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Information on EC 1.4.1.16 - diaminopimelate dehydrogenase and Organism(s) Corynebacterium glutamicum and UniProt Accession P04964

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Corynebacterium glutamicum
UNIPROT: P04964 not found.
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The taxonomic range for the selected organisms is: Corynebacterium glutamicum
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
meso-diaminopimelate dehydrogenase, meso-dapdh, diaminopimelate dehydrogenase, meso-2,6-diaminopimelate dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
meso-alpha,epsilon-diaminopimelate dehydrogenase
-
-
-
-
meso-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
meso-2,6-diaminoheptanedioate + H2O + NADP+ = L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
show the reaction diagram
enzyme may exhibit a random order of addition of substrates
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
meso-2,6-diaminoheptanedioate:NADP+ oxidoreductase (deaminating)
-
CAS REGISTRY NUMBER
COMMENTARY hide
60894-21-5
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-oxovalerate + NH3 + NADPH + H+
? + H2O + NADP+
show the reaction diagram
-
-
-
?
3-methyl-2-oxobutanoate + NH3 + NADPH + H+
? + H2O + NADP+
show the reaction diagram
-
-
-
?
4-methyl-2-oxopentanoate + NH3 + NADPH + H+
? + H2O + NADP+
show the reaction diagram
-
-
-
?
L-2-amino-6-oxoheptanedioate + NH3 + NAD(P)H
meso-2,6-diaminoheptanedioate + H2O + NAD(P)+
show the reaction diagram
L-DELTA1-tetrahydrodipicolinate + NH4+ + NADPH
meso-2,6-diaminoheptanedioate + NADP+
show the reaction diagram
-
-
-
?
meso-2,6-diaminoheptanedioate + H2O + NADP+
L-2-amino-6-oxoheptanedioate + NH3 + NADPH + H+
show the reaction diagram
-
-
-
?
meso-2,6-diaminoheptanedioate + NADP+
L-DELTA1-tetrahydrodipicolinate + NH4+ + NADPH
show the reaction diagram
-
-
-
?
oxaloacetate + NH3 + NADPH + H+
? + H2O + NADP+
show the reaction diagram
-
-
-
?
pyruvate + NH3 + NADPH + H+
D-alanine + H2O + NADP+
show the reaction diagram
-
-
-
?
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 + NAD+
L-2-amino-6-oxoheptanedioate + NH3 + NADH + H+
show the reaction diagram
-
-
-
-
r
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-2-amino-6-oxoheptanedioate + NH3 + NADPH
meso-2,6-diaminoheptanedioate + H2O + NADP+
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADPH
NADH
-
3% activity of that with NADP+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2S,5S)-2-amino-3(3-carboxy-2-isoxazolin-5-yl)propanoic acid
-
Cu2+
-
0.01 mM, 82% inhibition
D-2,6-diaminopimelate
-
10 mM, 49% inhibition
HgCl2
-
0.01 mM, 92% inhibition
iodoacetate
-
1 mM, 77% inhibition
L-2,6-diaminopimelate
-
10 mM, 27% inhibition
L-cysteine
-
5 mM, 99% inhibition
Li+
-
1 mM, 32% inhibition
N-ethylmaleimide
-
1 mM, 39% inhibition
Ni2+
-
1 mM, 36% inhibition
p-chloromercuribenzoate
-
-
thioglycolate
-
5 mM, 62% inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
36.16 - 57.04
2-oxovalerate
97.88 - 119.2
3-methyl-2-oxobutanoate
26.88 - 33.51
4-methyl-2-oxopentanoate
0.27
L-DELTA1-tetrahydrodipicolinate
pH 8.5, 30°C
-
0.43 - 2.8
meso-2,6-diaminoheptanedioate
39.2
NH4+
pH 8.5, 30°C
29.92 - 31.5
oxaloacetate
294.9 - 337.6
pyruvate
0.28
L-2-amino-6-oxopimelate
-
-
3.1
meso-diaminopimelate
-
-
2 - 10
NAD+
0.083 - 0.14
NADP+
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.91 - 0.93
2-oxovalerate
0.27 - 0.38
3-methyl-2-oxobutanoate
0.1 - 0.12
4-methyl-2-oxopentanoate
41.9
L-DELTA1-tetrahydrodipicolinate
pH 8.5, 30°C
-
51.99 - 115.4
meso-2,6-diaminoheptanedioate
768.3
NH4+
pH 8.5, 30°C
0.087 - 0.11
oxaloacetate
1.35 - 2.27
pyruvate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016 - 1.57
2-oxovalerate
0.0028 - 1.14
3-methyl-2-oxobutanoate
0.0034 - 1.15
4-methyl-2-oxopentanoate
155
L-DELTA1-tetrahydrodipicolinate
pH 8.5, 30°C
-
0.96 - 120.3
meso-2,6-diaminoheptanedioate
23.8
NH4+
pH 8.5, 30°C
