Literature summary for 2.2.1.9 extracted from

Bashiri, G.; Nigon, L.V.; Jirgis, E.N.M.; Ho, N.A.T.; Stanborough, T.; Dawes, S.S.; Baker, E.N.; Bulloch, E.M.M.; Johnston, J.M.
Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogen Mycobacterium tuberculosis (2020), J. Biol. Chem., 295, 3759-3770 .

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Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Mycobacterium smegmatis mc2 4,517 cells	Mycobacterium tuberculosis

Crystallization (Commentary)

Crystallization (Comment)	Organism
sitting drop vapor diffusion method, using 0.1 M MOPS/HEPES, pH 7.5, 20% (v/v) glycerol, 8% (w/v) PEG 4000, and a 0.02 M mixture of sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium oxamate, and potassium sodium tartrate tetrahydrate	Mycobacterium tuberculosis

Protein Variants

Protein Variants	Comment	Organism
R277A	the mutant has 18% of the wild type enzyme activity	Mycobacterium tuberculosis
R303A	the mutant has 56% of the wild type enzyme activity	Mycobacterium tuberculosis
R97A	the mutant has 50% of the wild type enzyme activity	Mycobacterium tuberculosis

Inhibitors

Inhibitors	Comment	Organism	Structure
dihydroxy-2-naphthoic acid	the potent inhibitor binds to domain II of the enzyme and inhibits its activity	Mycobacterium tuberculosis

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	dependent on	Mycobacterium tuberculosis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
isochorismate + 2-oxoglutarate	Mycobacterium tuberculosis	-	5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2	-	?
isochorismate + 2-oxoglutarate	Mycobacterium tuberculosis H37Rv	-	5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2	-	?

Organism

Organism	UniProt	Comment	Textmining
Mycobacterium tuberculosis	-	-	-
Mycobacterium tuberculosis H37Rv	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
HisTrap column chromatography and Superdex S200 gel filtration	Mycobacterium tuberculosis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
isochorismate + 2-oxoglutarate	-	Mycobacterium tuberculosis	5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2	-	?
isochorismate + 2-oxoglutarate	-	Mycobacterium tuberculosis H37Rv	5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2	-	?

Subunits

Subunits	Comment	Organism
homotetramer	-	Mycobacterium tuberculosis

Synonyms

Synonyms	Comment	Organism
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase	-	Mycobacterium tuberculosis
MenD	-	Mycobacterium tuberculosis
Rv0555	-	Mycobacterium tuberculosis
SEPHCHC synthase	-	Mycobacterium tuberculosis

Cofactor

Cofactor	Comment	Organism	Structure
thiamine diphosphate	-	Mycobacterium tuberculosis

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor	Structure
0.000053	-	wild type enzyme, at pH 8.0 and 25°C	Mycobacterium tuberculosis	dihydroxy-2-naphthoic acid
0.00032	-	mutant enzyme R303A, at pH 8.0 and 25°C	Mycobacterium tuberculosis	dihydroxy-2-naphthoic acid
0.00103	-	mutant enzyme R97A, at pH 8.0 and 25°C	Mycobacterium tuberculosis	dihydroxy-2-naphthoic acid

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Release 2023.1 (January 2023)