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Information on EC 4.1.1.20 - diaminopimelate decarboxylase
for references in articles please use BRENDA:EC4.1.1.20
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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.
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
- 4.1.1.20
- aspartokinase
- decarboxylases
- dihydrodipicolinate
- sphaericus
- nutrition
-
plp-dependent
showSynonyms
diaminopimelate decarboxylase, dapdc, lysa2, meso-diaminopimelate decarboxylase, dap-decarboxylase, dap decarboxylase, diaminopimelic acid decarboxylase, cgdapdc, lysa1, at3g14390, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Ba-DAPDC
BAS1329
CgDAPDC
Cgl1180
DAP decarboxylase
-
-
-
-
DAP-decarboxylase
-
-
-
-
DAPDC
Decarboxylase, diaminopimelate
-
-
-
-
diaminopimelate decarboxylase
Diaminopimelic acid decarboxylase
-
-
-
-
Ec-DAPDC
LysA
meso-DAP decarboxylase
meso-diaminopimelate decarboxylase
meso-diaminopimelic acid decarboxylase
Mt-DAPDC
TM_1517
Vc-DAPDC
diaminopimelate decarboxylase
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
-
meso-diaminopimelate decarboxylase
-
-
-
-
meso-diaminopimelic acid decarboxylase
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
meso-2,6-Diaminoheptanedioate = L-lysine + CO2
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
MetaCyc
L-lysine biosynthesis I, L-lysine biosynthesis II, L-lysine biosynthesis III, L-lysine biosynthesis VI
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SYSTEMATIC NAME
IUBMB Comments
meso-2,6-diaminoheptanedioate carboxy-lyase (L-lysine-forming)
A pyridoxal-phosphate protein.
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CAS REGISTRY NUMBER
COMMENTARY
9024-75-3
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
DD-2,6-diaminoheptanedioate
L-lysine + CO2
Substrates: DD-2,6-diaminoheptanedioate is a reasonable substrate for DAPDC but with an about 100fold lower kcat/Km value than DL-DAP
Products: -
Products: -
?
DL-2,6-diaminoheptanedioate
L-lysine + CO2
Substrates: -
Products: -
Products: -
?
2-aminopimelate
6-aminocaproate + CO2
Substrates: substrate of mutant E315T, very poor substrate of wild-type
Products: -
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?
2-aminopimelate
6-aminocaproate + CO2
Substrates: substrate of mutant E315T, very poor substrate of wild-type
Products: -
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?
alpha-aminoadipate
? + CO2
Substrates: substrate of mutant E315N
Products: -
Products: -
?
alpha-aminoadipate
? + CO2
Substrates: substrate of mutant E315N
Products: -
Products: -
?
D,D-2,6-diaminoheptanedioate
L-lysine + CO2
Substrates: -
Products: -
Products: -
?
D,D-2,6-diaminoheptanedioate
L-lysine + CO2
Substrates: -
Products: -
Products: -
?
diaminopimelate
L-lysine + CO2
Substrates: a step in the lysine biosynthetic pathway, overview
Products: -
Products: -
?
diaminopimelate
L-lysine + CO2
Substrates: -
Products: -
Products: -
?
diaminopimelate
L-lysine + CO2
Substrates: a step in the lysine biosynthetic pathway, overview
Products: -
Products: -
?
L-ornithine
putrescine + CO2
Substrates: substrate of wild-type, no substrate of mutants in residue E315
Products: -
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?
L-ornithine
putrescine + CO2
Substrates: substrate of wild-type, no substrate of mutants in residue E315
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
Priestia megaterium CII 19
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: final step in L-lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Escherichia coli K-12 / MG1655
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Escherichia coli K-12 / MG1655
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: last step in L-lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: commercial meso-2,6-diaminoheptanedioate is a mixture of 50% DL-2,6-diaminoheptanedioate, 25% DD-2,6-diaminoheptanedioate and 25% LL-2,6-diaminoheptanedioate
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Mycobacterium tuberculosis ATCC 25618 / H37Rv
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Mycobacterium tuberculosis ATCC 25618 / H37Rv
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Priestia megaterium CII 19
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
Substrates: -
Products: -
Products: -
ir
additional information
?
-
A0A1S0QVH4
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
-
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
A0A1S0QVH4
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
-
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
A0A1S0QVH4
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
A0A1S0QVH4
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
-
Substrates: 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
Products: -
Products: -
?
additional information
?
