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Information on EC 5.4.3.5 - D-ornithine 4,5-aminomutase and Organism(s) Acetoanaerobium sticklandii and UniProt Accession E3PY96

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EC Tree
     5 Isomerases
         5.4 Intramolecular transferases
             5.4.3 Transferring amino groups
                5.4.3.5 D-ornithine 4,5-aminomutase
IUBMB Comments
A pyridoxal-phosphate protein that requires a cobamide coenzyme for activity.
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This record set is specific for:
Acetoanaerobium sticklandii
UNIPROT: E3PY96
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Word Map
The taxonomic range for the selected organisms is: Acetoanaerobium sticklandii
The enzyme appears in selected viruses and cellular organisms
Synonyms
ornithine 4,5-aminomutase, d-ornithine aminomutase, d-ornithine 4,5-aminomutase, 4,5-oam, adenosylcobalamin-dependent ornithine 4,5-aminomutase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
adenosylcobalamin-dependent ornithine 4,5-aminomutase
-
ornithine 4,5-aminomutase
-
adenosylcobalamin-dependent ornithine 4,5-aminomutase
Aminomutase, D-ornithine 4,5-
-
-
-
-
D-ornithine aminomutase
-
-
ornithine 4,5-aminomutase
ornithine aminomutase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-ornithine = (2R,4S)-2,4-diaminopentanoate
show the reaction diagram
D-ornithine = (2R,4S)-2,4-diaminopentanoate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
PATHWAY SOURCE
PATHWAYS
-
-
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
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-ornithine
(2R,4S)-2,4-diaminopentanoate
show the reaction diagram
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
DL-ornithine
(2R,4S)-2,4-diaminopentanoate
show the reaction diagram
-
-
-
r
additional information
?
-
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
D-ornithine
(2R,4S)-2,4-diaminopentanoate
show the reaction diagram
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
adenosylcobalamin
pyridoxal 5'-phosphate
5'-deoxyadenosylcobalamin
adenosylcobalamin
pyridoxal 5'-phosphate
vitamin B12
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
in the paramagnetic Co2+ metal center of the cob(II)alamin cofactor
Co2+
in the paramagnetic Co2+ metal center of the cob(II)alamin cofactor
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,4-diaminobutyric acid
-
2,4-diamino-n-butyric acid
-
competitive
2,4-diaminobutyrate
2,4-diaminobutyric acid
-
2,4-Diaminopentanoic acid
-
product inhibition above 0.7 mM
DL-2,4-diaminobutryic acid
-
-
DL-2,4-diaminobutyric acid
DAB, a competitive inhibitor
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
0.03 - 0.453
D-ornithine
0.44 - 6.7
D-Orn
0.029 - 4.9
D-ornithine
0.068 - 0.567
DL-Ornithine
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.032 - 7.6
D-ornithine
0.002 - 1072
D-ornithine
0.0023 - 2.9
DL-Ornithine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.07 - 15.2
D-ornithine
0.014 - 190
D-ornithine
0.034 - 5.11
DL-Ornithine
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0046 - 0.098
2,4-diaminobutyric acid
0.096
2,4-diamino-n-butyric acid
-
-
0.0046 - 2
2,4-diaminobutyrate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4 - 9.7
-
half maximal activities at pH 7.4 and 9.7
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23 - 49
-
half maximal activities at 23°C and 49°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
the enzyme catalyzes the second step in the oxidative breakdown of the amino acid, converting D-ornithine to 2,4-diaminopentanoic acid
evolution
-
the enzyme belongs to the class III dAdoCbl-dependent isomerase family
malfunction
metabolism
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
12800
82900
12800
180000
-
gel electrophoresis, gel filtration, sucrose density gradient centrifugation
201000
-
gel filtration
82900
90000
-
2 * 12800, subunit OraS + 2 * 90000, subunit OraE, alpha2beta2
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterotetramer
alpha2beta2, OraS, OraE, 2 * 12800 + 2 * 82900
tetramer
2 * 12800, subunit OraS + 2 * 82900, subunit OraE, alpha2beta2
dimer
-
2 * 95000-98000, SDS-PAGE
heterotetramer
tetramer
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
analysis of the crystal structure of the active site of ornithine 4,5-aminomutase complexed with the natural substrate D-ornithine, PDB ID 3KOZ
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
PROTEIN VARIANTS
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
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 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
H225A
site-directed mutagenesis
H225Q
site-directed mutagenesis
C700S
site-directed mutagenesis, the beta-subunit mutant shows similar kinetics and activity as the wild-type enzyme
