Information on EC 5.4.3.3 - lysine 5,6-aminomutase

for references in articles please use BRENDA:EC5.4.3.3
Word Map on EC 5.4.3.3
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:

The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.4.3.3
-
RECOMMENDED NAME
GeneOntology No.
lysine 5,6-aminomutase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate
show the reaction diagram
D-lysine = (2R,5S)-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
L-lysine fermentation to acetate and butanoate
-
-
lysine metabolism
-
-
Lysine degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
(3S)-3,6-diaminohexanoate 5,6-aminomutase
This enzyme is a member of the 'AdoMet radical' (radical SAM) family. It requires pyridoxal 5'-phosphate and adenosylcobalamin for activity. A 5'-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of adenosylcobalamin, which is regenerated at the end of the reaction.
CAS REGISTRY NUMBER
COMMENTARY hide
9075-69-8
-
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
(3R)-3,6-diaminohexanoate
(3R,5S)-3,5-diaminohexanoate
show the reaction diagram
-
-
-
-
r
(3S)-3,6-diaminohexanoate
(3S,5S)-3,5-diaminohexanoate
show the reaction diagram
(R)-lysine
?
show the reaction diagram
-
best substrate
-
-
?
(S)-beta-lysine
3,5-diaminohexanoate
show the reaction diagram
(S)-lysine
?
show the reaction diagram
-
-
-
-
?
3,6-Diaminohexanoate
3,5-Diaminohexanoate
show the reaction diagram
4-thia-(R)-lysine
?
show the reaction diagram
-
4-thia-(R)-lysine reacts with the complex of pyridoxal 5'-phosphate, adenosylcobalamin, and lysine 5,6-aminomutase to generate cob(II)alamin, 5'-deoxyadenosine, and 4-thialysine-based free radicals
-
-
?
4-thia-(S)-lysine
?
show the reaction diagram
-
4-thia-(S)-lysine reacts with the complex of pyridoxal 5'-phosphate, adenosylcobalamin, and lysine 5,6-aminomutase to generate cob(II)alamin, 5'-deoxyadenosine, and 4-thialysine-based free radicals
-
-
?
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-beta-lysine
L-3,5-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
-
-
alpha-(adenyl)-Co-5'-deoxyadenosyl cobamide
-
tightly bound
Cobalamin
pyridoxal 5'-phosphate
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
-
Mg2+ or Mn2+ required
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
-
-
Diethanolamine/HCl
-
-
DL-citrulline
-
-
DL-delta-hydroxylysine
-
-
DL-epsilon-N-Acetyllysine
-
-
glycoprotein intrinsic factor
-
-
-
Hydroxyadenylcobamide
-
formed during isolation by degradation of enzyme-bound cobamide, strong inhibitor, tightly bound to the protein. Incubation with cobalamin, Mg2+, a mercaptan, and pyridoxal 5'-phosphate displaces the hydroxyadenylcobamide and markedly activates the enzyme
iodoacetamide
Isonicotinic acid hydrazide
-
-
L-2,4-diamino-n-butyrate
-
-
L-beta-Lysine
-
-
N-Acetylimidazole
-
-
phenylhydrazine
-
-
S-aminoethylcysteine
-
-
Tetranitromethane
-
-
Tris
-
and analogs
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2'-deoxyATP
2-oxobutanoate
-
can partially replace pyruvate, which is required for reaction
mercaptan
pyruvate
-
required
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
20
(3R)-3,6-diaminohexanoate
-
pH and temperature not specified in the publication
8.7
(3S)-3,6-diaminohexanoate
-
pH and temperature not specified in the publication
0.3
3,6-Diaminohexanoate
-
-
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
0.0004
(3R)-3,6-diaminohexanoate
-
pH and temperature not specified in the publication
0.48
(3S)-3,6-diaminohexanoate
-
pH and temperature not specified in the publication
0.63
(R)-lysine
-
pH and temperature not specified in the publication
0.48
(S)-beta-lysine
-
pH and temperature not specified in the publication
0.00043
(S)-lysine
-
pH and temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
19.5
-
unit defined as the amounts which allows the formation of 0.001 mM NADPH per min in a coupled assay system
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.8
-
highest activity in triethanolamine/HCl buffer
8.5
-
electron paramagnetic resonance, EPR, sample preparation
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
PDB
SCOP
CATH
ORGANISM
UNIPROT
Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29191
-
alpha2,beta2, 2 * 57261 + 2 * 29191, deduced from nucleotide sequence
30000
-
alpha2,beta2, 2 * 55000 + 2 * 30000, SDS-PAGE
32000
-
2 * 32000 + 2 * 52000, SDS-PAGE
52000
-
2 * 32000 + 2 * 52000, SDS-PAGE
57261
-
alpha2,beta2, 2 * 57261 + 2 * 29191, deduced from nucleotide sequence
60000
-
x * 60000, gel filtration, sulfhydryl component, x * about approximately 150000, gel filtration, cobamide protein component
170000
-
gel filtration
250000
-
gel filtration
300000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 60000, gel filtration, sulfhydryl component, x * about approximately 150000, gel filtration, cobamide protein component
heterodimer
heterotetramer
-
alpha2beta2
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis
-
hanging-drop vapor diffusion method, X-ray structure of substrate-free form, space group P3(1)2(1) with one alphabeta heterodimer per asymmetric unit, a = b = 99.7 A, c = 168.8 A, 2.8 A resolution
-
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
70
-
10 min, sulfhydryl component is destroyed, cobamide protein component loses about 40% of its activity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
highly purified sulfhydryl-enzyme-component is relatively unstable in dilute solutions of low ionic strength. The presence of mercaptans in buffers tends to prevent aggregation. The cobamide enzyme component is stable to a variety of storage conditions even when highly purified
-
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
-
-18°C, partially purified enzyme in solutions containing phosphate or ammonium sulfate
-
-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
-
-22°C, stable for at least 3 months. After 6 months, with repeated freezing and thawing, two-third of the original activity remains
-
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
for expression in Escherichia coli cells
-
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
Show AA Sequence (150 entries)
Please use the Sequence Search for a specific query.