-
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Substrates: 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
Products: -
Products: -
?
additional information
?
-
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
-
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
-
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Escherichia coli K-12 / MG1655
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Escherichia coli K-12 / MG1655
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
-
Substrates: the reaction catalyzed by diaminopimelate decarboxylase on D stereocenters could be a concerted, backside electrophilic substitution reaction with simultaneous CO2 loss from Calpha and proton donation to the backside of Calpha from Lys72
Products: -
Products: -
?
additional information
?
-
Substrates: the reaction catalyzed by diaminopimelate decarboxylase on D stereocenters could be a concerted, backside electrophilic substitution reaction with simultaneous CO2 loss from Calpha and proton donation to the backside of Calpha from Lys72
Products: -
Products: -
?
additional information
?
-
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
-
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
-
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Mycobacterium tuberculosis ATCC 25618 / H37Rv
Substrates: optimization of a simple quantitative assay for measuring DAPDC catalytic activity using saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, method, overview. SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Mycobacterium tuberculosis ATCC 25618 / H37Rv
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Substrates: the reaction catalyzed by diaminopimelate decarboxylase on D stereocenters could be a concerted, backside electrophilic substitution reaction with simultaneous CO2 loss from Calpha and proton donation to the backside of Calpha from Lys72
Products: -
Products: -
?
additional information
?
-
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
additional information
?
-
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
Substrates: usage of a quantitative assay for measuring DAPDC catalytic activity with saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae as the coupling enzyme, SDH has optimal activity at 37°C, pH 8.0, and in Tris buffer
Products: -
Products: -
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
diaminopimelate
L-lysine + CO2
Substrates: a step in the lysine biosynthetic pathway, overview
Products: -
Products: -
?
diaminopimelate
L-lysine + CO2
Substrates: -
Products: -
Products: -
?
diaminopimelate
L-lysine + CO2
Substrates: a step in the lysine biosynthetic pathway, overview
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
Priestia megaterium CII 19
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
?
-
Substrates: lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
A0A1S0QVH4
Substrates: -
Products: -
Products: -
ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: final step in L-lysine biosynthesis
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
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meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Escherichia coli K-12 / MG1655
Substrates: -
Products: -
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?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Escherichia coli K-12 / MG1655
Substrates: -
Products: -
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meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: last step in L-lysine biosynthesis
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?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
-
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
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meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Mycobacterium tuberculosis ATCC 25618 / H37Rv
Substrates: -
Products: -
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?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Mycobacterium tuberculosis ATCC 25618 / H37Rv
Substrates: -
Products: -
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ir
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
Substrates: -
Products: -
Products: -
ir
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
dependent on, the DAPDC1 protein contains a PLP binding consensus site, overview
pyridoxal 5'-phosphate
dependent on, the DAPDC1 protein contains a PLP binding consensus site, overview
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
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-(3-chloro-2-methylanilino)benzoic acid
0.04 mM, 44% inhibition, MIC for growth of Brucella melitensis 0.025 mM
4-imino-4-[2-(4-methoxyphenyl)-1H-benzimidazol-6-yl]-3-methylbutanamide
0.04 mM, 47.3% inhibition, MIC for growth of Brucella melitensis 0.05 mM
bis(azanido)platinum-cyclobutane-1,1-dicarboxylic acid
0.04 mM, 65% inhibition, MIC for growth of Brucella melitensis 0.0002 mM
L,L-2,6-diaminoheptanedioate
no detectable amounts of decarboxylation products
N-(2-chloro-6-methylphenyl)-2-([6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl]amino)-1,3-thiazole-5-carboxamide
0.04 mM, 67% inhibition, MIC for growth of Brucella melitensis 0.1 mM
N-[1-(3-chlorophenyl)-2-hydroxyethyl]-4-[5-chloro-2-[(propan-2-yl)amino]pyridin-4-yl]-1H-pyrrole-2-carboxamide
0.04 mM, 47% inhibition, MIC for growth of Brucella melitensis 0.025 mM
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Tuberculosis
An optimized coupled assay for quantifying diaminopimelate decarboxylase activity.
Tuberculosis
Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture.
Tuberculosis
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of LysA (Rv1293) from Mycobacterium tuberculosis.
Tuberculosis
Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis.
Tuberculosis
Dimerization of Bacterial Diaminopimelate Decarboxylase is Essential for Catalysis.
Tuberculosis
Inhibition of diaminopimelic acid decarboxylase activity in Mycobacterium tuberculosis by isonicotinic acid hydrazide.
