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Information on EC 4.1.1.20 - diaminopimelate decarboxylase and Organism(s) Corynebacterium glutamicum and UniProt Accession P09890

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.1 Carboxy-lyases
                4.1.1.20 diaminopimelate decarboxylase
IUBMB Comments
A pyridoxal-phosphate protein.
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This record set is specific for:
Corynebacterium glutamicum
UNIPROT: P09890
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The taxonomic range for the selected organisms is: Corynebacterium glutamicum
The enzyme appears in selected viruses and cellular organisms
Synonyms
diaminopimelate decarboxylase, dapdc, lysa2, meso-diaminopimelate decarboxylase, dap-decarboxylase, dap decarboxylase, diaminopimelic acid decarboxylase, cgdapdc, lysa1, at3g14390, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
meso-diaminopimelic acid decarboxylase
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DAP decarboxylase
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DAP-decarboxylase
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Decarboxylase, diaminopimelate
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Diaminopimelic acid decarboxylase
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-
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meso-DAP decarboxylase
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meso-diaminopimelate decarboxylase
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
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-
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SYSTEMATIC NAME
IUBMB Comments
meso-2,6-diaminoheptanedioate carboxy-lyase (L-lysine-forming)
A pyridoxal-phosphate protein.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-75-3
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
show the reaction diagram
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-
-
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
show the reaction diagram
additional information
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
show the reaction diagram
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-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
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
pyridoxal 5'-phosphate
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
95000
recombinant His6-tagged enzyme, gel filtration
47000
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x * 47000, estimated from amino acid sequence
50290
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x * 50290, recombinant protein, estimated from SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 * 47400, recombinant His6-tagged enzyme, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E375A
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
M408A
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
R302A
site-directed mutagenesis of a substrate binding site residue, the mutant shows about 65% reduced activity compared to wild-type
R343A
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
Y347A
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
Y412A
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene lysA, sequence comparisons, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
expressed in Escherichia coli BL21(DE3) cells
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expression in Escherichia coli
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
a 2fold increase in L-lysine production is observed after introduction of the cloned LysA gene into Escherichia coli
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sen, S.K.; Chatterjee, M.; Chatterjee, S.P.; Banerjee, A.K.
Activity of diaminopimelic acid decarboxylase in bacteria producing lysine
Acta Biotechnol.
3
217-220
1983
Arthrobacter globiformis, Corynebacterium glutamicum, Enterococcus faecalis, Micrococcus luteus, Staphylococcus aureus, Kocuria varians
-
Manually annotated by BRENDA team
Yeh, P.; Sicard, A.M.; Sinskey, A.J.
General organization of the genes specifically involved in the diaminopimelate-lysine biosynthetic pathway of Corynebacterium glutamicum
Mol. Gen. Genet.
212
105-111
1988
Corynebacterium glutamicum
Manually annotated by BRENDA team
Cheraghi, S.; Akbarzade, A.; Farhangi, A.; Chiani, M.; Saffari, Z.; Ghassemi, S.; Rastegari, H.; Mehrabi, M.
Improved production of L-lysine by over-expression of meso-diaminopimelate decarboxylase enzyme of Corynebacterium glutamicum in Escherichia coli
Pak. J. Biol. Sci.
13
504-508
2010
Corynebacterium glutamicum, Corynebacterium glutamicum ATC21799
Manually annotated by BRENDA team
Son, H.F.; Kim, K.J.
Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum
Biochem. Biophys. Res. Commun.
495
1815-1821
2018
Corynebacterium glutamicum (P09890), Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 (P09890)
Manually annotated by BRENDA team