Information on EC 1.4.1.16 - diaminopimelate dehydrogenase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.4.1.16
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RECOMMENDED NAME
GeneOntology No.
diaminopimelate dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
meso-2,6-diaminoheptanedioate + H2O + NADP+ = L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
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redox reaction
-
-
-
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reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-lysine biosynthesis III
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NIL
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lysine metabolism
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Lysine biosynthesis
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Metabolic pathways
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Biosynthesis of secondary metabolites
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SYSTEMATIC NAME
IUBMB Comments
meso-2,6-diaminoheptanedioate:NADP+ oxidoreductase (deaminating)
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CAS REGISTRY NUMBER
COMMENTARY hide
60894-21-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Achromobacter polymorph
very low activity
-
-
Manually annotated by BRENDA team
Achromobacter superficialis
very low activity
-
-
Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
Alcaligenes viscolactis
low activity
-
-
Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
Bacterium mycoides
very low activity
-
-
Manually annotated by BRENDA team
low activity
-
-
Manually annotated by BRENDA team
strain ICR 7000
-
-
Manually annotated by BRENDA team
low activity
-
-
Manually annotated by BRENDA team
strain AS019
-
-
Manually annotated by BRENDA team
strain RRL-5
-
-
Manually annotated by BRENDA team
low activity
-
-
Manually annotated by BRENDA team
Erwinia aroidea
low activity
-
-
Manually annotated by BRENDA team
Flavobacterium suaveolens
low activity
-
-
Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
low activity
-
-
Manually annotated by BRENDA team
no activity in Chlamydomonas reinhardtii
-
-
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Manually annotated by BRENDA team
no activity in Escherichia coli
strains ICR 0010, K12, ICR 0050 and IFO 3301
-
-
Manually annotated by BRENDA team
no activity in Glycine max
-
-
-
Manually annotated by BRENDA team
no activity in Klebsiella pneumoniae
strains IFO 125059 and 12019
-
-
Manually annotated by BRENDA team
no activity in Nicotiana tabacum
-
-
-
Manually annotated by BRENDA team
no activity in Staphylococcus aureus
-
-
-
Manually annotated by BRENDA team
no activity in Zea mays
-
-
-
Manually annotated by BRENDA team
low activity
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
Pseudomonas alkanolytica
very low activity
-
-
Manually annotated by BRENDA team
low activity
-
-
Manually annotated by BRENDA team
-
-
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Manually annotated by BRENDA team
very low activity
-
-
Manually annotated by BRENDA team
Sarcina subflava
low activity
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-
Manually annotated by BRENDA team
very low activity
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2,6-diaminoheptanedioic acid + H2O + NADP+
2-amino-6-oxopimelate + NH3 + NADPH
show the reaction diagram
-
mixture of all possible stereoisomers, 4% of activity with meso-2,6-diaminopimelate
-
r
2-amino-6-(hydroxyamino)heptanedioic acid + H2O + NADP+
2-hydroxyamino-6-oxopimelate + NH3 + NADPH
show the reaction diagram
-
mixture of all possible stereoisomers, 22% of activity with meso-2,6-diaminopimelate
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r
4-methylene diaminopimelate + H2O + NADP+
4-methyleneamino-6-oxopimelate + NH3 + NADPH
show the reaction diagram
-
mixture of all possible stereoisomers, 4% of activity with meso-2,6-diaminopimelate
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r
L-2-amino-6-oxoheptanedioate + NH3 + NAD(P)H
meso-2,6-diaminoheptanedioate + H2O + NAD(P)+
show the reaction diagram
L-2-amino-6-oxoheptanedioate + NH3 + NADPH
meso-2,6-diaminoheptanedioate + H2O + NADP+
show the reaction diagram
meso-2,6-diaminoheptanedioate + H2O + NADP+
L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
show the reaction diagram
phenylpyruvate + NH3 + NADPH + H+
phenylalanine + NADP+
show the reaction diagram
-
-
-
-
?
pyruvate + NH3 + NADPH + H+
D-alanine + NADP+
show the reaction diagram
-
-
-
?
additional information
?