Tuberculosis
The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.43
DL-2,6-Diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
0.03
meso-2,6-diaminoheptanedioate
mutant enzyme I148L, in 100 mM Tris, pH 8.0
0.11
meso-2,6-diaminoheptanedioate
mutant enzyme I148F, in 100 mM Tris, pH 8.0
0.35
meso-2,6-diaminoheptanedioate
mutant enzyme I148A, in 100 mM Tris, pH 8.0
0.36
meso-2,6-diaminoheptanedioate
mutant enzyme I148K, in 100 mM Tris, pH 8.0
0.36
meso-2,6-diaminoheptanedioate
mutant enzyme I148G, in 100 mM Tris, pH 8.0
0.39
meso-2,6-diaminoheptanedioate
wild type enzyme, in 100 mM Tris, pH 8.0
0.68
meso-2,6-diaminoheptanedioate
A0A1S0QVH4
pH 8.0, 37°C, recombinant enzyme
0.72
meso-2,6-diaminoheptanedioate
mutant enzyme I148D, in 100 mM Tris, pH 8.0
0.97
meso-2,6-diaminoheptanedioate
pH 8.0, 37°C, recombinant enzyme
1.6
meso-2,6-diaminoheptanedioate
pH 8.0, 37°C, recombinant enzyme
1.62
meso-2,6-diaminoheptanedioate
pH 8.0, 37°C, recombinant enzyme
1.9
meso-2,6-diaminoheptanedioate
pH 8.0, 37°C, recombinant enzyme
additional information
additional information
Michaelis-Menten kinetics, recombinant enzyme
-
additional information
additional information
-
Michaelis-Menten kinetics, recombinant enzyme
-
additional information
additional information
Michaelis-Menten kinetics, recombinant enzyme
-
additional information
additional information
-
Michaelis-Menten kinetics, recombinant enzyme
-
additional information
additional information
A0A1S0QVH4
Michaelis-Menten kinetics, recombinant enzyme
-
additional information
additional information
-
Michaelis-Menten kinetics, recombinant enzyme
-
additional information
additional information
Michaelis-Menten kinetics, recombinant enzyme
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.8
DD-2,6-diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
7.1
DL-2,6-Diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
0.07
meso-2,6-diaminoheptanedioate
mutant enzyme I148D, in 100 mM Tris, pH 8.0
0.07
meso-2,6-diaminoheptanedioate
mutant enzyme I148G, in 100 mM Tris, pH 8.0
0.28
meso-2,6-diaminoheptanedioate
mutant enzyme I148K, in 100 mM Tris, pH 8.0
0.33
meso-2,6-diaminoheptanedioate
mutant enzyme I148A, in 100 mM Tris, pH 8.0
0.38
meso-2,6-diaminoheptanedioate
mutant enzyme I148L, in 100 mM Tris, pH 8.0
0.68
meso-2,6-diaminoheptanedioate
mutant enzyme I148F, in 100 mM Tris, pH 8.0
2 - 8
meso-2,6-diaminoheptanedioate
pH 8.0, 37°C, recombinant enzyme
2 - 8
meso-2,6-diaminoheptanedioate
-
pH 8.0, 37°C, recombinant enzyme
7.1
meso-2,6-diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
15.65
meso-2,6-diaminoheptanedioate
wild type enzyme, in 100 mM Tris, pH 8.0
22
meso-2,6-diaminoheptanedioate
pH 8.0, 37°C, recombinant enzyme
55
meso-2,6-diaminoheptanedioate
pH 8.0, 37°C, recombinant enzyme
58
meso-2,6-diaminoheptanedioate
A0A1S0QVH4
pH 8.0, 37°C, recombinant enzyme
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
16
DL-2,6-Diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.6
LL-2,6-Diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
26
D-Lysine
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
1.8
L-lysine
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
111
substrate meso-2,6-diaminoheptanedioate, mutant E315M, pH 7.8, 30°C
22.6
substrate meso-2,6-diaminoheptanedioate, mutant E315P, pH 7.8, 30°C
26.3
substrate meso-2,6-diaminoheptanedioate, mutant E315T, pH 7.8, 30°C
32.7
substrate meso-2,6-diaminoheptanedioate, mutant E315L, pH 7.8, 30°C
36
substrate meso-2,6-diaminoheptanedioate, mutant E315F, pH 7.8, 30°C
42
substrate meso-2,6-diaminoheptanedioate, mutant E315N, pH 7.8, 30°C
675
substrate meso-2,6-diaminoheptanedioate, wild-type, pH 7.8, 30°C
82
substrate meso-2,6-diaminoheptanedioate, mutant E315Q, pH 7.8, 30°C
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25 - 45
-
relative rates of decarboxylation at 25C, 37C, 45C are 0.17 : 1.0 : 1.6
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
additional information
DAPDC1 spatial expression pattern in various tissues, overview
brenda
additional information
DAPDC1 spatial expression pattern in various tissues, overview
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
the enzyme contains a transit peptide-like sequence at the N-terminus
brenda
the enzyme contains a transit peptide-like sequence at the N-terminus
brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
additional information
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
metabolism
diaminopimelate decarboxylase (DAPDC) catalyzes the conversion of meso-2,6-diaminopimelate to lysine and carbon dioxide in the final step of the diaminopimelate (DAP) pathway
metabolism
diaminopimelate decarboxylase (DAPDC) catalyzes the conversion of meso-2,6-diaminopimelate to lysine and carbon dioxide in the final step of the diaminopimelate (DAP) pathway
metabolism
A0A1S0QVH4
diaminopimelate decarboxylase (DAPDC) catalyzes the conversion of meso-2,6-diaminopimelate to lysine and carbon dioxide in the final step of the diaminopimelate (DAP) pathway
metabolism
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
metabolism
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
metabolism
A0A1S0QVH4
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
metabolism
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
metabolism
