Information on EC 5.4.3.3 - beta-lysine 5,6-aminomutase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.4.3.3
-
RECOMMENDED NAME
GeneOntology No.
beta-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
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 degradation
-
-
lysine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
(3S)-3,6-diaminohexanoate 5,6-aminomutase
Requires a cobamide coenzyme.
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
-
-
?
D-lysine
2,5-diaminohexanoate
show the reaction diagram
L-beta-lysine
L-3,5-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-lysine
2,5-diaminohexanoate
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-deoxyadenosylcobalamin
adenosylcobalamin
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
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4-thia-D-lysine
-
suicide inhibitor
4-thia-L-lysine
-
suicide inhibitor
Diethanolamine/HCl
-
-
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
hydroxylamine
-
-
iodoacetamide
Isonicotinic acid hydrazide
-
-
phenylhydrazine
-
-
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
-
required
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
-
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0004
(3R)-3,6-diaminohexanoate
Clostridium sticklandii
-
pH and temperature not specified in the publication
194882
0.48
(3S)-3,6-diaminohexanoate
Clostridium sticklandii
-
pH and temperature not specified in the publication
20573
0.63
(R)-lysine
Porphyromonas gingivalis
-
pH and temperature not specified in the publication
166192
0.48
(S)-beta-lysine
Porphyromonas gingivalis
-
pH and temperature not specified in the publication
85569
0.00043
(S)-lysine
Porphyromonas gingivalis
-
pH and temperature not specified in the publication
6887
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
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32000
-
2 * 32000 + 2 * 52000, SDS-PAGE
52000
-
2 * 32000 + 2 * 52000, SDS-PAGE
60000
-
x * 60000, gel filtration, sulfhydryl component, x * about approximately 150000, gel filtration, cobamide protein component
170000
-
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
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-18°C, partially purified enzyme in solutions containing phosphate or ammonium sulfate
-
-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
recombinant 5,6-LAM
-
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
-
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