PDBsum entry 5ej4

Transferase

PDB id: 5ej4

Contents

Protein chains

(+ 2 more) 556 a.a.

Ligands

TD6 ×8

GOL ×16

FMT ×8

Metals

_MN ×8

Waters ×4357

PDB id:

5ej4

Name:

Transferase

Title:

Ecmend-thdp-mn2+ complex soaked with 2-ketoglutarate for 15 min

Structure:

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase. Chain: a, b, c, d, e, f, g, h. Synonym: thdp-dependent enzyme mend,sephchc synthase,menaquinone biosynthesis protein mend. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k12 substr. Mg1655. Gene: mend, b2264, jw5374. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.77Å R-factor: 0.178 R-free: 0.217

Authors:

H.G.Song,C.Dong,Y.Z.Chen,Y.R.Sun,Z.H.Guo

Key ref:

H.Song et al. (2016). A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis. J Am Chem Soc, 138, 7244-7247. PubMed id: 27213829 DOI: 10.1021/jacs.6b03437

Date:

01-Nov-15 Release date: 01-Jun-16

Protein chains

P17109  (MEND_ECOLI) -  2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase from Escherichia coli (strain K12)

Seq: 556 a.a.

Struc: 556 a.a.

Enzyme reactions

• Enzyme class: E.C.2.2.1.9 - 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid
• Reaction: isochorismate + 2-oxoglutarate + H⁺ = 5-enolpyruvoyl-6-hydroxy-2- succinyl-cyclohex-3-ene-1-carboxylate + CO2

isochorismate (Bound ligand (Het Group name = GOL) matches with 45.45% similarity) + 2-oxoglutarate + H(+) = 5-enolpyruvoyl-6-hydroxy-2- succinyl-cyclohex-3-ene-1-carboxylate + CO2 (Bound ligand (Het Group name = FMT) corresponds exactly)

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/jacs.6b03437

J Am Chem Soc 138:7244-7247 (2016)

PubMed id: 27213829

A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis.

H.Song, C.Dong, M.Qin, Y.Chen, Y.Sun, J.Liu, W.Chan, Z.Guo.

ABSTRACT

Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. However, this intermediate is not found in the thiamine-dependent catalysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and was structurally determined at 1.34 Å resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring nitrogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 Å. 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.