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 hide
5.4.3.4
-
RECOMMENDED NAME
GeneOntology No.
D-lysine 5,6-aminomutase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-Lysine = 2,5-diaminohexanoate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
group transfer
-
-
intramolecular, amino group
-
isomerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Lysine degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
D-2,6-diaminohexanoate 5,6-aminomutase
Requires a cobamide coenzyme.
CAS REGISTRY NUMBER
COMMENTARY hide
9075-70-1
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
subsp. shermanii
-
-
Manually annotated by BRENDA team
subsp. shermanii
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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
(3S)-3,6-diaminohexanoate
(3S,5S)-3,5-diaminohexanoate
show the reaction diagram
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
?
show the reaction diagram
-
enzyme of lysine fermentation pathway
-
-
-
D-lysine
2,5-diaminohexanoate
show the reaction diagram
D-lysine
D-2,5-diaminohexanoate
show the reaction diagram
-
-
-
-
?
L-lysine
2,5-diaminohexanoate
show the reaction diagram
L-lysine
L-2,5-diaminohexanoate
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
(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
L-lysine
2,5-diaminohexanoate
show the reaction diagram
-
first step in D-lysine catabolism
-
r
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-deoxyadenosylcobalamin
adenosylcobalamin
adenosylcobalamine
-
-
Cobalamin
FAD
-
slight activation
pyridoxal 5'-phosphate
additional information
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
stimulation by monovalent cations, K+ or NH4+
NH4+
-
stimulation by monovalent cations, K+ or NH4+
Zn2+
-
purified KamDE contains a substantial quantity of metal ions, primarily Zn2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
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-citrulline
-
-
DL-delta-hydroxylysine
-
-
DL-epsilon-N-Acetyllysine
-
-
glycoprotein intrinsic factor
-
-
-
hydroxylamine
-
-
iodoacetamide
-
-
Isonicotinic acid hydrazide
-
-
L-2,4-diamino-n-butyrate
-
-
L-beta-Lysine
-
-
N-Acetylimidazole
-
-
n-Hexanoate
-
-
S-aminoethylcysteine
-
-
Tetranitromethane
-
-
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
mercaptan
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.02
D-Lysine
-
pH and temperature not specified in the publication
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.63
D-Lysine
Clostridium sticklandii
-
pH and temperature not specified in the publication
1531
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9 - 9.2
-
Tris/HCl buffer
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
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
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
enzyme assay
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
250000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterotetramer
-
alpha2beta2
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4
-
dissociation of complex
3401
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
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
LITERATURE
inactivated by irradiation
-
STORAGE STABILITY
ORGANISM
UNIPROT
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
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 5,6-LAM
-
recombinant and native KamDE
-
recombinant enzyme from Escherichia coli
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme expression in Escherichia coli
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
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Y263F
-
the mutation abolishes the enzymatic activity
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