Information on EC 4.3.1.12 - ornithine cyclodeaminase

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

EC NUMBER
COMMENTARY hide
4.3.1.12
-
RECOMMENDED NAME
GeneOntology No.
ornithine cyclodeaminase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-ornithine = L-proline + NH3
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Arginine and proline metabolism
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-
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
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L-arginine degradation VII (arginase 3 pathway)
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-
L-ornithine degradation I (L-proline biosynthesis)
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arginine metabolism
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-
SYSTEMATIC NAME
IUBMB Comments
L-ornithine ammonia-lyase (cyclizing; L-proline-forming)
Requires NAD+. The enzyme is a member of the mu-crystallin protein family [4]. The reaction is stimulated by the presence of ADP or ATP and is inhibited by O2 [2].
CAS REGISTRY NUMBER
COMMENTARY hide
9054-76-6
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain ATCC 13032
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
2011, wild-type
-
-
Manually annotated by BRENDA team
41, wild-type
-
-
Manually annotated by BRENDA team
GR4, wild-type
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
NCBInr database XP_00131964; causes sexually transmitted disease (STD), ornithine cyclodeamidase isoforms are exclusively expressed by the highly virulent isolate
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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T-DNA mutants of atocd and AtOCD RNAi plants have 15% higher proline accumulation at low water potential while p5cs1-4/atocd double mutants have 40% higher proline than p5cs1 at low water potential but no change in proline metabolism gene expression
metabolism
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catalyzes step 10 in the ornithine fermentation pathway
physiological function
-
AtOCD is stress and proline induced and lack of AtOCD expression increases proline accumulation
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
L-ornithine
?
show the reaction diagram
L-ornithine
L-proline + NH3
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
L-ornithine
?
show the reaction diagram
L-ornithine
L-proline + NH3
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ADP
-
stimulates
ATP
-
stimulates
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
iodoacetate
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-
N-ethylmaleimide
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2 mM, complete inhibition
p-chloromercuribenzoate
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1 mM, complete inhibition
proline
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10 mM: 30% inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
L-arginine
additional information
-
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25 - 11.1
L-ornithine
0.0061
NAD+
-
-
additional information
additional information
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 8.5
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OCD, Ach5
8 - 9.5
8.5 - 9
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in the presence of L-arginine
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.6 - 9.8
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50% of maximal activity at pH 6.6 and pH 9.8
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 35
30 - 35
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OCD, Ach5
38 - 42
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
33 - 52
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50% of maximal activity at 33°C and 52°C
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.34
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theoretical value
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
lysates of parasite culture isolates FF28JT-Rio (low virulent) and FMV-1 (highly virulent)
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
36130
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calculated by the database algorithmn, confirmed by PAGE
39500
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2 * 39500, OCD, Ach5, calculation from sequence of amino acid
41500
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2 * 41500, SDS-PAGE
42000
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2 * 42000, OCD, Ach5, SDS-PAGE
80220
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amino acid analysis
81000
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equilibrium sedimentation
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor diffusion method, crystal structure of the enzyme in complex with NADH, refined to 1.8 A resolution, crystal structure of crystals grown in presence of L-ornithine, refined to 1.6 A resolution
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vapor-diffusion method, the best diffraction-quality crystals are obtained from solutions of 40%(v/v) 2-methyl-2,4-pentanediol buffered at pH 6.0 with 0.1 M MES and diffracted X-rays to 1.68 A resolution. Crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 70.0, b = 78.3, c = 119.4 A
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
low concentrations of ornithine stabilize
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ornithine, NAD+ and dithiothreitol stabilize
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
addition of dithiothreitol and subsequent incubation in argon atmosphere completely reverses the inhibition caused by oxygen
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34265
enzyme activity in the presence of air is 80 to 90% of those in argon atmosphere
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34264
enzyme is sensitive to either pure oxygen or air
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34265
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-10°C, rapid loss of activity during storage
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-20°C, OCD, Arch5, and OCD, C58, stable for several months without loss of activity
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4°C, 50% loss of activity under argon atmosphere within 3 days
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crude extracts can be frozen and thawed without significant loss of activity
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enzyme can be frozen and thawed repeatedly without loss of activity
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stable for at least 1 year when stored in sealed ampoules in argon atmosphere in liquid nitrogen
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in an ornithine overproducing platform strain with deletions of argR and argF (ORN1) from Corynebacterium glutamicum
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expression in Escherichia coli
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expression in Escherichia coli XL-2-Blue
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expression in Escherichia coli; OCD, Arch5, and OCD, C58
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression of AtOCD is induced by low water potential stress and by exogenous proline
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
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expression of ocd from Pseudomonas putida in an ornithine overproducing platform strain with deletions of argR and argF (ORN1) from Corynebacterium glutamicum results in proline production with yields up to 0.31 g proline/g glucose
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