binding of PLP initiates rearrangements within the active site, specifically the reorientation of Arg169, His218, and His22, which is propagated to the active-site loop, through Arg169. The substrate, meso-diaminopimelate, is positioned through interactions with conserved active-site residues to form an additional hydrogen bond to His220. This stabilizes the closed active-site loop conformation, mediated through Arg169, and can only occur when the D-stereocenter is oriented for decarboxylation
metabolism
-
diaminopimelate decarboxylase (DAPDC) catalyzes the conversion of meso-2,6-diaminopimelate to lysine and carbon dioxide in the final step of the diaminopimelate (DAP) pathway
-
metabolism
-
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
-
metabolism
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
diaminopimelate decarboxylase (DAPDC) catalyzes the conversion of meso-2,6-diaminopimelate to lysine and carbon dioxide in the final step of the diaminopimelate (DAP) pathway
-
metabolism
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
-
metabolism
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
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
-
metabolism
Escherichia coli K-12 / MG1655
-
diaminopimelate decarboxylase (DAPDC) catalyzes the conversion of meso-2,6-diaminopimelate to lysine and carbon dioxide in the final step of the diaminopimelate (DAP) pathway
-
metabolism
Escherichia coli K-12 / MG1655
-
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
-
metabolism
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
the enzyme catalyzes the irreversible and stereospecific decarboxylation of meso-diaminopimelate (meso-DAP) in the final step of the diaminopimelate (DAP) biosynthesis pathway
-
physiological function
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
physiological function
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
physiological function
A0A1S0QVH4
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
physiological function
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
physiological function
expression of DAPDC1 rescues Escherichia coli that harbors a mutation in the gene encoding DAPDC. DAPDC1 is only able to rescue the mutant when its expression is repressed by glucose
physiological function
expression of DAPDC2 rescues Escherichia coli that harbors a mutation in the gene encoding DAPDC. DAPDC2 is only able to rescue the mutant when its expression is repressed by glucose
physiological function
-
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
-
physiological function
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
-
physiological function
Escherichia coli K-12 / MG1655
-
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
-
physiological function
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
the product of the reaction, L-lysine, is an important building block for the biosynthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria
-
additional information
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
A0A1S0QVH4
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
-
additional information
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
-
additional information
Escherichia coli K-12 / MG1655
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
-
additional information
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
100000
200000
50000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
homotetramer
monomer
additional information
dimer
and monmer, 2 * 53807, calculated from sequence. Dimer is predominant
dimer
and monmer, 2 * 54240, calculated from sequence. Dimer is predominant
dimer
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
2 * 47400, recombinant His6-tagged enzyme, SDS-PAGE
-
dimer
2 * 50000, wild-type enzyme, about, SDS-PAGE, 2 x 49000, recombinant mutants N381A and R385A, SDS-PAGE
dimer
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
2 * 50000, wild-type enzyme, about, SDS-PAGE, 2 x 49000, recombinant mutants N381A and R385A, SDS-PAGE
-
homotetramer
an equilibrium may exist between the dimeric and the tetrameric form, X-ray crystallography
homotetramer
-
an equilibrium may exist between the dimeric and the tetrameric form, X-ray crystallography
-
monomer
and dimer, 1 * 53807, calculated from sequence. Dimer is predominant
monomer
and dimer, 1 * 54240, calculated from sequence. Dimer is predominant
additional information
A0A1S0QVH4
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
-
additional information
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
additional information
Escherichia coli K-12 / MG1655
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
-
additional information
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
additional information
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
-
additional information
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
additional information
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis, secondary and quaternary structure analysis of soluble recombinant enzyme, analysis by SDS-PAGE, fluorescence-detected analytical ultracentrifugation, mass spectrometry, and circular dichroism spectroscopy, detailed overview
-
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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
