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Information on EC 4.1.1.20 - diaminopimelate decarboxylase and Organism(s) Mycobacterium tuberculosis and UniProt Accession P9WIU7
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4.1.1.20 diaminopimelate decarboxylaseIUBMB Comments
A pyridoxal-phosphate protein.
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Word Map
- 4.1.1.20
- aspartokinase
- decarboxylases
- dihydrodipicolinate
- sphaericus
- nutrition
-
plp-dependent
The taxonomic range for the selected organisms is: Mycobacterium tuberculosis
The enzyme appears in selected viruses and cellular organisms
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, 
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topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
DAP decarboxylase
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-
-
-
DAP-decarboxylase
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-
-
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Decarboxylase, diaminopimelate
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-
-
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Diaminopimelic acid decarboxylase
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-
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meso-diaminopimelate decarboxylase
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
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-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
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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
9024-75-3
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
DD-2,6-diaminoheptanedioate
L-lysine + CO2
DD-2,6-diaminoheptanedioate is a reasonable substrate for DAPDC but with an about 100fold lower kcat/Km value than DL-DAP
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-
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
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
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-
?
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
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-
-
?
additional information
?
-
-
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
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-
?
additional information
?
-
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
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-
?
additional information
?
-
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
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-
?
additional information
?
-
-
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
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-
?
additional information
?
-
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
-
-
?
additional information
?
-
-
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
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
L,L-2,6-diaminoheptanedioate
no detectable amounts of decarboxylation products
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
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
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
7.1
meso-2,6-diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
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
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
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
1.6
LL-2,6-Diaminoheptanedioate
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
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
additional information
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
additional information
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
additional information
-
dimerization of bacterial diaminopimelate decarboxylase is essential for catalysis
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
an equilibrium may exist between the dimeric and the tetrameric form, X-ray crystallography
additional information
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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
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
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
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
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)
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)
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
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)
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