Information on EC 5.4.3.5 - D-ornithine 4,5-aminomutase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY hide
5.4.3.5
-
RECOMMENDED NAME
GeneOntology No.
D-ornithine 4,5-aminomutase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-ornithine = (2R,4S)-2,4-diaminopentanoate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
group transfer
-
-
intramolecular, amino group
-
isomerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
D-Arginine and D-ornithine metabolism
-
-
L-ornithine degradation II (Stickland reaction)
-
-
urea cycle
-
-
SYSTEMATIC NAME
IUBMB Comments
D-ornithine 4,5-aminomutase
A pyridoxal-phosphate protein that requires a cobamide coenzyme for activity.
CAS REGISTRY NUMBER
COMMENTARY hide
62213-30-3
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain QYMF
-
-
Manually annotated by BRENDA team
strain OhlLAs
-
-
Manually annotated by BRENDA team
strain OhlLAs
-
-
Manually annotated by BRENDA team
strain JW/NM-WN-LF
-
-
Manually annotated by BRENDA team
strain JW/NM-WN-LF
-
-
Manually annotated by BRENDA team
strain 630
-
-
Manually annotated by BRENDA team
strain 630
-
-
Manually annotated by BRENDA team
strain SJ95
-
-
Manually annotated by BRENDA team
strain SJ95
-
-
Manually annotated by BRENDA team
strain KPA171202
-
-
Manually annotated by BRENDA team
strain KPA171202
-
-
Manually annotated by BRENDA team
strain MB4
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
-
the enzyme belongs to the class III dAdoCbl-dependent isomerase family
metabolism
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
D-Orn
?
show the reaction diagram
-
enzyme of ornithine fermentation
-
-
-
D-Orn
L(4S)-2,4-Diaminopentanoate
show the reaction diagram
-
r
-
-
D-ornithine
(2R,4S)-2,4-diaminopentanoate
show the reaction diagram
additional information
?
-
-
subunit OraS of the enzyme is capable of forming a complex with recombinant enzyme (KamDE) containing only E1 of lysine 5,6-aminomutase, EC 5.4.3.4, and restores its allosteric regulation by ATP
-
-
-
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
D-Orn
?
show the reaction diagram
-
enzyme of ornithine fermentation
-
-
-
D-ornithine
(2R,4S)-2,4-diaminopentanoate
show the reaction diagram
additional information
?
-
-
subunit OraS of the enzyme is capable of forming a complex with recombinant enzyme (KamDE) containing only E1 of lysine 5,6-aminomutase, EC 5.4.3.4, and restores its allosteric regulation by ATP
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-deoxyadenosylcobalamin
adenosylcobalamin
pyridoxal 5'-phosphate
vitamin B12
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
in the paramagnetic Co2+ metal center of the cob(II)alamin cofactor; in the paramagnetic Co2+ metal center of the cob(II)alamin cofactor
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,4-diamino-n-butyric acid
-
competitive
-
2,4-diaminobutyric acid
-
;
2,4-Diaminopentanoic acid
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product inhibition above 0.7 mM
DL-2,4-diaminobutryic acid
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-
DL-alpha-Lys
-
-
-
iodoacetate
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-
L-alpha-Orn
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-
potassium phosphate
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
mercaptan
-
keeps essential labile sulfhydryl groups reduced and protects from oxygen
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.44 - 6.7
D-Orn
0.03 - 0.453
D-ornithine
additional information
additional information
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.032 - 7.6
D-ornithine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.07 - 15.2
D-ornithine
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.096
2,4-diamino-n-butyric acid
-
-
-
0.0046 - 0.098
2,4-diaminobutyric acid
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
assay at; assay at
8.5
-
assay at; assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4 - 9.7
-
half maximal activities at pH 7.4 and 9.7
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
assay at; assay at
30
-
assay at; assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23 - 49
-
half maximal activities at 23C and 49C
PDB
SCOP
CATH
ORGANISM
UNIPROT
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
180000
-
gel electrophoresis, gel filtration, sucrose density gradient centrifugation
201000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
2 * 95000-98000, SDS-PAGE
heterotetramer
alpha2beta2, OraS, OraE, 2 * 12800 + 2 * 82900; alpha2beta2, OraS, OraE, 2 * 12800 + 2 * 82900
tetramer
additional information
-
protein KamDE comprised of the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase is catalytically active in absence of the third 12800 kDa subunit, but ATP no longer has a regulatory effect on it. The S subunit of D-ornithine aminomutase, OraS, is capable of forming a complex with KamDE and restores the enzymes ATP-dependent allosteric regulation
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis
-
