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Literature summary 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)

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

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.2.1.9 Mg2+ required Escherichia coli

Natural Substrates/ Products (Substrates)

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

Organism

EC Number Organism UniProt Comment Textmining
2.2.1.9 Escherichia coli P17109
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
2.2.1.9 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
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.2.1.9 isochorismate + 2-oxoglutarate
-
 Escherichia coli 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate + CO2
-
 ?
2.2.1.9 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

EC Number Synonyms Comment Organism
2.2.1.9 (1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
-
 Escherichia coli
2.2.1.9 MenD
-
 Escherichia coli
2.2.1.9 SEPHCHC synthase
-
 Escherichia coli

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.2.1.9 7
-
 assay at Escherichia coli

Cofactor

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

General Information

EC Number General Information Comment Organism
2.2.1.9 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
2.2.1.9 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
2.2.1.9 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