5eja: Difference between revisions

Revision as of 15:40, 1 June 2016

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EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and soaked with isochorismate for 7 min

Structural highlights

5eja is a 8 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GOL, MN, TD6
Related:	5ej4, 5ej5, 5ej6, 5ej7, 5ej8, 5ej9, 5ejm
Activity:	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase, with EC number 2.2.1.9
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Warning: this is a large structure, and loading might take a long time or not happen at all.

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:https://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:https://dx.doi.org/10.1021/jacs.6b03437

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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:https://dx.doi.org/10.1021/bi700810x

[3] 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:https://dx.doi.org/10.1021/jacs.6b03437

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+{{Large structure}}
+==EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and soaked with isochorismate for 7 min==
+<StructureSection load='5eja' size='340' side='right' caption='[[5eja]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5eja]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EJA 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TD6:(4S)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3LAMBDA~5~-THIAZOL-2-YL}-4-HYDROXYBUTANOIC+ACID'>TD6</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ej4|5ej4]], [[5ej5|5ej5]], [[5ej6|5ej6]], [[5ej7|5ej7]], [[5ej8|5ej8]], [[5ej9|5ej9]], [[5ejm|5ejm]]</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-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid_synthase 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.2.1.9 2.2.1.9] </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=5eja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eja OCA], [http://pdbe.org/5eja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eja RCSB], [http://www.ebi.ac.uk/pdbsum/5eja PDBsum]</span></td></tr>
+</table>
+{{Large structure}}
+== Function ==
+[[http://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.
-The entry 5eja is ON HOLD  until Paper Publication
+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>
-Authors: Song, H.G., Dong, C., Chen, Y.Z., Sun, Y.R., Guo, Z.H.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description: EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and soaked with isochorismate for 7 min
+<div class="pdbe-citations 5eja" style="background-color:#fffaf0;"></div>
-[[Category: Unreleased Structures]]
+== References ==
-[[Category: Sun, Y.R]]
+<references/>
-[[Category: Guo, Z.H]]
+__TOC__
+</StructureSection>
+[[Category: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase]]
+[[Category: Chen, Y Z]]
 [[Category: Dong, C]]
-[[Category: Chen, Y.Z]]
+[[Category: Guo, Z H]]
-[[Category: Song, H.G]]
+[[Category: Song, H G]]
+[[Category: Sun, Y R]]
+[[Category: Post-decarboxylation intermediate]]
+[[Category: Transferase]]

5eja: Difference between revisions

Revision as of 15:40, 1 June 2016

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and soaked with isochorismate for 7 min

Structural highlights

Function

Publication Abstract from PubMed

References

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