Information on EC 1.5.1.11 - D-octopine dehydrogenase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.5.1.11
-
RECOMMENDED NAME
GeneOntology No.
D-octopine dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
N2-(D-1-carboxyethyl)-L-arginine + NAD+ + H2O = L-arginine + pyruvate + NADH + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
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reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
pyruvate fermentation to opines
-
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Arginine and proline metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
N2-(D-1-carboxyethyl)-L-arginine:NAD+ oxidoreductase (L-arginine-forming)
In the reverse direction, acts also on L-ornithine, L-lysine and L-histidine.
CAS REGISTRY NUMBER
COMMENTARY hide
37256-27-2
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
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Manually annotated by BRENDA team
Anthopleura pacifica
-
-
-
Manually annotated by BRENDA team
-
-
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Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Cardium tuberculatum
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Chlamys opercularis
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
2 allozymic forms are distributed in a highly population-specific manner, enzyme variants: ss, ff, and sf
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-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
crown-gall tumor-tissue induced by Agrobacterium tumefaciens
-
-
Manually annotated by BRENDA team
no activity in Amphitrite sp.
-
-
-
Manually annotated by BRENDA team
no activity in Bugula neritina
-
-
-
Manually annotated by BRENDA team
no activity in Chaetopleura apiculata
-
-
-
Manually annotated by BRENDA team
no activity in Chaetopterus variopedatus
-
-
-
Manually annotated by BRENDA team
no activity in Clymenella torquata
-
-
-
Manually annotated by BRENDA team
no activity in Crepidula fornicata
-
-
-
Manually annotated by BRENDA team
no activity in Diodora cayenensis
-
-
-
Manually annotated by BRENDA team
no activity in Glottidia pyramidata
-
-
-
Manually annotated by BRENDA team
no activity in Glycera sp.
-
-
-
Manually annotated by BRENDA team
no activity in Hydroides sp.
-
-
-
Manually annotated by BRENDA team
no activity in Laqueus californianus
-
-
-
Manually annotated by BRENDA team
no activity in Lepidonotus sp.
-
-
-
Manually annotated by BRENDA team
no activity in Littorina littorea
-
-
-
Manually annotated by BRENDA team
no activity in Lyonsia hyalina
-
-
-
Manually annotated by BRENDA team
no activity in Membranipora tenuis
-
-
-
Manually annotated by BRENDA team
no activity in Mopalia muscosa
-
-
-
Manually annotated by BRENDA team
no activity in Mya arenaria
-
-
-
Manually annotated by BRENDA team
no activity in Nereis sp.
-
-
-
Manually annotated by BRENDA team
no activity in Phascolopsis sp.
-
-
-
Manually annotated by BRENDA team
no activity in Phascolosoma sp.
-
-
-
Manually annotated by BRENDA team
no activity in Phoronis architecta
-
-
-
Manually annotated by BRENDA team
no activity in Phoronis vancouverensis
-
-
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Manually annotated by BRENDA team
no activity in Schizoporella floridana
-
-
-
Manually annotated by BRENDA team
no activity in Tectura testudinalis
-
-
-
Manually annotated by BRENDA team
no activity in Tegula funebralis
-
-
-
Manually annotated by BRENDA team
no activity in Terebratalia transversa
-
-
-
Manually annotated by BRENDA team
no activity in Themiste sp.
-
-
-
Manually annotated by BRENDA team
no activity in Turbo castanea
-
-
-
Manually annotated by BRENDA team
no activity in Urechis sp.
-
-
-
Manually annotated by BRENDA team
no activity in Urosalpinx cinerea
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
crown-gall tumor-tissue induced by Agrobacterium tumefaciens
-
-
Manually annotated by BRENDA team
Priapulus sp.
-
-
-
Manually annotated by BRENDA team
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Manually annotated by BRENDA team
2 isoenzymes: a polymorphic anodal form and a hepatopancreas-specific cathodally migrating form
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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
beta-alanine + pyruvate + NADH + H+
?
show the reaction diagram
-
-
-
-
?
canavanine + pyruvate + NADH
? + NAD+ + H2O
show the reaction diagram
24.74% activity with canavanine compared to L-Arg
-
-
?
