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5ej9

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EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min

Structural highlights

5ej9 is a 8 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.72Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MEND_ECOLI Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).^[1] ^[2]

Publication Abstract from PubMed

Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. How-ever, this intermediate is not found in the thiamine-dependent catal-ysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and structurally determined at 1.34 A resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring ni-trogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 A. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.

A thiamine-dependent enzyme utilizes an active tetrahedral intermediate in vitamin K biosynthesis.,Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z J Am Chem Soc. 2016 May 23. PMID:27213829^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Palaniappan C, Sharma V, Hudspeth ME, Meganathan R. Menaquinone (vitamin K2) biosynthesis: evidence that the Escherichia coli menD gene encodes both 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase and alpha-ketoglutarate decarboxylase activities. J Bacteriol. 1992 Dec;174(24):8111-8. PMID:1459959
↑ Jiang M, Cao Y, Guo ZF, Chen M, Chen X, Guo Z. Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry. 2007 Sep 25;46(38):10979-89. Epub 2007 Aug 31. PMID:17760421 doi:http://dx.doi.org/10.1021/bi700810x
↑ Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z. A thiamine-dependent enzyme utilizes an active tetrahedral intermediate in vitamin K biosynthesis. J Am Chem Soc. 2016 May 23. PMID:27213829 doi:http://dx.doi.org/10.1021/jacs.6b03437

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ej9"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5ej9 is ON HOLD
+==EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min==
+<StructureSection load='5ej9' size='340' side='right'caption='[[5ej9]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5ej9]] is a 8 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=5EJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EJ9 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=5ej9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej9 OCA], [https://pdbe.org/5ej9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ej9 RCSB], [https://www.ebi.ac.uk/pdbsum/5ej9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MEND_ECOLI MEND_ECOLI] Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).<ref>PMID:1459959</ref> <ref>PMID:17760421</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. How-ever, this intermediate is not found in the thiamine-dependent catal-ysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and structurally determined at 1.34 A resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring ni-trogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 A. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.
-Authors: Song, H.G., Dong, C., Chen, Y.Z., Sun, Y.R., Guo, Z.H.
+A thiamine-dependent enzyme utilizes an active tetrahedral intermediate in vitamin K biosynthesis.,Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z J Am Chem Soc. 2016 May 23. PMID:27213829<ref>PMID:27213829</ref>
-Description: EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Sun, Y.R]]
+<div class="pdbe-citations 5ej9" style="background-color:#fffaf0;"></div>
-[[Category: Guo, Z.H]]
+== References ==
-[[Category: Dong, C]]
+<references/>
-[[Category: Chen, Y.Z]]
+__TOC__
-[[Category: Song, H.G]]
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Chen YZ]]
+[[Category: Dong C]]
+[[Category: Guo ZH]]
+[[Category: Song HG]]
+[[Category: Sun YR]]

5ej9

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Current revision

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and isochorismate for 13 min

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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