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Literature summary for extracted from

  • 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 (2016), J. Am. Chem. Soc., 138, 7244-7247 .
    View publication on PubMed

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant enzyme complexed with its tetrahedral reaction intermediate, X-ray diffraction structure determination and analysis Escherichia coli


Metals/Ions Comment Organism Structure
Mg2+ required Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
isochorismate + 2-oxoglutarate Escherichia coli
5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate + CO2


Organism UniProt Comment Textmining
Escherichia coli P17109


Reaction Comment Organism Reaction ID
isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2 proposed mechanism for formation of the tetrahedral intermediate in MenD catalysis. The strong interaction at the terminal carboxylate is proposed to restrict the rotation around C2-C2alpha so that no hydrogen bond is formed between C2alpha-OH and N4' of the cofactor throughout the reaction process. This disables the formation of the enamine intermediate and enables the formation of the tetrahedral intermediate. Modeling, overview Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
isochorismate + 2-oxoglutarate
Escherichia coli 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate + CO2
isochorismate + 2-oxoglutarate via a tetrahedral enamine/acyl anion intermediate, overview Escherichia coli 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate + CO2


Synonyms Comment Organism
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Escherichia coli
Escherichia coli
SEPHCHC synthase
Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
assay at Escherichia coli


Cofactor Comment Organism Structure
thiamine diphosphate ThDP-dependent enzyme Escherichia coli

General Information

General Information Comment Organism
evolution the enzyme Men D is not significantly different from other ThDP-dependent enzymes in active-site architecture, cofactor binding, or overall three-dimensional structure, suggesting the use of the canonical enamine intermediate in its catalysis Escherichia coli
metabolism MenD is a thiamine diphosphate-dependent enzyme that catalyzes a distinctive Stetterlike 1,4-addition reaction in bacterial biosynthesis of vitamin K2 Escherichia coli
additional information in the covalent tetrahedral enamine intermediate, all of the bond lengths and angles of its planar thiazolium ring are comparable to those of a similar enzyme-free thiamine diphosphate adduct, complex crystal structure determination and analysis, NMR structure analysis and modeling, overview Escherichia coli