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3t89

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

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 <StructureSection load='3t89' size='340' side='right'caption='[[3t89]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == 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]] 1.949&#8491;</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>
 </table>
 == 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3t89" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[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]]
-[[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]]

3t89

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

Structural highlights

Function

References

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