Canavanine + pyruvate + NADH
N2-(D-1-Carboxyethyl)-canavanine + NAD+ + H2O
show the reaction diagram
Canavanine + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-canavanine + NADP+ + H2O
show the reaction diagram
-
at 56% of the activity with L-Arg
-
-
-
glycine + pyruvate + NADH + H+
?
show the reaction diagram
-
-
-
-
?
Homoarginine + pyruvate + NADH
N2-(D-1-Carboxyethyl)-homoarginine + NAD+ + H2O
show the reaction diagram
Homoarginine + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-homoarginine + NADP+ + H2O
show the reaction diagram
-
at 62% of the activity with L-Arg
-
-
-
L-alanine + pyruvate + NADH
? + NAD+ + H2O
show the reaction diagram
0.29% activity with L-alanine compared to L-Arg
-
-
?
L-alanine + pyruvate + NADH + H+
?
show the reaction diagram
-
-
-
-
?
L-Arg + 2-oxobutanoate + NADH
N2-(D-2-Carboxypropyl)-L-Arg + NAD+ + H2O
show the reaction diagram
L-Arg + 2-oxobutanoate + NADPH
N2-(D-2-Carboxypropyl)-L-Arg + NADP+ + H2O
show the reaction diagram
-
at 21% of the activity with pyruvate
-
-
-
L-Arg + 2-oxobutyrate + NADH
?
show the reaction diagram
-
-
-
?
L-Arg + 2-oxovalerate + NADH
?
show the reaction diagram
-
-
-
?
L-Arg + glyoxylate + NADPH
?
show the reaction diagram
-
at 5% of the activity with pyruvate
-
-
-
L-Arg + NADH
N2-(D-1-carboxyethyl)-L-Arg + NAD+ + H2O
show the reaction diagram
100% activity with L-Arg
-
-
?
L-Arg + oxaloacetate + NADH
?
show the reaction diagram
L-Arg + pyruvate + NADH
N2-(D-1-carboxyethyl)-L-Arg + NAD+ + H2O
show the reaction diagram
L-Arg + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-L-Arg + NADP+ + H2O
show the reaction diagram
L-arginine + pyruvate + NADH + H+
N2-(D-1-carboxyethyl)-L-arginine + NAD+ + H2O
show the reaction diagram
L-Citrulline + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-L-citrulline + NADP+ + H2O
show the reaction diagram
-
-
-
-
-
L-Cys + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-L-Cys + NADP+ + H2O
show the reaction diagram
-
at 27% of the activity with L-Arg
-
-
-
L-cysteine + pyruvate + NADH
? + NAD+ + H2O
show the reaction diagram
1.18% activity with L-cysteine compared to L-Arg
-
-
?
L-Gln + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-L-Gln + NADP+ + H2O
show the reaction diagram
L-His + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-L-His + NADP+ + H2O
show the reaction diagram
-
at 78% of the activity with L-Arg
-
-
-
L-Lys + pyruvate + NADH
Lysopine + NAD+ + H2O
show the reaction diagram
L-Lys + pyruvate + NADPH
Lysopine + NADP+ + H2O
show the reaction diagram
L-lysine + pyruvate + NADH + H+
?
show the reaction diagram
-
-
-
-
?
L-Met + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-L-Met + NADP+ + H2O
show the reaction diagram
L-serine + pyruvate + NADPH
N2-(D-1-carboxyethyl)-L-Ser + NADP+ + H2O
show the reaction diagram
-
at 25% of the activity with L-Arg
-
-
-
norvaline + pyruvate + NADH
? + NAD+ + H2O
show the reaction diagram
0.15% activity with norvaline compared to L-Arg
-
-
?
Orn + pyruvate + NADH
N2-(D-1-Carboxyethyl)-L-Orn + NAD+ + H2O
show the reaction diagram
Orn + pyruvate + NADPH
N2-(D-1-Carboxyethyl)-L-Orn + NADP+ + H2O
show the reaction diagram
-
at 30% of the activity with L-Arg
-
-
-
ornithine + pyruvate + NADH
? + NAD+ + H2O
show the reaction diagram
0.26% activity with ornithine compared to L-Arg
-
-
?
