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
5.4.3.5
-
RECOMMENDED NAME
GeneOntology No.
D-ornithine 4,5-aminomutase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
D-ornithine = (2R,4S)-2,4-diaminopentanoate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
group transfer
-
-
intramolecular, amino group
-
isomerization
-
-
-
-
isomerization
-, Q8VPJ5, Q8VPJ6
;
PATHWAY
KEGG Link
MetaCyc Link
D-Arginine and D-ornithine metabolism
-
ornithine degradation II (Stickland reaction)
-
SYSTEMATIC NAME
IUBMB Comments
D-ornithine 4,5-aminomutase
A pyridoxal-phosphate protein that requires a cobamide coenzyme for activity.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Aminomutase, D-ornithine 4,5-
-
-
-
-
D-ornithine aminomutase
Alkaliphilus oremlandii OhlLAs
-
-
-
D-ornithine aminomutase
-
-
-
D-ornithine aminomutase
-
-
D-ornithine aminomutase
-
-
-
D-ornithine aminomutase
-
-
D-ornithine aminomutase
-
-
-
D-ornithine aminomutase
-
-
D-ornithine aminomutase
Thermoanaerobacter pseudethanolicus MB4
-
-
-
D-ornithine aminomutase
-
-
D-ornithine aminomutase
-
-
-
OAM
Q8VPJ5, Q8VPJ6
-
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraE
Alkaliphilus oremlandii OhlLAs
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraE
Clostridium difficile, Clostridium sticklandii
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4 and or-5 are placed elsewhere in the genome
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE and or-4, or-5 is placed elsewhere in the genome
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE and or-4, or-5 is placed elsewhere in the genome
-
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4 and or-5 are placed elsewhere in the genome
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4 and or-5 are placed elsewhere in the genome
-
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraE
Thermoanaerobacter pseudethanolicus MB4
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4 and or-5 are placed elsewhere in the genome
oraE
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4 and or-5 are placed elsewhere in the genome
-
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraS
Alkaliphilus oremlandii OhlLAs
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraS
Clostridium difficile, Clostridium sticklandii
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraS
Thermoanaerobacter pseudethanolicus MB4
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
oraS
-
gene name, one of the two subunits, gene is in synteny with further genes of the ornithine fermentation pathway: or-1, or-2, or-4, oraS, oraE, or-4, or-5
-
ornithine 4,5-aminomutase
-
-
ornithine 4,5-aminomutase
Q8VPJ5, Q8VPJ6
-
CAS REGISTRY NUMBER
COMMENTARY
62213-30-3
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
strain OhlLAs
-
-
Manually annotated by BRENDA team
Alkaliphilus oremlandii OhlLAs
strain OhlLAs
-
-
Manually annotated by BRENDA team
Clostridium difficile
strain 630
-
-
Manually annotated by BRENDA team
-
Q8VPJ5, Q8VPJ6
UniProt
Manually annotated by BRENDA team
strain ATCC 12662
-
-
Manually annotated by BRENDA team
strain DSM 619
-
-
Manually annotated by BRENDA team
strain JW/NM-WN-LF
-
-
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
Thermoanaerobacter pseudethanolicus MB4
strain MB4
-
-
Manually annotated by BRENDA team
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
5'-deoxyadenosylcobalamin
-
Km value 0.00043
adenosylcobalamin
-
dependent on
adenosylcobalamin
-, Q8VPJ5, Q8VPJ6
;
pyridoxal 5'-phosphate
-
required, Km: 0.00036 mM
pyridoxal 5'-phosphate
-
Km value 0.0015
pyridoxal 5'-phosphate
-
dependent on
pyridoxal 5'-phosphate
-, Q8VPJ5, Q8VPJ6
;
vitamin B12
-
required
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2,4-diamino-n-butyric acid
-
competitive
-
2,4-diaminobutyrate
-, Q8VPJ5, Q8VPJ6
;
2,4-Diaminopentanoic acid
-
product inhibition above 0.7 mM
DL-2,4-diaminobutryic acid
-
-
DL-alpha-Lys
-
-
-
potassium phosphate
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
mercaptan
-
keeps essential labile sulfhydryl groups reduced and protects from oxygen
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.44
-
D-Orn
-
coupled assay with C4 dehydrogenase
6.7
-
D-Orn
-
radiochemical assay
0.045
-
D-ornithine
-
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
6.3
-
D-ornithine
-
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.096
-
2,4-diamino-n-butyric acid
-
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.4
9.7
-
half maximal activities at pH 7.4 and 9.7
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
23
49
-
half maximal activities at 23°C and 49°C
PDB
SCOP
CATH
ORGANISM
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
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
12800
-
-, Q8VPJ5, Q8VPJ6
OraS
82900
-
-, Q8VPJ5, Q8VPJ6
OraE
180000
-
-
gel electrophoresis, gel filtration, sucrose density gradient centrifugation
201000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-
2 * 95000-98000, SDS-PAGE
tetramer
-
alpha2beta2, 2 * 12800 + 2 * 82900, deduced from nucleotide sequence
heterotetramer
-, Q8VPJ5, Q8VPJ6
alpha2beta2, OraS, OraE, 2 * 12800 + 2 * 82900; alpha2beta2, OraS, OraE, 2 * 12800 + 2 * 82900
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 enzyme’s ATP-dependent allosteric regulation
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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; 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
-, Q8VPJ5, Q8VPJ6
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
45
-
-
rapid inactivation above 45°C
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
glycerol stabilizes during storage and purification
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
LITERATURE
;
-, Q8VPJ5, Q8VPJ6
enzyme S subunit OraS, expression in Escherichia coli
-
Ni2+ -NTA column chromatography and Q-Sepharose resin chromatography
-
recombinant refolded D-ornithine aminomutase
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
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; for expression in Escherichia coli cells
-, Q8VPJ5, Q8VPJ6
genes oraE and oraS for subunits OraS and OraE, expression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
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 enzyme’s ATP-dependent allosteric regulation. OraS protein alone lowers the Km of KamDE for adenosylcobalamin and pyridoxal phosphate