D627A
site-directed mutagenesis, the beta-subunit mutant shows similar kinetics and slightly reduced activity compared to the wild-type enzyme
E338A
E338D
E338Q
E81A
site-directed mutagenesis, inactive beta-subunit mutant
E81D
site-directed mutagenesis, almost inactive beta-subunit mutant
E81Q
site-directed mutagenesis, the beta-subunit mutant shows highly reduced activity compared to wild-type
G128D
site-directed mutagenesis, inactive beta-subunit mutant
G339W
site-directed mutagenesis, the beta-subunit mutant shows altered kinetics and highly reduced activity compared to the wild-type enzyme
H225A
site-directed mutagenesis
H225Q
site-directed mutagenesis
I424E
site-directed mutagenesis, the beta-subunit mutant shows altered kinetics and reduced activity compared to the wild-type enzyme
N226D
site-directed mutagenesis, the beta-subunit mutant shows highly reduced activity compared to wild-type
P343W
site-directed mutagenesis, the beta-subunit mutant shows altered kinetics and highly reduced activity compared to the wild-type enzyme
R297K
site-directed mutagenesis, almost inactive beta-subunit mutant
S162A
site-directed mutagenesis, the beta-subunit mutant shows highly reduced activity compared to wild-type
Y160F
site-directed mutagenesis, almost inactive beta-subunit mutant
Y187A
site-directed mutagenesis, the beta-subunit mutant shows 1260fold reduced activity, compared to wild-type, attributed to a slower rate of external aldimine formation and a diminution of adenosylcobalamin Co-C bond homolysis
Y187F
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
rapid inactivation above 45°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
glycerol stabilizes during storage and purification
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, at a concentration of 0.7 mg/ml, 35% loss of activity after 1 month
-
-80°C, the purified enzyme can be stored in concentrated solution in the presence of 50% glycerol for several months
-
4°C, 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
-
Ni2+ -NTA column chromatography and Q-Sepharose resin chromatography
-
recombinant His-tagged wild-type and beta-subunit mutant enzymes from Escherichia coli
recombinant refolded D-ornithine aminomutase
-
recombinant wild-type and beta-subunit mutant enzymes
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
for expression in Escherichia coli cells
recombinant expression of wild-type and mutant enzymes
enzyme S subunit OraS, expression in Escherichia coli
-
expressed in Escherichia coli strain Rosetta(DE3)pLysS
-
expression of oraA and oraE genes encoding D-ornithine aminomutase in Escherichia coli
-
for expression in Escherichia coli cells
genes oraE and oraS for subunits OraS and OraE, expression in Escherichia coli
-
genes oraS and oraE encode the alpha- and beta-subunit, respectively
genes oraS and oraE encode the alpha- and beta-subunit, respectively, recombinant expression of His-tagged wild-type and beta-subunit mutant enzymes in Escherichia coli strain XL-1 Blue
genes oraS and oraE encoding the alpha- and beta-subunit, recombinant expression of wild-type and beta-subunit mutant enzymes
recombinant expression of wild-type and beta-subunit mutant enzymes
recombinant expression of wild-type and mutant enzymes
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Somack, R.; Costilow, R.N.
Purification and properties of a pyridoxal phosphate and coenzyme B12 dependent D-alpha-ornithine 5,4-aminomutase
Biochemistry
12
2597-2604
1973
Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Chen, H.P.; Wu, S.H.; Lin, Y.L.; Chen, C.M.; Tsay, S.S.
Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-ornithine aminomutase from Clostridium sticklandii
J. Biol. Chem.
276
44744-44750
2001
Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Chen, H.P.; Hsui, F.C.; Lin, L.Y.; Ren, C.T.; Wu, S.H.
Coexpression, purification and characterization of the E and S subunits of coenzyme B(12) and B(6) dependent Clostridium sticklandii D-ornithine aminomutase in Escherichia coli
Eur. J. Biochem.
271
4293-4297
2004
Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Tseng, C.H.; Yang, C.H.; Lin, H.J.; Wu, C.; Chen, H.P.
The S subunit of D-ornithine aminomutase from Clostridium sticklandii is responsible for the allosteric regulation in D-alpha-lysine aminomutase
FEMS Microbiol. Lett.
274
148-153
2007
Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Wolthers, K.R.; Rigby, S.E.; Scrutton, N.S.
Mechanism of radical-based catalysis in the reaction catalyzed by adenosylcobalamin-dependent ornithine 4,5-aminomutase
J. Biol. Chem.
283
34615-34625
2008
Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Fonknechten, N.; Perret, A.; Perchat, N.; Tricot, S.; Lechaplais, C.; Vallenet, D.; Vergne, C.; Zaparucha, A.; Le Paslier, D.; Weissenbach, J.; Salanoubat, M.
