'>MLI</scene></td></tr>		</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=MLI:MALONATE+ION'>MLI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2262 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2262 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Naphthoate_synthase Naphthoate~~ synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-dihydroxy-2-naphthoyl-CoA_synthase 1,4-dihydroxy-2-naphthoyl-CoA synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [http://www.ebi.ac.uk/pdbsum/3t89 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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [http://pdbe.org/3t89 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [http://www.ebi.ac.uk/pdbsum/3t89 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t89 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 3t89" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
-	[[Category: ~~Naphthoate~~ synthase]]	+	[[Category: 1,4-dihydroxy-2-naphthoyl-CoA synthase]]
	[[Category: Garcia-Diaz, M]]		[[Category: Garcia-Diaz, M]]
	[[Category: Kisker, C]]		[[Category: Kisker, C]]

OCA at 06:42, 25 December 2014

OCA — Thu, 25 Dec 2014 06:42:18 GMT

←Older revision		Revision as of 06:42, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T89 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T89 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=MLI:MALONATE+ION'>MLI</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=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2262 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2262 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Naphthoate_synthase Naphthoate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Naphthoate_synthase Naphthoate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [http://www.ebi.ac.uk/pdbsum/3t89 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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [http://www.ebi.ac.uk/pdbsum/3t89 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MENB_ECOLI MENB_ECOLI]] Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).<ref>PMID:1091286</ref> <ref>PMID:20643650</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.,Li HJ, Li X, Liu N, Zhang H, Truglio JJ, Mishra S, Kisker CF, Garcia-Diaz M, Tonge PJ Biochemistry. 2011 Aug 10. PMID:21830810<ref>PMID:21830810</ref>		Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.,Li HJ, Li X, Liu N, Zhang H, Truglio JJ, Mishra S, Kisker CF, Garcia-Diaz M, Tonge PJ Biochemistry. 2011 Aug 10. PMID:21830810<ref>PMID:21830810</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 23:		Line 25:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Naphthoate synthase]]		[[Category: Naphthoate synthase]]
-	[[Category: Garcia-Diaz, M.]]	+	[[Category: Garcia-Diaz, M]]
-	[[Category: Kisker, C.]]	+	[[Category: Kisker, C]]
-	[[Category: Li, H-J.]]	+	[[Category: Li, H-J]]
-	[[Category: Li, X.]]	+	[[Category: Li, X]]
-	[[Category: Liu, N.]]	+	[[Category: Liu, N]]
-	[[Category: Mishra, S.]]	+	[[Category: Mishra, S]]
-	[[Category: Tonge, P.]]	+	[[Category: Tonge, P]]
-	[[Category: Truglio, J.]]	+	[[Category: Truglio, J]]
-	[[Category: Zhang, H.]]	+	[[Category: Zhang, H]]
	[[Category: Crotonase superfamily]]		[[Category: Crotonase superfamily]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 06:35, 5 June 2014

OCA — Thu, 05 Jun 2014 06:35:04 GMT

←Older revision		Revision as of 06:35, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3t89.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis==
		+	<StructureSection load='3t89' size='340' side='right' caption='[[3t89]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3t89]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T89 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=MLI:MALONATE+ION'>MLI</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t88\|3t88]], [[3t8a\|3t8a]], [[3t8b\|3t8b]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2262 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Naphthoate_synthase Naphthoate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.36 4.1.3.36] </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=3t89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t89 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t89 RCSB], [http://www.ebi.ac.uk/pdbsum/3t89 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 A structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate alpha-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase, is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in alpha-proton acidity.

-	~~<!--~~	+	Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.,Li HJ, Li X, Liu N, Zhang H, Truglio JJ, Mishra S, Kisker CF, Garcia-Diaz M, Tonge PJ Biochemistry. 2011 Aug 10. PMID:21830810<ref>PMID:21830810</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3t89", creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded)~~,	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3t89\| PDB=3t89 \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~Escherichia coli MenB,~~ the ~~1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21830810}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21830810 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21830810}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3t89]] is a 6 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021830810<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Naphthoate synthase]]		[[Category: Naphthoate synthase]]

OCA at 11:06, 16 November 2011

OCA — Wed, 16 Nov 2011 11:06:00 GMT

←Older revision		Revision as of 11:06, 16 November 2011
Line 1:		Line 1:
-	[[Image:3t89.~~jpg~~\|left\|200px]]	+	[[Image:3t89.png\|left\|200px]]

	<!--		<!--

OCA at 07:27, 24 August 2011

OCA — Wed, 24 Aug 2011 07:27:35 GMT

←Older revision		Revision as of 07:27, 24 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3t89.jpg\|left\|200px]]

-	The ~~entry 3t89~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3t89", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3t89\| PDB=3t89 \| SCENE= }}

-	~~Authors: Li~~, ~~H-J.~~, ~~Li, X., Liu, N., Zhang, H., Truglio, J., Mishra, S., Kisker, C., Garcia~~-~~Diaz, M., Tonge, P.~~	+	===Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis===

-	~~Description: Crystal structure of Escherichia coli MenB~~, the 1,4-~~dihydroxy~~-~~2-naphthoyl~~-~~CoA~~ synthase ~~in vitamin K2 biosynthesis~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21830810}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21830810 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21830810}}
		+
		+	==About this Structure==
		+	[[3t89]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T89 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021830810</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
		+	[[Category: Naphthoate synthase]]
		+	[[Category: Garcia-Diaz, M.]]
		+	[[Category: Kisker, C.]]
		+	[[Category: Li, H-J.]]
		+	[[Category: Li, X.]]
		+	[[Category: Liu, N.]]
		+	[[Category: Mishra, S.]]
		+	[[Category: Tonge, P.]]
		+	[[Category: Truglio, J.]]
		+	[[Category: Zhang, H.]]
		+	[[Category: Crotonase superfamily]]
		+	[[Category: Lyase]]

OCA at 05:54, 17 August 2011

OCA — Wed, 17 Aug 2011 05:54:42 GMT

←Older revision		Revision as of 05:54, 17 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3t89 is ON HOLD	+	The entry 3t89 is ON HOLD until Paper Publication

	Authors: Li, H-J., Li, X., Liu, N., Zhang, H., Truglio, J., Mishra, S., Kisker, C., Garcia-Diaz, M., Tonge, P.		Authors: Li, H-J., Li, X., Liu, N., Zhang, H., Truglio, J., Mishra, S., Kisker, C., Garcia-Diaz, M., Tonge, P.

	Description: Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis		Description: Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis

OCA: Protected "3t89" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2011 05:36:51 GMT

Protected "3t89" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:36, 10 August 2011