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
L-arginine + pyruvate + NADH + H+
N2-(D-1-carboxyethyl)-L-arginine + NAD+ + H2O
show the reaction diagram
-
-
-
-
r
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADPH
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
-
-
1-Ethyl-3(3-dimethylaminopropyl)carbodiimide hydrochloride
-
-
2,2'-dipyridyl
-
-
3-hydroxypyruvate
-
inhibitor of octopine formation
5,5'-dithiobis(2-nitrobenzoate)
-
-
5,5'-dithiobis(2-nitrobenzoic acid)
-
-
5-Guanidinopentanoate
-
-
AMP
-
dead-end inhibition
diethyldicarbonate
-
reversal of the inhibition by hydroxylamine
diethyldithiocarbamate
-
-
epsilon-aminohexanoate
-
-
glyoxylate
-
inhibitor of octopine formation
Guanidinobutane
-
-
homoarginine
-
inhibitor of octopine formation
L-Arg
Methyl octopine
-
-
NADH
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substrate inhibition
NADP+
NADPH
-
substrate inhibition
octopine
p-chloromercuribenzoate
-
-
p-Chloromercuriphenyl sulfonic acid
Propanoate
-
-
pyruvate
additional information
-
ODH is not inhibited by 5 or 10 mM iodacetamide
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6.2 - 7.8
2-oxobutanoate
5.9
2-oxobutyrate
wild type enzyme, in 50 mM triethanolamine buffer, pH 7.0, at 25C
49.8
2-oxovalerate
wild type enzyme, in 50 mM triethanolamine buffer, pH 7.0, at 25C
0.3 - 2.8
Arg
3.2 - 6.4
D-lysopine
0.1 - 5.2
D-octopine
0.5 - 159
L-Arg
3.9
L-canavanine
-
with pyruvate and NADPH as cosubstrates
22
L-citrulline
-
L-Met, with pyruvate and NADPH as cosubstrate; with pyruvate and NADPH as cosubstrates
5.4
L-Cys
-
with pyruvate and NADPH as cosubstrate
2.7
L-Gln
-
with pyruvate and NADPH as cosubstrates
23
L-His
-
with pyruvate and NADPH as cosubstrate
3.3 - 6.1
L-Lys
1.4 - 1.8
L-lysine
11.2
L-Met
-
-
0.7 - 28
L-Orn
1.8
Lys
0.014 - 110
NAD+
0.01 - 18
NADH
0.015
NADP+
-
-
0.001 - 0.01
NADPH
-
-
0.09 - 2.8
octopine
6
Orn
-
-
1 - 2.6
oxaloacetate
0.25 - 162
pyruvate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
526
2-oxobutanoate
Pecten maximus
Q9BHM6
wild type enzyme, in 50 mM triethanolamine buffer, pH 7.0, at 25C
272
2-oxovalerate
Pecten maximus
Q9BHM6
wild type enzyme, in 50 mM triethanolamine buffer, pH 7.0, at 25C
2 - 640
L-Arg
7.3 - 652
NADH
13 - 775
pyruvate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.45
-
crude extract enzyme, using beta-alanine as substrate, in 100 mM citrate phosphate buffer, pH 6.2, temperature not specified in the publication
1.5
-
crude extract enzyme, using L-alanine as substrate, in 100 mM citrate phosphate buffer, pH 6.2, temperature not specified in the publication
1.7
-
crude extract enzyme, using glycine as substrate, in 100 mM citrate phosphate buffer, pH 6.2, temperature not specified in the publication
10.1
-
recombinant enzyme, using glycine as substrate, in 100 mM citrate phosphate buffer, pH 6.2, temperature not specified in the publication
10.4
-
crude extract enzyme, using L-arginine as substrate, in 100 mM citrate phosphate buffer, pH 6.2, temperature not specified in the publication
33.3
-
recombinant enzyme, using L-alanine as substrate, in 100 mM citrate phosphate buffer, pH 6.2, temperature not specified in the publication
63
-
crude extract, at 18C
324.8
-
recombinant enzyme, using L-arginine as substrate, in 100 mM citrate phosphate buffer, pH 6.2, temperature not specified in the publication
464
-
His-tagged recombinant enzyme, after purification, at 18C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2
-
with Lys or Orn as substrate
6 - 6.6
-
with Arg or His as substrate
6.5
-
enzyme form A and B, octopine formation
6.7
-
octopine formation
6.8
-
octopine formation
8.7
-
octopine oxidation
9.2
-
octopine oxidation
9.5
-
octopine oxidation
9.7
-
enzyme form A and B, octopine oxidation
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
-
about 70% of maximal activity at pH 6 and pH 8
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.35
-
theoretical value
5.9
-
calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
hepatopancreas-specific cathodally migrating form
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37000
-
gel filtration
38000
-
equilibrium sedimentation
40000
-
gel filtration
43000
-
His-tagged recombinant enzyme, SDS-PAGE
43300
-
calculated from sequence of cDNA
52000
-
gel filtration
70000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 44300, calculated from amino acid sequence; x * 70000, GST-tagged enzyme, SDS-PAGE
