Information on EC 1.5.1.11 - D-octopine dehydrogenase

for references in articles please use BRENDA:EC1.5.1.11
Word Map on EC 1.5.1.11
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:


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

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
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
pyruvate fermentation to opines
-
-
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
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Cardium tuberculatum
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Chlamys opercularis
-
-
-
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
-
-
-
Manually annotated by BRENDA team
2 allozymic forms are distributed in a highly population-specific manner, enzyme variants: ss, ff, and sf
-
-
Manually annotated by BRENDA team
from Hawaii
-
-
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
-
-
-
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
collected in the straits of Messina area (central Mediterranean) between May and June of 2011, from two nearby marine and brackish-water sites, two populations
-
-
Manually annotated by BRENDA team
Priapulus sp.
-
-
-
Manually annotated by BRENDA team
-
-
-
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
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
-
bivalves have evolved diverse and highly specialised strategies for surviving in hypoxic episodes including pathways that are efficient both in terms of ATP production, and in minimising H+ and toxic end product accumulation. Under these circumstances, glycogen is metabolized to pyruvate and the cytosolic NADH/NAD+ redox ratio is balanced by the reduction of pyruvate to lactate. Alternatively, NAD+ can be recycled more efficiently by coupling an amino acid to pyruvate, with formation of opines such as alanopine, tauropine, octopine, and strombine. Specimens utilizing the octopine rather than the alanopine pathway will increase energy flow rapidly, developing a major ability to counteract environmental variations. The high ratio between malate dehydrogenase/lactate dehydrogenase is due to the ability of Pinna nobilis to turn on anaerobic metabolism as a consequence of environmental or anthropogenic stresses. Anaerobic pathways are not all equivalent in terms of energy production based upon maximum rates for ATP output (lactate > octopine > alanopine = strombine). The ODH pathway is probably able to realize a higher rate of energy production than either the SDH or ADH pathways
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
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
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
-
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
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
the enzyme activity in adductor muscle increases following the marine-brackish gradient
-
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 25°C
49.8
2-oxovalerate
wild type enzyme, in 50 mM triethanolamine buffer, pH 7.0, at 25°C
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
wild type enzyme, in 50 mM triethanolamine buffer, pH 7.0, at 25°C
272
2-oxovalerate
wild type enzyme, in 50 mM triethanolamine buffer, pH 7.0, at 25°C
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 18°C
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 18°C
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
7.2
-
assay at
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
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
assay at
28
-
assay at
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
-
ODH is the major opine dehydrogenase in the adductor muscle
Manually annotated by BRENDA team
additional information
-
enzyme tissue distribution and expression analysis
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
34900
-
1 * 34900, SDS-PAGE
35800
-
1 * 35800, equilibrium sedimentation with guanidine hydrochloride
37000
-
gel filtration
40000
-
gel filtration
41500
-
1 * 41500, SDS-PAGE
43300
-
calculated from sequence of cDNA
44300
-
x * 44300, calculated from amino acid sequence
46000
-
1 * 46000, SDS-PAGE
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 12°C
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8.5
-
4°C, 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
-30°C, 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
-
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, ultrafiltration, dialysis, and 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
-
gene ocs, DNA and amino acid sequence determination, analysis, and comparisons, genetic structure, phylogenetic analysis, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
-
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