Information on EC 5.4.3.4 - D-lysine 5,6-aminomutase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
5.4.3.4
-
RECOMMENDED NAME
GeneOntology No.
D-lysine 5,6-aminomutase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
group transfer
-
-
intramolecular, amino group
-
isomerization
-
-
-
-
isomerization
-
-
PATHWAY
KEGG Link
MetaCyc Link
Lysine degradation
-
SYSTEMATIC NAME
IUBMB Comments
D-2,6-diaminohexanoate 5,6-aminomutase
Requires a cobamide coenzyme.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
alpha-Lysine mutase
-
-
-
-
Aminomutase, D-lysine 5,6-
-
-
-
-
D-alpha-Lysine mutase
-
-
-
-
lysine 5,6-aminomutase
-
-
Mutase, D-alpha-lysine mutase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9075-70-1
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
lysine 5,6-aminomutase participates in the fermentation of L- or D-lysine as carbon and nitrogen sources in anaerobic bacteria
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(3S)-3,6-diaminohexanoate
(3S,5S)-3,5-diaminohexanoate
show the reaction diagram
-
-, 5,6-LAM has both beta-lysine 5,6-aminomutase and D-lysine 5,6-aminomutase activity
-
?
4-thia-D-lysine
?
show the reaction diagram
-
substrate analogue, suicide inhibitor
-
-
?
4-thia-L-lysine
?
show the reaction diagram
-
substrate analogue, suicide inhibitor
-
-
?
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
-
-
-
-
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
-
-
-
-
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
-
-
-
-
D-alpha-Lysine
2,5-Diaminohexanoate
show the reaction diagram
-
-
-
-
D-alpha-Lysine
?
show the reaction diagram
-
enzyme of lysine fermentation pathway
-
-
-
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
equilibrium constant of 1.2
-
?
D-lysine
D-2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
L-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-, first step in D-lysine catabolism
-
r
L-lysine
L-2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(3S)-3,6-diaminohexanoate
(3S,5S)-3,5-diaminohexanoate
show the reaction diagram
-
-
-
?
D-alpha-Lysine
?
show the reaction diagram
-
enzyme of lysine fermentation pathway
-
-
-
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
D-lysine
2,5-diaminohexanoate
show the reaction diagram
-
equilibrium constant of 1.2
-
?
L-lysine
2,5-diaminohexanoate
show the reaction diagram
-
first step in D-lysine catabolism
-
r
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
5'-deoxyadenosylcobalamin
-
-
adenosylcobalamin
-
-
adenosylcobalamin
-
Km value 6.1 mM, in presence of S-subunit of D-ornithine aminomutase, Km value 3.5 mM, in presence of ATP and S-subunit of D-ornithine aminomutase, Km value 1.9 mM
adenosylcobalamine
-
-
ATP
-
or phosphonic acid analogs, stimulates, allosteric effector
Cobalamin
-
required, directly involved in the catalysis of the amino group migration
Cobalamin
-
coenzyme serves as carrier of the hydrogen that is transferred
FAD
-
slight activation
pyridoxal 5'-phosphate
-
required
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
-
Km value 3.9 mM, in presence of S-subunit of D-ornithine aminomutase, Km value 3.0 mM, in presence of ATP and S-subunit of D-ornithine aminomutase, Km value 2.4 mM
pyridoxal 5'-phosphate
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
K+
-
stimulation by monovalent cations, K+ or NH4+
Mg2+
-
required
Mg2+
-
stimulates
NH4+
-
stimulation by monovalent cations, K+ or NH4+
Zn2+
-
purified KamDE contains a substantial quantity of metal ions, primarily Zn2+
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1,4-diaminobutane
-
-
1-Aminoproline
-
D- and L-form
2-Amino-n-butanoate
-
-
2-amino-n-pentanoic acid
-
-
2-aminoisobutanoate
-
-
3,5-diaminohexanoate
-
-
3-amino-n-butanoate
-
-
3-aminoisobutanoate
-
-
4-amino-n-butanoate
-
-
4-thia-D-lysine
-
suicide inhibitor
4-thia-L-lysine
-
suicide inhibitor
6-Amino-n-hexanoic acid
-
-
DL-delta-hydroxylysine
-
-
DL-epsilon-N-Acetyllysine
-
-
glycoprotein intrinsic factor
-
-
-
Isonicotinic acid hydrazide
-
-
L-2,4-diamino-n-butyrate
-
-
N-Acetylimidazole
-
-
S-aminoethylcysteine
-
-
Tetranitromethane
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
ATP
-
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 128000 Da 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. ATP lowers the Km value of the KamDE-OraS complex for adenosylcobalamin and pyridoxal phosphate
mercaptan
-
e.g. 1,4-dimercaptothreitol required
mercaptan
-
required
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
9
9.2
-
Tris/HCl buffer
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
8
10.5
-
pH 8.0: about 55% of maximal activity, pH 10.5: about 65% of maximal activity, no activity at pH 7
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
-
enzyme assay
PDB
SCOP
CATH
ORGANISM
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
250000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
tetramer
-
alpha2,beta2, 2 * 55000 + 2 * 30000, SDS-PAGE; alpha2,beta2, 2 * 57261 + 2 * 29191, deduced from nucleotide sequence
heterotetramer
-
alpha2beta2
additional information
-
protein KamDE comprised of the 30 and 51 kDa subunits of the E1 component of D-alpha-lysine aminomutase is catalytically active in absence of the third 12.8 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
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4
-
-
dissociation of complex
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
35
55
-
approx. 50% loss of activity at 43°C after 5 min, almost complete loss of activity at 55°C after 5 min
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
inactivated by irradiation
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-15°C, Tris buffer, pH 8.5-9.0, protein concentration of no less than 3 mg/ml, 20-40% loss of activity after 1 month
-
-20°C, 50% glycerol, protein KamDE comprised of the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase can be stored for several months with significant loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
protein KamDE comprised of the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase, expression in Escherichia coli
-
recombinant and native KamDE
-
recombinant 5,6-LAM
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli
-
genes kamDE coding for the 30000 and 51000 Da subunits of the E1 component of D-alpha-lysine aminomutase, expression in Escherichia coli
-
expression in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C235S
-
9% of wild-type activity
K144Q
-
no activity
K23Q
-
75% of wild-type activity
K377Q
-
0.6% of wild-type activity
K446Q
-
25% of wild-type activity
K58Q
-
33% of wild-type activity
K90Q
-
72% of wild-type activity
additional information
-
protein KamDE comprised of the 30000 and 51000 kDa 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