vapor-diffusion at room temperature, crystals are grown from 0.002 mL DDC solution in 50 mM sodium MES, pH 6.0 and 0.1 mM pyridoxal 5'-phosphate mixed with 0.002 ml well solution consisting of 1.44-1.54 M lithium sulfate, 50 mM MES, pH 6.0, and 0.1 mM pyridoxal 5'-phosphate
-
hanging drop vapour diffusion method, in 100 mM bicine, pH 8.0, and 1.6 M ammonium sulfate, at 4°C
co-crystals of DAPDC and azelaic acid and L-lysine at 2.6 A and 2.0 A resolution, respectively, hanging drop vapor-diffusion, 12% polyethylene glycol 6000, 100 mm Tris-Cl, pH 8.0, 20 mM MgCl2 and 10 mM L-lysine
-
hanging drop vapor diffusion method, using 20-23% (w/v) PEG-MME 5000, 0.1 M MES pH 6.1-6.6, and 60 mM (NH4)2SO4
hanging-drop vapour-diffusion method, crystals grown in absence of substrate or cofactor are colourless and appear to contain one homotetramer of LysA in the asymmetric unit
-
vapor-diffusion in hanging drops at 18°C, crystals grow within 3-7 days in 0.004 ml hanging-drops containing 0.002 ml of DAPDC at 10 mg/ml and 5 mM lysine, equilibration against 0.5 ml well solution containing 24% polyethylene glycol mono-methylester 5000, 100 mM MES, pH 6.3, and 60 mM ammonium sulfate, crystals diffract to 2.6 A
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
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
E375A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
-
M408A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
-
R343A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
-
Y347A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
-
Y412A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis of a substrate binding site residue, the mutant is almost completely inactive
-
I148A
mutant shows 2% catalytic efficiency compared to the wild type enzyme
I148D
mutant shows 0.2% catalytic efficiency compared to the wild type enzyme
I148F
mutant shows 15% catalytic efficiency compared to the wild type enzyme
I148G
mutant shows 0.5% catalytic efficiency compared to the wild type enzyme
I148K
mutant shows 2% catalytic efficiency compared to the wild type enzyme
I148L
mutant shows 28% catalytic efficiency compared to the wild type enzyme
E315T
N381A
site-directed mutagenesis, the mutant shows impaired dimerization and is significantly attenuated in catalytic activity
R385A
site-directed mutagenesis, the mutant shows impaired dimerization and is significantly attenuated in catalytic activity
N381A
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
site-directed mutagenesis, the mutant shows impaired dimerization and is significantly attenuated in catalytic activity
-
R385A
Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961
-
site-directed mutagenesis, the mutant shows impaired dimerization and is significantly attenuated in catalytic activity
-
E315T
mutant has lost most of the activity toward 2,6-diamonopimelate and has the highest activity toward 2-aminopimelate observed
E315T
-
mutant has lost most of the activity toward 2,6-diamonopimelate and has the highest activity toward 2-aminopimelate observed
-
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, sodium phosphate buffer, pH 6.8, 4 months, about 50% loss of activity
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant DAPDC
recombinant enzyme from Escherichia coli strain BL21(DE3) by anion exchange and hydrophobic interaction chromatography, and gel filtration
A0A1S0QVH4
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3)
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and gel filtration
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)
A0A1S0QVH4
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and gel filtration
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene DAPDC, location on chromosome II, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic tree, overview, functional complementation of lysine biosynthesis-defective Escherichia coli strains in minimal medium
gene DAPDC1, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic tree, overview
gene DAPDC2, localization on chromosome V, DNA and amino acid sequence determination and analysis, sequence comparisons and phylogenetic tree, overview
gene lysA, recombinant enzyme expression in Escherichia coli strain BL21(DE3)
A0A1S0QVH4
gene lysA, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)
gene lysA, sequence comparisons, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
gene lysA, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)
gene lysA, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
A0A1S0QVH4
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
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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
a 2fold increase in L-lysine production is observed after introduction of the cloned LysA gene into Escherichia coli
-
a 2fold increase in L-lysine production is observed after introduction of the cloned LysA gene into Escherichia coli
-
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
nutrition
analysis
development of a quantitative SDH-DAPDC coupled assay and adaptation for use in a 348-well format
analysis
-
development of a quantitative SDH-DAPDC coupled assay and adaptation for use in a 348-well format
-
nutrition
-
lysine complementation of calf nutrition by lysine-overproducing rumen bacteria, considered
nutrition
Clostridium spp.