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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
L-2-amino-6-oxoheptanedioate + NH3 + NADPH
meso-2,6-diaminoheptanedioate + H2O + NADP+
show the reaction diagram
meso-2,6-diaminoheptanedioate + H2O + NADP+
L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
MnSO4
slight activation, mutant enzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2S,5S)-2-amino-3(3-carboxy-2-isoxazolin-5-yl)propanoic acid
2-mercaptoethanol
complete inhibition at 5 mM
4,4'-Dithiopyridine
-
complete inactivation
4-chloromercuribenzoate
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complete inhibition at 0.1 mM
5,5'-dithiobis(2-nitrobenzoate)
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complete inactivation
D-2,6-diaminopimelate
glyoxylate
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5 mM, 30% inhibition of reductive amination
HgCl2
iodoacetate
L-2,6-diaminopimelate
L-2-amino-6-methylene-pimelate
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competitive inhibition
L-alpha,epsilon-diaminopimelate
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-
L-cysteine
Li+
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1 mM, 32% inhibition
meso-alpha,delta-Diaminoadipate
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-
meso-diaminopimelate
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N-ethylmaleimide
p-chloromercuribenzoate
thioglycolate
Thioglycollate
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strong inhibition at 5 mM
Zn2+
strong inhibition at 1 mM
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.21 - 0.28
L-2-amino-6-oxopimelate
1.9 - 16.7
meso-2,6-diaminoheptanedioate
2.5 - 6.25
meso-2,6-diaminopimelate
3.1
meso-diaminopimelate
-
-
2 - 10
NAD+
0.00083 - 0.14
NADP+
0.13 - 0.23
NADPH
12.5 - 62.5
NH3
11 - 24.3
phenylpyruvate
12.2 - 24.8
pyruvate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6780 - 127000
meso-2,6-diaminoheptanedioate
0.11 - 3.98
phenylpyruvate
664 - 10100
pyruvate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0042 - 0.023
(2S,5S)-2-amino-3(3-carboxy-2-isoxazolin-5-yl)propanoic acid
2
D-2,6-diaminopimelate
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4
D-alpha,epsilon-diaminopimelate
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-
8.5
L-2,6-diaminopimelate
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-
0.005
L-2-amino-6-methylene-pimelate
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-
3.12
L-alpha,epsilon-diaminopimelate
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-
4.16
meso-alpha,delta-Diaminoadipate
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-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.013
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activity in crude extracts at pH 8.0
0.03
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reductive amination of 2-amino-6-oxopimelate in crude extracts at pH 7.5 in the presence of 1.67 mM meso-diaminopimelate
0.07
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recombinant wild-type enzyme, pH 8.5, 30C
0.12
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activity in crude extracts
0.13
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strain AS019 transformed with plasmid harboring cloned gene
0.16
-
activity in strain RRL-5
0.237
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reductive amination of 2-amino-6-oxopimelate in crude extracts at pH 7.5
0.25
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reductive amination of 2-amino-6-oxopimelate in crude extracts at pH 7.5
0.28
-
recombinant mutant T171S/R181F, pH 8.5, 30C
0.287
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oxidative deamination of meso-diaminopimelate in crude extracts at pH 10.5
0.34
-
activity in crude extracts at pH 10.5
0.44
-
recombinant mutant R181F, pH 8.5, 30C
0.45
-
oxidative deamination of meso-diaminopimelate in crude extracts at pH 10.5
0.53
-
activity in crude extracts
0.74
-
recombinant mutant T171S/H227V, pH 8.5, 30C
1.02
-
recombinant mutant T171S/R181F/H227V, pH 8.5, 30C
1.03
-
recombinant mutant H227C, pH 8.5, 30C
1.35
-
recombinant mutant R181F/H227V, pH 8.5, 30C
2.22
-
activity in strain RRL-5 transformed with plasmid harboring cloned gene
2.39
-
recombinant mutant H227V, pH 8.5, 30C
8.28
-
purified enzyme, pH 7.2, 50C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
2-amino-6-oxopimelate + NH3 + NADPH
7.9
-
reductive amination of 2-amino-6-oxopimelate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.9 - 10
-
2-amino-6-oxopimelate + NH3 + NADPH
6.8 - 11
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meso-2,6-diaminopimelate + H2O + NADP+
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Clostridium tetani (strain Massachusetts / E88)
Clostridium tetani (strain Massachusetts / E88)
Clostridium tetani (strain Massachusetts / E88)
Clostridium tetani (strain Massachusetts / E88)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Symbiobacterium thermophilum (strain T / IAM 14863)
Symbiobacterium thermophilum (strain T / IAM 14863)
Symbiobacterium thermophilum (strain T / IAM 14863)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
78500 - 80000
80000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallization in the presence of NADP+, only monoclinic crystals are suitable for X-ray diffraction, 2.2 A resolution
