Information on EC 4.1.1.20 - Diaminopimelate decarboxylase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY hide
4.1.1.20
-
RECOMMENDED NAME
GeneOntology No.
Diaminopimelate decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
meso-2,6-Diaminoheptanedioate = L-lysine + CO2
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
L-lysine biosynthesis I
-
-
L-lysine biosynthesis II
-
-
L-lysine biosynthesis III
-
-
L-lysine biosynthesis VI
-
-
Lysine biosynthesis
-
-
lysine metabolism
-
-
Metabolic pathways
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Microbial metabolism in diverse environments
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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
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Chlamydomonas sp.
-
-
-
Manually annotated by BRENDA team
Clostridium spp.
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
soy bean
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
duckweed
-
-
Manually annotated by BRENDA team
duckweed
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum
-
-
-
Manually annotated by BRENDA team
parental strain AS1 and its G49 derivative
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
tobacco
-
-
Manually annotated by BRENDA team
a single DAPDC gene
SwissProt
Manually annotated by BRENDA team
wheat
-
-
Manually annotated by BRENDA team
bean
-
-
Manually annotated by BRENDA team
corn
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D,D-2,6-diaminoheptanedioate
L-lysine + CO2
show the reaction diagram
DD-2,6-diaminoheptanedioate
L-lysine + CO2
show the reaction diagram
-
DD-2,6-diaminoheptanedioate is a reasonable substrate for DAPDC but with an about 100fold lower kcat/Km value than DL-DAP
-
-
?
diaminopimelate
L-lysine + CO2
show the reaction diagram
DL-2,6-diaminoheptanedioate
L-lysine + CO2
show the reaction diagram
-
-
-
-
?
Lanthionine
?
show the reaction diagram
-
slowly
-
-
-
meso-2,6-Diaminoheptanedioate
?
show the reaction diagram
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
diaminopimelate
L-lysine + CO2
show the reaction diagram
meso-2,6-Diaminoheptanedioate
?
show the reaction diagram
meso-2,6-Diaminoheptanedioate
L-Lysine + CO2
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
activates
Na+
-
activates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,5-Diaminopentane
-
-
1,6-diaminohexane
-
-
1,7-Diaminoheptane
-
-
2,3-Diaminopropionic acid
-
-
Aminooxyacetate
-
-
D,L-alpha-aminoheptanedioate
-
-
D-Lysine
diaminoheptanedioic acid
-
analogs
glutamic acid
-
-
L,L-2,6-diaminoheptanedioate
-
no detectable amounts of decarboxylation products
L-2,4-diaminobutyrate
L-cystine
L-lysine
L-ornithine
-
-
L-S-aminoethylcysteine
-
-
LL-2,6-Diaminoheptanedioate
-
-
mercuribenzoic acid
-
-
meso-2,6-diaminoheptanedioate
-
substrate inhibition
n-butylamine
-
-
N-Hydroxydiaminoheptanedioate
NH2OH
-
-
p-chloromercuribenzoate
-
-
Penicillamine
-
no effect at 10fold pyridoxal phosphate concentration
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,3-Dimercaptopropan-1-ol
D-Lysine
-
activates
dithiothreitol
-
activates
EDTA
-
activates
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1 - 7
D,D-2,6-diaminoheptanedioate
-
pH 7.8, 25°C
0.43
DL-2,6-Diaminoheptanedioate
-
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
1.7
meso-2,6-diamininoheptanedioate
0.03 - 1
meso-2,6-diaminoheptanedioate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.8
D,D-2,6-diaminoheptanedioate
7.1
DL-2,6-Diaminoheptanedioate
Mycobacterium tuberculosis
-
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
0.07 - 15.65
meso-2,6-diaminoheptanedioate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1
D,D-2,6-diaminoheptanedioate
Mycobacterium tuberculosis
-
pH 7.8, 25°C
194866
16
DL-2,6-Diaminoheptanedioate
Mycobacterium tuberculosis
-
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
20250
18
meso-2,6-diaminoheptanedioate
Mycobacterium tuberculosis
-
pH 7.8, 25°C
1400
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.004
1,5-Diaminopentane
-
-
0.0024
1,6-diaminohexane
-
-
0.0025
1,7-Diaminoheptane
-
-
0.13
adipic acid
-
-
0.089
azelaic acid
-
-
0.21
caproic acid
-
-
26
D-Lysine
-
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication; pH 7.8, 25°C
1.6
L,L-2,6-diaminoheptanedioate
-
pH 7.8, 25°C
1.8
L-lysine
-
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication; pH 7.8, 25°C
1.6
LL-2,6-Diaminoheptanedioate
-
in 100 mM TEA-HCl pH 7.8, temperature not specified in the publication
0.91
N-Hydroxydiaminoheptanedioate
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.01
Chlamydomonas sp.
-
-
0.017
-
-
0.046 - 0.058
-
-
0.048
-
-
0.09
-
wild-type strain AS1
0.209
Clostridium spp.
-
-
0.45
-
mutant G49 strain
7
-
recombinant DDC, 37°C
9
-
native DDC
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 9
-
more than half-maximal activity between 7.5 and pH 9.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
enzyme assay at
30
-
enzyme assay at
57
Methanothermobacter thermautotrophicum
-
assayed at
additional information
-
-
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 45
-
relative rates of decarboxylation at 25C, 37C, 45C are 0.17 : 1.0 : 1.6
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.54
sequence calculation
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
-
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Aquifex aeolicus (strain VF5)
Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Psychromonas ingrahamii (strain 37)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
52500
-
gel filtration, recombinant DDC
80000
-
gel filtration
105000
-
gel filtration
189000
-
X-ray scattering
200000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
homotetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
to 2.0 A resolution; to 2.3 A resolution
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
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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
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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
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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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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
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
stable for 10 min at pH 6.0-7.5
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
stable to freezing and thawing
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, sodium phosphate buffer, pH 6.8, 4 months, about 50% loss of activity
-
2¦C, sodium phosphate buffer, pH 6.8, several days
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography
-
Ni-NTA resin column chromatography
recombinant DAPDC
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
-
expressed in Escherichia coli BL21(DE3) cells
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expressed in Escherichia coli strain BL21 (DE3)
expression in Escherichia coli
expression in Escherichia coli; expression in Escherichia coli
expression in FR3T3 and other mammalian cells
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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
overexpression in Escherichia coli
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
a 2fold increase in L-lysine production is observed after introduction of the cloned LysA gene into Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
nutrition
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