-
lysine complementation of calf nutrition by lysine-overproducing rumen bacteria, considered
nutrition
-
lysine complementation of calf nutrition by lysine-overproducing rumen bacteria, considered
nutrition
-
lysine complementation of calf nutrition by lysine-overproducing rumen bacteria, considered
nutrition
-
lysine complementation of calf nutrition by lysine-overproducing rumen bacteria, considered
nutrition
-
lysine complementation of calf nutrition by lysine-overproducing rumen bacteria, considered
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Chatterjee, S.P.; White, P.J.
Activities and regulation of the enzymes of lysine biosynthesis in a lysine-excreting strain of Bacillus megaterium
J. Gen. Microbiol.
128
1073-1081
1982
Priestia megaterium
-
brenda
Chatterjee, S.P.; Singh, B.K.; Gilvarg, C.
Biosynthesis of lysine in plants: the putative role of meso-diaminopimelate dehydrogenase
Plant Mol. Biol.
26
285-290
1994
Chlamydomonas sp., Glycine max, Nicotiana tabacum, Zea mays
brenda
Denman, R.F.; Hoare, D.S.; Work, E.
Diaminopimelic acid decarboxylase in pyridoxin-deficient Escherichia coli
Biochim. Biophys. Acta
16
442-443
1955
Escherichia coli
brenda
Vogel, H.J.; Hirvonen, A.P.
Diaminopimelate decarboxylase
Methods Enzymol.
17B
146-150
1971
Landoltia punctata, Lemna perpusilla
-
brenda
White, P.J.
Diaminopimelate decarboxylase (Escherichia coli)
Methods Enzymol.
17B
140-145
1971
Escherichia coli
-
brenda
Rosner, A.
Control of lysine biosynthesis in Bacillis subtilis: inhibition of diaminopimelate decarboxylase by lysine
J. Bacteriol.
121
20-28
1975
Bacillus subtilis, Brevibacterium sp.
brenda
Mazelis, M.N.; Miflin, B.J.; Prati, H.M.
A chloroplast-localized diaminopimelate decarboxylase in higher plants
FEBS Lett.
64
197-200
1976
Vicia faba
brenda
Schroder, D.; Wolfel, L.; Schoeter, A.; Mach, F.
Lysinbiosynthese bei Pseudomonas aeruginosa PAO 1:1. Einfluss von Cetyl-trimethyl-ammoniumbromid auf P. aeruginosa PAO 1 bei der Bestimmung der DAP-Decarboxylaseaktivitt
Z. Allg. Mikrobiol.
18
361-364
1978
Pseudomonas aeruginosa
brenda
Schroeder, D.; Woelfel, L.; Schroeter, A.; Mach, F.
Lysinbiosynthese bei Pseudomonas aeruginosa PAO 1 II. Erste Untersuchungen der DAP-Decarboxylase Lysin-auxotropher Mutanten von P. aeruginosa PAO 1
Z. Allg. Mikrobiol.
18
453-456
1978
Pseudomonas aeruginosa
brenda
Asada, Y.; Tanizawa, K.; Kawabata, Y.; Misuno, H.; Soda, K.
Purification and properties of meso-alpha,epsilon-diaminopimelate decarboxylase from Bacillus sphaericus
Agric. Biol. Chem.
45
1513-1514
1981
Lysinibacillus sphaericus
-
brenda
Asada, Y.; Tanizawa, K.; Sawada, S.; Suzuki, T.; Misono, H.; Soda, K.