monomer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
His-tag-induced crystallization of OcDH is found to be dependent on the length of the His tag. OcDH-tagless and His6-tagged OcDH do not yield crystals. The purified His5-tagged OcDH yields small crystals. Together with the coenzyme NADH the crystals obtained are single and diffract to 2.1 A resolution. Two distinct domains can be found in OcDH: an NADH-dependent glycerol-3-phosphate dehydrogenase-like domain (domain I) and an octopine dehydrogenase specific domain (domain II; Interpro database). Each domain comprises approximately half of the protein, with domain I containing the classic Rossman fold of dinucleotide-binding proteins
-
in complex with NADH and agmatine, to 2.8 A resolution
-
in complex with NADH, hanging drop vapour diffusion method, using 100 mM MES, pH 7.0, and Na-citrate ranging from 1.0 to 1.2 M in a 1:1 ratio, at 12C
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8.5
-
4C, stable. Loses most of its activity after 24 h at lower or higher pH-values
13323
additional information
-
enzyme form B is more sensitive to alkaline treatments than enzyme form A
13314
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41
-
half-denaturation time: 40 min, enzyme forms A and B
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the apoenzyme is protected against inactivation by NADP+
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
irreversible inactivation by photooxidation in presence of rose bengal
-
13308
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-30C, buffer containing glycerol, NADPH and 2-mercaptoethanol, stable for many weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2 isoenzymes: A and B
-
ammonium sulfate precipitation, Ni2+-NTA column chromatography, and Sephadex G-100 gel filtration
crown-gall tumor-tissue induced by Agrobacterium tumefaciens
glutathione Sepharose column chromatography
-
His5-tagged OcDH and His6-tagged OcDH are purified by Ni-NTA chromatography, yielding almost 20 mg homogenous enzyme per litre of cell culture (purity greater than 98%). The purification of OcDH-tagless requires several chromatographic steps and yields 3-5 mg per litre of cell culture, with a purity of more than 98%
-
Ni-NTA affinity chromatography and Sephadex G-100 gel filtration
-
the biospecific chromatographic affinity purification is not applicable to the purification of the enzyme from Monodonta lineate
-
the biospecific chromatographic affinity purification is not applicable to the purification of the enzyme from Mytilus edulis
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 cells
-
expressed in Escherichia coli ER2566 cells
expressed in Escherichia coli strain ER2566
-
expressed in Escherichia coli with a C-terminal penta His-tag
-
OcDH is cloned and expressed tagless (OcDH-tagless), as a His5-tagged OcDH (OcDH-His5) and as a His6-tagged OcDH variant (OcDHLEHis6) in Escherichia coli. The His tag is always placed at the C-terminus
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C148A
-
the mutant shows reduced activity
C148S
-
the mutant shows reduced activity and is only slightly inhibited by 5,5'-dithiobis(2-nitrobenzoic acid) and p-chloromercuribenzoate
D329A
-
the mutation results in strong increases in Km and decreases in kcat values for pyruvate and L-arginine, but has little effect on the Km and kcat values for NADH
H212A
-
the mutation results in strong increases in Km and decreases in kcat values for pyruvate and L-arginine, but has little effect on the Km and kcat values for NADH
Q118A
reduced activity
Q118D
reduced activity
R324A
-
the mutation results in strong increases in Km and decreases in kcat values for pyruvate and L-arginine, but has little effect on the Km and kcat values for NADH
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
kinetic of renaturation. A fast process involves the formation of a structured intermediate
-
refolding kinetics. Upon reactivation after short denaturation of less than 8 s, about 25% of the activity is recovered in a fast initial phase of 20 s. The slow phase of reactivation, which predominates after long-term denaturation, is determined by a single-first-order reaction
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
molecular biology
-
His-tag-induced crystallization of OcDH is found to be dependent on the length of the His tag