Literature summary for 4.1.1.20 extracted from

Son, H.F.; Kim, K.J.
Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum (2018), Biochem. Biophys. Res. Commun., 495, 1815-1821 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene lysA, sequence comparisons, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)	Corynebacterium glutamicum

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant enzyme complexed with pyridoxal 5'-phosphate cofactor alone or with pyridoxal 5'-phosphate cofactor and product L-lysine, sitting drop vapor diffusion method, mixing of 0.001 ml of 60 mg/ml protein in 40 mM Tris-HCl, pH 8.0, and 150 mM NaCl with 0.001 ml of reservoir solution, containing 0.8 M sodium citrate tribasic and 0.1 M sodium cacodylate, pH 6.5, and equilibration against 005 ml of reservoir solution, soaking of crystals in 10 mM ligand-containing mother liquor, X-ray diffraction structure determination and analysis at 1.72-2.40 A resolution, molecular replacement using the structure of Mycobacterium tuberculosis meso-diaminopimelate decarboxylase structure, PDB ID 1HKV, as search model, modeling	Corynebacterium glutamicum

Crystallization (Comment)

Organism

purified recombinant enzyme complexed with pyridoxal 5'-phosphate cofactor alone or with pyridoxal 5'-phosphate cofactor and product L-lysine, sitting drop vapor diffusion method, mixing of 0.001 ml of 60 mg/ml protein in 40 mM Tris-HCl, pH 8.0, and 150 mM NaCl with 0.001 ml of reservoir solution, containing 0.8 M sodium citrate tribasic and 0.1 M sodium cacodylate, pH 6.5, and equilibration against 005 ml of reservoir solution, soaking of crystals in 10 mM ligand-containing mother liquor, X-ray diffraction structure determination and analysis at 1.72-2.40 A resolution, molecular replacement using the structure of Mycobacterium tuberculosis meso-diaminopimelate decarboxylase structure, PDB ID 1HKV, as search model, modeling

Corynebacterium glutamicum

Protein Variants

Protein Variants	Comment	Organism
E375A	site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive	Corynebacterium glutamicum
M408A	site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive	Corynebacterium glutamicum
R302A	site-directed mutagenesis of a substrate binding site residue, the mutant shows about 65% reduced activity compared to wild-type	Corynebacterium glutamicum
R343A	site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive	Corynebacterium glutamicum
Y347A	site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive	Corynebacterium glutamicum
Y412A	site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive	Corynebacterium glutamicum

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
95000	-	recombinant His6-tagged enzyme, gel filtration	Corynebacterium glutamicum

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
meso-2,6-Diaminoheptanedioate	Corynebacterium glutamicum	-	L-Lysine + CO2	-	?
meso-2,6-Diaminoheptanedioate	Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025	-	L-Lysine + CO2	-	?

Organism

Organism	UniProt	Comment	Textmining
Corynebacterium glutamicum	P09890	-	-
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025	P09890	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration	Corynebacterium glutamicum

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
meso-2,6-Diaminoheptanedioate	-	Corynebacterium glutamicum	L-Lysine + CO2	-	?
meso-2,6-Diaminoheptanedioate	-	Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025	L-Lysine + CO2	-	?
additional information	the position of the alpha15 helix in CgDAPDC and the residues located on the helix are crucial for determining the substrate specificities of the amino acid decarboxylases. Substrate binding mode of enzyme CgDAPDC, substrate binding site involves residues Arg302, Arg343, Tyr347, Glu375, Tyr404, Met408, and Tyr412	Corynebacterium glutamicum	?	-	?
additional information	the position of the alpha15 helix in CgDAPDC and the residues located on the helix are crucial for determining the substrate specificities of the amino acid decarboxylases. Substrate binding mode of enzyme CgDAPDC, substrate binding site involves residues Arg302, Arg343, Tyr347, Glu375, Tyr404, Met408, and Tyr412	Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025	?	-	?

Subunits

Subunits	Comment	Organism
dimer	2 * 47400, recombinant His6-tagged enzyme, SDS-PAGE	Corynebacterium glutamicum

Synonyms

Synonyms	Comment	Organism
CgDAPDC	-	Corynebacterium glutamicum
Cgl1180	-	Corynebacterium glutamicum
DAPDC	-	Corynebacterium glutamicum
LysA	-	Corynebacterium glutamicum
meso-diaminopimelic acid decarboxylase	-	Corynebacterium glutamicum

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	PLP, the PLP cofactor is tightly bound at the center of the barrel domain and forms a Schiff base with the catalytic Lys75 residue, binding structure analysis, overview	Corynebacterium glutamicum

General Information

General Information	Comment	Organism
metabolism	enzyme meso-diaminopimelic acid decarboxylase (DAPDC) catalyzes the final step in the de novo L-lysine biosynthetic pathway by converting meso-diaminopimelic acid (meso-DAP) into L-lysine by decarboxylation reaction	Corynebacterium glutamicum