0.0029 - 1.24
oxaloacetate
0.0046 - 1.46
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
-
-
8.5
L-2,6-diaminopimelate
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.13
-
strain AS019 transformed with plasmid harboring cloned gene
0.15
-
activity in crude extracts of cells grown on complex medium
0.16
-
activity in strain RRL-5
2.22
-
activity in strain RRL-5 transformed with plasmid harboring cloned gene
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.9
-
reductive amination of 2-amino-6-oxopimelate
9
-
oxidative deamination of meso-2,6-diaminopimelate
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35099
-
2 * 35099, nucleotide sequencing
35198
-
2 * 35198, electrospray MS, deduced from amino acid sequence
39000
-
2 * 39000, SDS-PAGE
70000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization in the presence of NADP+, only monoclinic crystals are suitable for X-ray diffraction, 2.2 A resolution
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
crystals of the ternary complex formed from the enzyme, NADP+ and the inhibitor L-2-amino-6-methylene-pimelate, 2.1 A resolution
-
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
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A69R
mutation to the correspondung residue of Symbiobacteium thermophilum DAPDH. Mutation improves the catalytic efficiencies toward 2-keto acids and does not affect the catalytic efficiency toward meso-DAP
additional information
-
systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane. Superior strains with desirable properties such as (i) the release from unwanted feedback regulation at the level of aspartokinase and pyruvate carboxylase by introducing the point mutations lysC311 and pycA458, (ii) an optimized supply of the key precursor oxaloacetate by amplifying the anaplerotic enzyme, pyruvate carboxylase, and deleting phosphoenolpyruvate carboxykinase which otherwise removes oxaloacetate, (iii) enhanced biosynthetic flux via combined amplification of aspartokinase, dihydrodipicolinate reductase, diaminopimelate dehydrogenase and diaminopimelate decarboxylase, and (iv) attenuated flux into the threonine pathway competing with production by the leaky mutation hom59 in the homoserine dehydrogenasegene
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 7
-
-
391505
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
unstable above
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 0.01 M potassium phosphate buffer, pH 7.4, 0.01% 2-mercaptoethanol, 10% glycerol, 1 year
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli and Corynebacterim glutamicum
-
gene ddh, overexpression in Corynebacterium glutamicum, co-expression with other enzyme of the metabolic pathway for cadaverine, i.e. N-acetyl-diaminopentane, production, overview
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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, Corynebacterium glutamicum AS019
Manually annotated by BRENDA team
Cremer, J.; Treptow, C.; Eggeling, L.; Sahm, H.
Regulation of enzymes of lysine biosynthesis in Corynebacterium glutamicum
J. Gen. Microbiol.
134
3221-3229
1988
Corynebacterium glutamicum
Manually annotated by BRENDA team
Ishino, S.; Mizukami, T.; Yamaguchi, K.; Katsumata, R.; Araki, K.
Cloning and sequencing of the meso-diaminopimelate-D-dehydrogenase (ddh) gene of Corynebacterium glutamicum
Agric. Biol. Chem.
52
2903-2909
1988
Corynebacterium glutamicum, Corynebacterium glutamicum RRL-5
-
Manually annotated by BRENDA team
Ishino, S.; Mizukami, T.; Yamaguchi, K.; Katsumata, R.; Araki, K.
Nucleotide sequence of the meso-diaminopimelate D-dehydrogenase gene from Corynebacterium glutamicum
Nucleic Acids Res.
15
3917
1987
Corynebacterium glutamicum
Manually annotated by BRENDA team
Misono, H.; Ogasawara, M.; Nagasaki, S.
Characterization of meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum and its distribution in bacteria
Agric. Biol. Chem.
