Literature summary for 4.1.1.7 extracted from

Andrews, F.H.; Horton, J.D.; Shin, D.; Yoon, H.J.; Logsdon, M.G.; Malik, A.M.; Rogers, M.P.; Kneen, M.M.; Suh, S.W.; McLeish, M.J.
The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes (2015), Biochim. Biophys. Acta, 1854, 1001-1009 .

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Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Escherichia coli Rosetta2(DE3)pLysS cells	Mycolicibacterium smegmatis

Crystallization (Commentary)

Crystallization (Comment)	Organism
sitting drop vapor diffusion method, using 4.0 M sodium formate	Mycolicibacterium smegmatis

Protein Variants

Protein Variants	Comment	Organism
I466A	the mutant shows increased catalytic efficiency for benzoylformate compared to the wild type enzyme	Mycolicibacterium smegmatis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
2	3	benzoylformate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
15	-	benzoylformate	mutant enzyme I466A, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
21	-	2-Oxohexanoate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
21	-	4-methylthio-2-oxobutanoate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis

Organism

Organism	UniProt	Comment	Textmining
Mycolicibacterium smegmatis	-	-	-
Mycolicibacterium smegmatis mc2155	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
HiTrap Ni2+ chelating column chromatography	Mycolicibacterium smegmatis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
2-oxohexanoate	best substrate	Mycolicibacterium smegmatis	valeraldehyde + CO2	-	?
2-oxohexanoate	best substrate	Mycolicibacterium smegmatis mc2155	valeraldehyde + CO2	-	?
4-methylthio-2-oxobutanoate	-	Mycolicibacterium smegmatis	3-(methylsulfanyl)propanal + CO2	-	?
4-methylthio-2-oxobutanoate	-	Mycolicibacterium smegmatis mc2155	3-(methylsulfanyl)propanal + CO2	-	?
benzoylformate	-	Mycolicibacterium smegmatis	benzaldehyde + CO2	-	?
benzoylformate	-	Mycolicibacterium smegmatis mc2155	benzaldehyde + CO2	-	?
additional information	very low activity with pyruvate, phenylpyruvate, 2-2oxopentanoate, 3-methyl-2-oxopentanoate, 2-oxobutanoate, and 3-methyl-2-oxobutanoate. No activity with 2-oxoglutarate	Mycolicibacterium smegmatis	?	-	?
additional information	very low activity with pyruvate, phenylpyruvate, 2-2oxopentanoate, 3-methyl-2-oxopentanoate, 2-oxobutanoate, and 3-methyl-2-oxobutanoate. No activity with 2-oxoglutarate	Mycolicibacterium smegmatis mc2155	?	-	?

Synonyms

Synonyms	Comment	Organism
BFDC	-	Mycolicibacterium smegmatis

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
4.6	-	benzoylformate	mutant enzyme I466A, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
5.1	-	benzoylformate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
20	-	2-Oxohexanoate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
20	-	4-methylthio-2-oxobutanoate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis

Cofactor

Cofactor	Comment	Organism	Structure
thiamine diphosphate	-	Mycolicibacterium smegmatis

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.22	-	benzoylformate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
0.3	-	benzoylformate	mutant enzyme I466A, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
0.94	-	2-Oxohexanoate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis
0.95	-	4-methylthio-2-oxobutanoate	wild type enzyme, at pH 6.0 and 30°C	Mycolicibacterium smegmatis

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Release 2023.1 (January 2023)