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crystals of the ternary complex formed from the enzyme, NADP+ and the inhibitor (2S,5S)-2-amino-3(3-carboxy-2-isoxazolin-5-yl)propanoic acid
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crystals of the ternary complex formed from the enzyme, NADP+ and the inhibitor L-2-amino-6-methylene-pimelate, 2.1 A resolution
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enzyme-NADP+ complex, hanging drop vapour diffusion, crystals of maximum dimensions of 0.05 x 0.05 x 0.5 mm are observed in 1 M ammonium sulfate, 1.2 M lithium sulfate, 100 mM HEPES, pH 7.5, crystals of dimensions 0.3 x 0.05 x 0.5 mm are obtained from 13-17% polyethylene glycol 8000 in 100 mM sodium cacodylate, pH 6.5 and 150-300 mM Mg(OAc)2
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 11
-
purified enzyme, 30 min, 50C, fully stable
723913
6.5 - 7
-
-
391505
7 - 9
-
at 40C
391507
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 60
-
purified recombinant enzyme, 30 min, fully stable in deamination activity
48
-
10 min, 10 mM potassium phosphate pH 7.4, unstable above
60
-
purified enzyme, 30 min, pH 7.2, fully stable
70
-
purified recombinant enzyme, 30, loss of 6% deamination activity
75
-
purified recombinant enzyme, 1 h, rapid inactivation
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 0.01 M potassium phosphate buffer, pH 7.4, 0.01% 2-mercaptoethanol, 10% glycerol, 1 year
4C, 0.01% 2-mercaptoethanol, 20% glycerol, 1 month
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate, DEAE-cellulose, hydroxyapatite, Sephadex G-150
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recombinant enzyme from Escherichia coli strain Rosetta (DE3) by heat treatment and affinity chromatography, native enzyme 47fold to homogeneity by ammonium sulfate fractionation, and hydrophobic interaction and anion exchange chromatography, followed by preparative slab PAGE
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recombinant soluble enzyme 3.4fold from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
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recombinant wild-type and mutant enzymes from Escherichia coli strain Bl21(DE3)
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recombinant wild-type enzyme and mutant Q154L/D158G/T173I/R199M/H249N from Escherichia coli strain Rosetta (DE3) by heat treatment and chelating affinity chromatograhy
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, expression in Escherichia coli strain Rosetta (DE3)
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DNA and amino acid sequence determmination and analysis, expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3), equally as a soluble protein and in inclusion bodies
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expression in Escherichia coli and Corynebacterim glutamicum
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gene ddh, expression of wild-type enzyme and mutant Q154L/D158G/T173I/R199M/H249N in Escherichia coli strain Rosetta (DE3)
gene ddh, overexpression in Corynebacterium glutamicum, co-expression with other enzyme of the metabolic pathway for cadaverine, i.e. N-acetyl-diaminopentane, production, overview
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recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
F146W
-
site-directed mutagenesis, the mutant shows altered activity levels with meso-2,6-diaminoheptanedioate and pyruvate as substrates
F146W/M152Q
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site-directed mutagenesis, the mutant shows altered activity levels with meso-2,6-diaminoheptanedioate and pyruvate as substrates
H227C
-
site-directed saturation mutagenesis, the mutant shows 15.1fold increased activity with phenylpyruvate compared to the wild-type enzyme
H227V
-
site-directed saturation mutagenesis, the mutant shows 35.1fold increased activity with phenylpyruvate compared to the wild-type enzyme
M152Q
-
site-directed mutagenesis, the mutant shows altered activity levels with meso-2,6-diaminoheptanedioate and pyruvate as substrates
R181F
-
site-directed saturation mutagenesis, the mutant shows 6.4fold increased activity with phenylpyruvate compared to the wild-type enzyme
R181F/H227V
-
site-directed saturation mutagenesis, the mutant shows 19.3fold increased activity with phenylpyruvate compared to the wild-type enzyme
T171P
-
site-directed saturation mutagenesis, the mutant shows 2.2fold increased activity with phenylpyruvate compared to the wild-type enzyme
T171S
-
site-directed saturation mutagenesis, the mutant shows 2.8fold increased activity with phenylpyruvate compared to the wild-type enzyme
T171S/H227V
-
site-directed saturation mutagenesis, the mutant shows 10.6fold increased activity with phenylpyruvate compared to the wild-type enzyme
T171S/R181F
-
site-directed saturation mutagenesis, the mutant shows 4.0fold increased activity with phenylpyruvate compared to the wild-type enzyme
T171S/R181F/H227V
-
site-directed saturation mutagenesis, the mutant shows 14.6fold increased activity with phenylpyruvate compared to the wild-type enzyme
Q154L/D158G/T173I/R199M/H249N
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
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high thermostability and relaxed substrate profile of Symbiobacterium thermophilum meso-DAPDH warrant it as an excellent starting enzyme for creating effective D-amino acid dehydrogenases by protein engineering
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