A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine
J. Bacteriol.
191
3162-3167
2009
Clostridioides difficile, Acetoanaerobium sticklandii, Cutibacterium acnes, Alkaliphilus metalliredigens, Fervidobacterium nodosum Rt17-B1, Alkaliphilus oremlandii, Petrotoga mobilis, Thermoanaerobacter pseudethanolicus, Natranaerobius thermophilus, Thermosipho melanesiensis, Natranaerobius thermophilus JW/NM-WN-LF, Clostridioides difficile 630, Thermosipho melanesiensis BI429, Petrotoga mobilis SJ95, Thermoanaerobacter pseudethanolicus MB4, Cutibacterium acnes KPA171202, Alkaliphilus oremlandii OhlLAs
Manually annotated by BRENDA team
Wolthers, K.R.; Levy, C.; Scrutton, N.S.; Leys, D.
Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase
J. Biol. Chem.
285
13942-13950
2010
Acetoanaerobium sticklandii (E3PY95), Acetoanaerobium sticklandii (E3PY96), Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Makins, C.; Pickering, A.V.; Mariani, C.; Wolthers, K.R.
Mutagenesis of a conserved glutamate reveals the contribution of electrostatic energy to adenosylcobalamin co-C bond homolysis in ornithine 4,5-aminomutase and methylmalonyl-CoA mutase
Biochemistry
52
878-888
2013
Acetoanaerobium sticklandii (E3PY95), Acetoanaerobium sticklandii (E3PY96), Acetoanaerobium sticklandii, Acetoanaerobium sticklandii DSM 519 (E3PY95), Acetoanaerobium sticklandii DSM 519 (E3PY96)
Manually annotated by BRENDA team
Makins, C.; Miros, F.N.; Scrutton, N.S.; Wolthers, K.R.
Role of histidine 225 in adenosylcobalamin-dependent ornithine 4,5-aminomutase
Bioorg. Chem.
40
39-47
2012
Acetoanaerobium sticklandii (E3PY95), Acetoanaerobium sticklandii (E3PY96), Acetoanaerobium sticklandii DSM 519 (E3PY95), Acetoanaerobium sticklandii DSM 519 (E3PY96)
Manually annotated by BRENDA team
Maity, A.N.; Chen, Y.H.; Ke, S.C.
Large-scale domain motions and pyridoxal-5-phosphate assisted radical catalysis in coenzyme B12-dependent aminomutases
Int. J. Mol. Sci.
15
3064-3087
2014
Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Pang, J.; Li, X.; Morokuma, K.; Scrutton, N.S.; Sutcliffe, M.J.
Large-scale domain conformational change is coupled to the activation of the Co-C bond in the B12-dependent enzyme ornithine 4,5-aminomutase: a computational study
J. Am. Chem. Soc.
134
2367-2377
2012
Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Makins, C.; Whitelaw, D.A.; Mu, C.; Walsby, C.J.; Wolthers, K.R.
Isotope effects for deuterium transfer and mutagenesis of Tyr187 provide insight into controlled radical chemistry in adenosylcobalamin-dependent ornithine 4,5-aminomutase
Biochemistry
53
5432-5443
2014
Acetoanaerobium sticklandii (E3PY95 AND E3PY96), Acetoanaerobium sticklandii
Manually annotated by BRENDA team
Makins, C.; Whitelaw, D.A.; McGregor, M.; Petit, A.; Mothersole, R.G.; Prosser, K.E.; Wolthers, K.R.
Optimal electrostatic interactions between substrate and protein are essential for radical chemistry in ornithine 4,5-aminomutase
Biochim. Biophys. Acta
1865
1077-1084
2017
Acetoanaerobium sticklandii (E3PY95 AND E3PY96), Acetoanaerobium sticklandii, Acetoanaerobium sticklandii DSM 519 (E3PY95 AND E3PY96)
Manually annotated by BRENDA team
Pang, J.; Scrutton, N.S.; Sutcliffe, M.J.
Quantum mechanics/molecular mechanics studies on the mechanism of action of cofactor pyridoxal 5-phosphate in ornithine 4,5-aminomutase
Chemistry
20
11390-11401
2014
Acetoanaerobium sticklandii (E3PY95 AND E3PY96)
Manually annotated by BRENDA team
Menon, B.R.; Menon, N.; Fisher, K.; Rigby, S.E.; Leys, D.; Scrutton, N.S.
Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase
FEBS J.
282
1242-1255
2015
Acetoanaerobium sticklandii (E3PY95 AND E3PY96)
Manually annotated by BRENDA team
Menon, B.R.; Fisher, K.; Rigby, S.E.; Scrutton, N.S.; Leys, D.
A conformational sampling model for radical catalysis in pyridoxal phosphate- and cobalamin-dependent enzymes
J. Biol. Chem.
289
34161-34174
2014
Acetoanaerobium sticklandii (E3PY95 AND E3PY96)
Manually annotated by BRENDA team