Stereochemistry of meso-'a,e'-diaminopimelate decarboxylase reaction: the first evidence for pyridoxal 5'phosphate dependent decarboxylation with inversion of configuration
Biochemistry
20
6881-6886
1981
Lysinibacillus sphaericus
brenda
Dierks-Ventling, C.
Lysine biosynthesis and utilization during seed development of normal and opaque-2 Zea mays L.
Planta
157
233-238
1983
Zea mays
brenda
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
Micrococcus luteus, Kocuria varians, Arthrobacter globiformis, Enterococcus faecalis, Corynebacterium glutamicum, Staphylococcus aureus
-
brenda
Bakhiet, N.; Forney, F.W.; Stahly, D.P.; Daniels, L.
Lysine biosynthesis in Methanobacterium thermoautotrophicum is by the diaminopimelic acid pathway
Curr. Microbiol.
10
195-198
1984
Methanothermobacter thermautotrophicus, Methanospirillum hungatei
-
brenda
Jouanneau, J.; Stragier, P.; Bouvier, J.; Patte, J.C.; Yaniv, M.
Expression in mammalian cells of the diaminopimelic acid decarboxylase of Escherichia coli permits cell growth in lysine-free medium
Eur. J. Biochem.
145
175-178
1985
Escherichia coli
-
brenda
Kelland, J.C.; Palcic, M.M.; Pickard, M.A.; Vederas, J.C.
Stereochemistry of lysine formation by meso-diaminopimelate decarboxylase from wheat germ: use of 1H-13C NMR shift correlation to detect stereospecific deuterium labeling
Biochemistry
24
3263-3267
1985
Triticum sp.
brenda
Kelland, J.C.; Arnold, L.D.; Palcic, M.M.; Pickard, M.A.; Vederas, J.C.
Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate decarboxylase from Bacillus sphaericus and wheat germ
J. Biol. Chem.
261
13216-13223
1986
Lysinibacillus sphaericus, Triticum sp.
brenda
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
brenda
Styriak, I.; Timashova-Kalcheva, E.O.; Kmet, V.; Maljuta, S.S.
DAP-decarboxylase activity and lysine production by rumen bacteria
Arch. Anim. Nutr.
42
71-77
1992
Butyrivibrio fibrisolvens, Clostridium spp., Fibrobacter succinogenes, Megasphaera elsdenii, Selenomonas ruminantium, Streptococcus equinus
brenda
White, P.J.
The regulation of diaminopimelate decarboxylase activity in Escherichia coli strain W
J. Gen. Microbiol.
96
51-62
1976
Escherichia coli
brenda
Mills, D.A.et al.
Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene from Bacillus methanolicus MGA 3 and comparison to other decarboxylase genes
Appl. Environ. Microbiol.
59
2927-2937
1993
Bacillus methanolicus
brenda
Momany, C.; Levdikov, V.; Blagova, L.; Crews, K.
Crystallization of diaminopimelate decarboxylase from Escherichia coli, a stereospecific D-amino-acid decarboxylase
Acta Crystallogr. Sect. D
58
549-552
2002
Escherichia coli
brenda
Gokulan, K.; Rupp, B.; Pavelka, M.S., Jr.; Jacobs, W.R., Jr.; Sacchettini, J.C.
Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis
J. Biol. Chem.
278
18588-18596
2003
Mycobacterium tuberculosis (P9WIU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WIU7)
brenda
Ray, S.S.; Bonanno, J.B.; Rajashankar, K.R.; Pinho, M.G.; He, G.; De Lencastre, H.; Tomasz, A.; Burley, S.K.
Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor
Structure
10
1499-1508
2002
Methanocaldococcus jannaschii
brenda
Kefala, G.; Perry, L.J.; Weiss, M.S.
Cloning, expression, purification, crystallization and preliminary x-ray diffraction analysis of LysA (Rv1293) from Mycobacterium tuberculosis
Acta Crystallogr. Sect. F
F61
782-784
2005
Mycobacterium tuberculosis
brenda
Gunji, Y.; Tsujimoto, N.; Shimaoka, M.; Ogawa-Miyata, Y.; Sugimoto, S.; Yasueda, H.
Characterization of the L-lysine biosynthetic pathway in the obligate methylotroph Methylophilus methylotrophus
Biosci. Biotechnol. Biochem.
68
1449-1460
2004
Methylophilus methylotrophus
brenda
Kim, J.
Diaminopimelate decarboxylase from Arabidopsis contains motifs for pyridoxal-5'-phosphate and substrate
Asian J. Plant Sci.