the structure of substrate-free ornithine 4,5-aminomutase is solved to a resolution of 2.0 A, furthermore the structures of the enzyme in complex with D-ornithine and in complex with the inhibitor 2,4-diaminobutyrate are determined; the structure of substrate-free ornithine 4,5-aminomutase is solved to a resolution of 2.0 A, furthermore the structures of the enzyme in complex with D-ornithine and in complex with the inhibitor 2,4-diaminobutyrate are determined
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
rapid inactivation above 45C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
glycerol stabilizes during storage and purification
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, at a concentration of 0.7 mg/ml, 35% loss of activity after 1 month
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-80C, the purified enzyme can be stored in concentrated solution in the presence of 50% glycerol for several months
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4C, 20% glycerol v/v or 0.02 mM coenzyme B12, enzyme concentration 1.0 mg/ml, 9% loss of activity after 2 d
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme S subunit OraS, expression in Escherichia coli
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Ni2+ -NTA column chromatography and Q-Sepharose resin chromatography
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recombinant refolded D-ornithine aminomutase
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme S subunit OraS, expression in Escherichia coli
-
expressed in Escherichia coli strain Rosetta(DE3)pLysS
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expression of oraA and oraE genes encoding D-ornithine aminomutase in Escherichia coli
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for expression in Escherichia coli cells; for expression in Escherichia coli cells
genes oraE and oraS for subunits OraS and OraE, expression in Escherichia coli
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recombinant expression of wild-type and mutant enzymes; recombinant expression of wild-type and mutant enzymes
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E338A
-
site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 670fold and catalytic efficiency 220fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate; site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 670fold and catalytic efficiency 220fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate
E338D
-
site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 380fold and catalytic efficiency 60fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows n detectable adenosylcobalamin homolysis upon binding of the physiological substrate; site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 380fold and catalytic efficiency 60fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate
E338Q
-
site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 90fold and catalytic efficiency 20fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate; site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 90fold and catalytic efficiency 20fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate
H225A
-
site-directed mutagenesis; site-directed mutagenesis
H225Q
-
site-directed mutagenesis; site-directed mutagenesis
E338A
-
site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 670fold and catalytic efficiency 220fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate; site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 670fold and catalytic efficiency 220fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate
-
E338D
-
site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 380fold and catalytic efficiency 60fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows n detectable adenosylcobalamin homolysis upon binding of the physiological substrate; site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 380fold and catalytic efficiency 60fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate
-
E338Q
-
site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 90fold and catalytic efficiency 20fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate; site-directed mutagenesis, substrate binding of the mutant is unaffected, but kcat is reduced 90fold and catalytic efficiency 20fold compared to the wild-type enzyme. The rate of external aldimine formation in the mutant is similar to that of the wild-type enzyme, but it shows no detectable adenosylcobalamin homolysis upon binding of the physiological substrate
-
H225A
-
site-directed mutagenesis; site-directed mutagenesis
-
H225Q
-
site-directed mutagenesis; site-directed mutagenesis
-
additional information
-
protein KamDE comprised of the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase is catalytically active in absence of the third 12800 kDa subunit, but ATP no longer has a regulatory effect on it. The S subunit of D-ornithine aminomutase, OraS, is capable of forming a complex with KamDE and restores the enzymes ATP-dependent allosteric regulation. OraS protein alone lowers the Km of KamDE for adenosylcobalamin and pyridoxal phosphate