50
2729-2734
1986
Achromobacter polymorph, Achromobacter superficialis, Agrobacterium tumefaciens, Alcaligenes viscolactis, Bacillus amyloliquefaciens, Bacillus cereus, Bacillus licheniformis, Bacterium mycoides, Brevibacillus brevis, Brevibacterium sp., Corynebacterium ammoniagenes, Corynebacterium glutamicum, Corynebacterium pseudodiphtheriticum, Enterobacter cloacae, Flavobacterium suaveolens, Glutamicibacter protophormiae, Hafnia alvei, Kocuria rosea, Lysinibacillus sphaericus, Micrococcus luteus, Morganella morganii, no activity in Escherichia coli, no activity in Klebsiella pneumoniae, no activity in Staphylococcus aureus, Providencia rettgeri, Pseudomonas aeruginosa, Pseudomonas alkanolytica, Pseudomonas chlororaphis subsp. aureofaciens, Pseudomonas cruciviae, Pseudomonas fragi, Pseudomonas putida, Terrabacter tumescens
-
Manually annotated by BRENDA team
Ishino, S.; Yamaguchi, K.; Shirahata, K.; Araki, K.
Involvement of meso-alpha,epsilon-diamino-pimelate D-dehydrogenase in lysine biosynthesis in Corynebacterium glutamicum
Agric. Biol. Chem.
48
2257-2260
1984
Corynebacterium glutamicum
-
Manually annotated by BRENDA team
Misono, H.; Togawa, H.; Soda, K.
meso-alpha,epsilon-Diaminopimelate D-dehydrogenase: distribution and the reaction product
J. Bacteriol.
137
22-27
1979
Brevibacterium sp., Corynebacterium glutamicum, Erwinia aroidea, Lysinibacillus sphaericus, Proteus mirabilis, Proteus vulgaris, Pseudomonas fluorescens, Sarcina subflava
Manually annotated by BRENDA team
Scapin, G.; Reddy, S.G.; Blanchard, J.S.
Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum
Biochemistry
35
13540-13551
1996
Corynebacterium glutamicum (P04964), Corynebacterium glutamicum
Manually annotated by BRENDA team
Reddy, S.G.; Scapin, G.; Blanchard, J.S.
Expression, purification, and crystallization of meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum
Proteins Struct. Funct. Genet.
25
514-516
1996
Corynebacterium glutamicum
Manually annotated by BRENDA team
Wang, F.; Scapin, G.; Blanchard, J.S.; Angeletti, R.H.
Substrate binding and conformational changes of Corynebacterium glutamicum diaminopimelate dehydrogenase revealed by hydrogen/deuterium exchange and electrospray mass spectrometry
Protein Sci.
7
293-299
1998
Corynebacterium glutamicum
Manually annotated by BRENDA team
Scapin, G.; Cirilli, M.; Reddy, S.G.; Gao, Y.; Vederas, J.C.; Blanchard, J.S.
Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase
Biochemistry
37
3278-3285
1998
Corynebacterium glutamicum (P04964), Corynebacterium glutamicum
Manually annotated by BRENDA team
Cirilli, M.; Scapin, G.; Sutherland, A.; Vederas, J.C.; Blanchard, J.S.
The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate
Protein Sci.
9
2034-2037
2000
Corynebacterium glutamicum, Lysinibacillus sphaericus
Manually annotated by BRENDA team
Kind, S.; Jeong, W.K.; Schroeder, H.; Wittmann, C.
Systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane
Metab. Eng.
12
341-351
2010
Corynebacterium glutamicum
Manually annotated by BRENDA team
Zhang, Y.; Ma, Q.; Dong, M.; Zhang, X.; Chen, Y.; Gao, X.; Song, Y.
Essential role of amino acid position 71 in substrate preference by meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum IAM14863
Enzyme Microb. Technol.
111
57-62
2018
Corynebacterium glutamicum (P04964), Corynebacterium glutamicum ATCC 13032 (P04964), Symbiobacterium thermophilum (Q67PI3)
Manually annotated by BRENDA team
Xu, J.Z.; Ruan, H.Z.; Liu, L.M.; Wang, L.P.; Zhang, W.G.
Overexpression of thermostable meso-diaminopimelate dehydrogenase to redirect diaminopimelate pathway for increasing L-lysine production in Escherichia coli
Sci. Rep.
9
2423
2019
Acetivibrio thermocellus (A3DDX7), Acetivibrio thermocellus ATCC 27405 (A3DDX7), Bacteroides fragilis (Q64PZ8), Bacteroides fragilis YCH46 (Q64PZ8), Corynebacterium glutamicum (P04964), Corynebacterium glutamicum ATCC 13032 (P04964), Lysinibacillus sphaericus (Q9KWR0), Symbiobacterium thermophilum (Q67PI3), Ureibacillus thermosphaericus (G1UII1)
Manually annotated by BRENDA team