5
260-265
2006
Arabidopsis thaliana (Q949X7), Arabidopsis thaliana (Q94A94)
-
brenda
Kim, J.; Lee, S.
Characterization of a gene encoding diaminopimelate decarboxylase from rice
Integr. Biosci.
10
197-201
2006
Oryza sativa (Q6ZG77)
-
brenda
Hu, T.; Wu, D.; Chen, J.; Ding, J.; Jiang, H.; Shen, X.
The catalytic intermediate stabilized by a "down" active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis
J. Biol. Chem.
283
21284-21293
2008
Helicobacter pylori (P56129), Helicobacter pylori
brenda
Weyand, S.; Kefala, G.; Svergun, D.I.; Weiss, M.S.
The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation
J. Struct. Funct. Genomics
10
209-217
2009
Mycobacterium tuberculosis (P9WIU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WIU7)
brenda
Fogle, E.J.; Toney, M.D.
Analysis of catalytic determinants of diaminopimelate and ornithine decarboxylases using alternate substrates
Biochim. Biophys. Acta
1814
1113-1119
2011
Mycobacterium tuberculosis, Mycobacterium tuberculosis (P9WIU7), Mycobacterium tuberculosis H37Rv (P9WIU7)
brenda
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
brenda
Oliver, M.R.; Crowther, J.M.; Leeman, M.M.; Kessans, S.A.; North, R.A.; Donovan, K.A.; Griffin, M.D.; Suzuki, H.; Hudson, A.O.; Kasanmascheff, M.; Dobson, R.C.
The purification, crystallization and preliminary X-ray diffraction analysis of two isoforms of meso-diaminopimelate decarboxylase from Arabidopsis thaliana
Acta Crystallogr. Sect. F
70
663-668
2014
Arabidopsis thaliana (Q949X7), Arabidopsis thaliana (Q94A94), Arabidopsis thaliana
brenda
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)
brenda
Peverelli, M.G.; Perugini, M.A.
An optimized coupled assay for quantifying diaminopimelate decarboxylase activity
Biochimie
115
78-85
2015
Bacillus anthracis (A0A1S0QVH4), Bacillus anthracis, Bacillus anthracis Sterne (A0A1S0QVH4), Escherichia coli (P00861), Escherichia coli, Escherichia coli K-12 / MG1655 (P00861), Mycobacterium tuberculosis (P9WIU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 / H37Rv (P9WIU7), no activity in Homo sapiens
brenda
Peverelli, M.G.; Soares da Costa, T.P.; Kirby, N.; Perugini, M.A.
Dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
J. Biol. Chem.
291
9785-9795
2016
Bacillus anthracis (A0A1S0QVH4), Bacillus anthracis, Bacillus anthracis Sterne (A0A1S0QVH4), Escherichia coli (P00861), Escherichia coli, Escherichia coli K-12 / MG1655 (P00861), Mycobacterium tuberculosis (P9WIU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 / H37Rv (P9WIU7), Vibrio cholerae serotype O1 (Q9KVL7), Vibrio cholerae serotype O1 ATCC 39315 / El Tor Inaba N16961 (Q9KVL7)
brenda
Bie, P.; Yang, X.; Zhang, C.; Wu, Q.
Identification of small-molecule inhibitors of Brucella diaminopimelate decarboxylase by using a high-throughput screening assay
Front. Microbiol.
10
2936
2020
Brucella melitensis (Q8YJJ9), Brucella melitensis 16M (Q8YJJ9)
brenda
Crowther, J.M.; Cross, P.J.; Oliver, M.R.; Leeman, M.M.; Bartl, A.J.; Weatherhead, A.W.; North, R.A.; Donovan, K.A.; Griffin, M.D.W.; Suzuki, H.; Hudson, A.O.; Kasanmascheff, M.; Dobson, R.C.J.
Structure-function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control
J. Biol. Chem.
294
8505-8515
2019
Arabidopsis thaliana (Q949X7), Arabidopsis thaliana (Q94A94)
brenda
Marjanovic, A.; Ramirez-Palacios, C.J.; Masman, M.F.; Drenth, J.; Otzen, M.; Marrink, S.J.; Janssen, D.B.
Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase
Protein Eng. Des. Sel.
34
gzab016
2021
Thermotoga maritima (Q9X1K5), Thermotoga maritima DSM 3109 (Q9X1K5)
brenda
EXTERNAL LINKS (specific for EC-Number 4.1.1.20)
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