Literature summary for 1.17.1.8 extracted from

Cirilli, M.; Zheng, R.; Scapin, G.; Blanchard, J.S.
The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity (2003), Biochemistry, 42, 10644-10650.

Cloned(Commentary)

Cloned (Comment)	Organism
gene dapB, expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)	Mycobacterium tuberculosis

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant wild-type enzyme in ternary complex with inhibitor 2,6-pyridinedicarboxylate and NADH or NADPH, hanging drop vapour diffusion method, room temperature, 0.003 ml protein solution containing 20 mg/ml enzyme, 2 mM NADH or NADPH, and 30 mM 2,6-pyridinedicarboxylate, mixed with 0.003 ml precipitant solution containing 2.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 3% PEG 400, 3 days, X-ray diffraction strcuture determination at 16°C and 2.2 A resolution and analysis	Mycobacterium tuberculosis

Crystallization (Comment)

Organism

purified recombinant wild-type enzyme in ternary complex with inhibitor 2,6-pyridinedicarboxylate and NADH or NADPH, hanging drop vapour diffusion method, room temperature, 0.003 ml protein solution containing 20 mg/ml enzyme, 2 mM NADH or NADPH, and 30 mM 2,6-pyridinedicarboxylate, mixed with 0.003 ml precipitant solution containing 2.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 3% PEG 400, 3 days, X-ray diffraction strcuture determination at 16°C and 2.2 A resolution and analysis

Mycobacterium tuberculosis

Protein Variants

Protein Variants	Comment	Organism
K11A	site-directed mutagenesis, increased activity with and specificty for NADH as cofactor, reduced activity with NADPH compared to the wild-type enzyme	Mycobacterium tuberculosis
K9A	site-directed mutagenesis, increased specificty for NADH as cofactor, reduced activity with NADPH compared to the wild-type enzyme	Mycobacterium tuberculosis

Inhibitors

Inhibitors	Comment	Organism	Structure
2,6-pyridinedicarboxylate	competitive, binding site structure	Mycobacterium tuberculosis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.0025	-	NADH	recombinant mutant K9A	Mycobacterium tuberculosis
0.0032	-	NADH	recombinant wild-type enzyme	Mycobacterium tuberculosis
0.0043	-	NADH	recombinant mutant K11A	Mycobacterium tuberculosis
0.0118	-	NADPH	recombinant wild-type enzyme	Mycobacterium tuberculosis
0.042	-	NADPH	recombinant mutant K9A	Mycobacterium tuberculosis
0.83	-	NADPH	recombinant mutant K11A	Mycobacterium tuberculosis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
2,3-dihydrodipicolinate + NAD(P)H	Mycobacterium tuberculosis	second step in the biosynthesis of meso-diaminopimelate, a bacterial cell wall component, and is involved in L-lysine biosynthesis	2,3,4,5-tetrahydrodipicolinate + NAD(P)+	-	?
2,3-dihydrodipicolinate + NAD(P)H	Mycobacterium tuberculosis H37Rv	second step in the biosynthesis of meso-diaminopimelate, a bacterial cell wall component, and is involved in L-lysine biosynthesis	2,3,4,5-tetrahydrodipicolinate + NAD(P)+	-	?

Organism

Organism	UniProt	Comment	Textmining
Mycobacterium tuberculosis	P9WP23	gene dapB	-
Mycobacterium tuberculosis H37Rv	P9WP23	gene dapB	-

Reaction

Reaction	Comment	Organism	Reaction ID
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+	substrate binding site structure	Mycobacterium tuberculosis	a

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
additional information	-	activity of recombinant wild-type and mutant enzymes with NADH or NADPH as cofactors	Mycobacterium tuberculosis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
2,3-dihydrodipicolinate + NAD(P)H	-	Mycobacterium tuberculosis	2,3,4,5-tetrahydrodipicolinate + NAD(P)+	-	?
2,3-dihydrodipicolinate + NAD(P)H	second step in the biosynthesis of meso-diaminopimelate, a bacterial cell wall component, and is involved in L-lysine biosynthesis	Mycobacterium tuberculosis	2,3,4,5-tetrahydrodipicolinate + NAD(P)+	-	?
2,3-dihydrodipicolinate + NAD(P)H	-	Mycobacterium tuberculosis H37Rv	2,3,4,5-tetrahydrodipicolinate + NAD(P)+	-	?
2,3-dihydrodipicolinate + NAD(P)H	second step in the biosynthesis of meso-diaminopimelate, a bacterial cell wall component, and is involved in L-lysine biosynthesis	Mycobacterium tuberculosis H37Rv	2,3,4,5-tetrahydrodipicolinate + NAD(P)+	-	?
2,3-dihydrodipicolinate + NADH + H+	-	Mycobacterium tuberculosis	2,3,4,5-tetrahydrodipicolinate + NAD+ + H2O	-	r
2,3-dihydrodipicolinate + NADH + H+	-	Mycobacterium tuberculosis H37Rv	2,3,4,5-tetrahydrodipicolinate + NAD+ + H2O	-	r

Subunits

Subunits	Comment	Organism
tetramer	homotetramer, crystal structure	Mycobacterium tuberculosis

Synonyms

Synonyms	Comment	Organism
DHPR	-	Mycobacterium tuberculosis
dihydrodipicolinate reductase	-	Mycobacterium tuberculosis

Cofactor

Cofactor	Comment	Organism	Structure
NADH	dependent on	Mycobacterium tuberculosis
NADPH	dependent on	Mycobacterium tuberculosis