Information on EC 5.4.3.2 - lysine 2,3-aminomutase

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The expected taxonomic range for this enzyme is: Bacteria, Archaea

EC NUMBER
COMMENTARY hide
5.4.3.2
-
RECOMMENDED NAME
GeneOntology No.
lysine 2,3-aminomutase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-lysine = (3S)-3,6-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
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-
Lysine degradation
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-
lysine metabolism
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-
SYSTEMATIC NAME
IUBMB Comments
L-lysine 2,3-aminomutase
Activity is stimulated by S-adenosyl-L-methionine and pyridoxal phosphate.
CAS REGISTRY NUMBER
COMMENTARY hide
9075-20-1
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
MG1655, gene yjeK
-
-
Manually annotated by BRENDA team
gene ablA
UniProt
Manually annotated by BRENDA team
gene ablA
UniProt
Manually annotated by BRENDA team
gene ablA
SwissProt
Manually annotated by BRENDA team
L-1689-23
-
-
Manually annotated by BRENDA team
L-1689-23
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(S)-lysine
(S)-beta-lysine
show the reaction diagram
alpha-lysine
beta-lysine
show the reaction diagram
-
-
-
-
?
L-2-aminobutyrate
L-3-aminobutyrate
show the reaction diagram
L-alanine
beta-alanine
show the reaction diagram
L-Lys
(3R)-3,6-diaminohexanoic acid
show the reaction diagram
-
hydrogen transfer is not rate-limiting in reaction. The radical intermediate has (R)-configuration, and stereochemistry is determined by the conformation of the lysine side chain in the active site
-
-
?
L-Lys
(3S)-3,6-Diaminohexanoic acid
show the reaction diagram
L-Lys
?
show the reaction diagram
L-lysine
(3S)-3,6-diaminohexanoate
show the reaction diagram
L-lysine
(3S)-3,6-diaminohexanoic acid
show the reaction diagram
S-adenosylmethionine
5'-deoxyadenosylmethionine
show the reaction diagram
-
-
-
-
r
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
alpha-lysine
beta-lysine
show the reaction diagram
-
-
-
-
?
L-Lys
?
show the reaction diagram
L-lysine
(3S)-3,6-diaminohexanoate
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
S-adenosyl-L-methionine
vitamin B6
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enzyme contains 0.9 M per 230000 MW protein
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cu2+
-
enzyme-bound, occupies cobalt sites in the enzyme under conditions of insufficient cobalt in the growth medium, even the best preparations contain a small amount
Fe
-
contains traces of iron, and activity is enhanced by addition of ferrous ions
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4,5-dehydro-(S)-lysine
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suicide inactivator
4-thia-L-lysine
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substrate analogue, generates a stable analogues of the alpha-Lys radical
Co2+
-
0.1 mM, 80% inhibition
iodoacetic acid
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-
S-adenosylhomocysteine
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competitive towards S-adenosylmethionine
S-aminoethylcysteine
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-
SDS
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50 mM, the rate of inactivation decreases in the presence of L-Lys, S-adenosylmethionine or S-adenosylhomocysteine. The SDS-dissociated enzyme can be slightly reactivated by removal of the detergent by gel filtration or dialysis
trans-4,5-dehydro-L-lysine
Urea
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4 M
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Dithionite
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activity absolutely depends on the addition of dithionite
ethylamine
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saturating ethylamine accelerates the L-alanine reaction 70fold
Ferredoxin
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enzyme activity is dependent on the presence of flavodoxin, ferredoxin, or flavodoxin-NADP+ reductase
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flavodoxin
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enzyme activity is dependent on the presence of flavodoxin, ferredoxin, or flavodoxin-NADP+ reductase
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L-cysteine
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required for in vitro activity
methylamine
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saturating methylamine accelerates the L-2-aminobutyrate reaction 47fold
pyridoxal 5'-phosphate
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required for in vitro activity
Reducing agent
-
required
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S-adenosyl-L-methionine
S-adenosylmethionine
Sodium dithionite
-
required for in vitro activity
sulfhydryl compound
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can reactivate oxygen-inactivated enzyme, optimal activation when 0.9 mM Fe2+ is present
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6.6
L-Lys
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-
8
L-lysine
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.083 - 83
L-Lys
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8
L-lysine
Clostridium subterminale
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at pH 8.0, 37°C, in 0.2 M Na-EPPS buffer
134
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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37°C, pH 8.0
62
recombinant wild-type with His-tag
88
wild-type, Fe-S centers reconstituted
additional information
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-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9.8
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about 50% of maximal activity at pH 6.0 and 9.8
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10 - 60
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about 25% of maximal activity at 10°C and 60°C
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
47000
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6 * 47000, SDS-PAGE
54061
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4 * 54061, electrospry ionization mass spectroscopy
224000
-
gel filtration
230000
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gel filtration
259000
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calculation from sedimentation and diffusion coefficient
285000
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gel filtration, disc gel electrophoresis
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
homodimer
tetramer
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4 * 54061, electrospry ionization mass spectroscopy
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor-diffucion, 2.1 A resolution, a L-selenomethionine-substituted complex of the enzyme with [4Fe-4S]2+, pyridoxal-5'-phosphate, S-adenosyl-L-methionine, and L-alpha-lysine. The unit cell contains a dimer of hydrogen-bonded, domain-swapped dimers
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
inactivation by purification in air, reactivation by prolonged anaerobic incubation with glutathione and dithionite
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3386
rapid inactivation by oxygen
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3375
the enzyme is extremely sensitive to oxidation by air and is active under anaerobic conditions
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714347
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-10°C, 20 mM potassium phosphate buffer, pH 6.7, partially purified enzyme, approximately 25% loss of activity in 2 months
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-10°C, under argon, 30 mM Tris/Cl buffer, pH 7.8, 0.01 mM pyridoxal phosphate, 15% v/v glycerol, 10-15% loss of activity after 3 months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant lysine 2,3-aminomutase, Streptomycin, ammonium sulfate, Sephacryl S-300, DEAE-Sephacryl
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recombinant protein, purification under anaerobic conditions
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Sephacryl S200 gel filtration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
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expression Escherichia coli
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expression in Escherichia coli
gene ablA, DNA and amino acid sequence determination and analysis, phylogenetic analysis, expression in Escherichia coli strain BL21(DE3)
gene yjeK, construction of polycistronic vectors encoding His-tagged or non-tagged EF-P, with YjeA, a class II lysyl-tRNA synthetase, and YjeK and overexpression in Escherichia coli strain BL21(DE3)
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
a deletion mutant is constructed
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expression of the abl operon is strictly salt dependent
expression of the abl operon is strictly salt dependent. Expression of ablA and ablB at the standard NaCl concentration of 38.5 mM is not detectable, but it increases drastically with increasing salt concentrations in the growth medium. The level of transcription of the abl operon is identical in cells grown with 400 or 800 mM NaCl
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D165N
about 0.1% of wild-type activity, 0.23 mol iron and 0.13 mol sulfur per mol of subunit
D172N
no catalytic activity, 0.43 mol iron and 0.13 mol sulfur per mol of subunit
D293N
no catalytic activity, 0.97 mol iron and 0.05 mol sulfur per mol of subunit. Involved in binding of epsilon-aminium and alpha-carboxylate groups of substrate
D330A
no catalytic activity, 1.9 mol iron and 1.3 mol sulfur per mol of subunit. Involved in binding of epsilon-aminium and alpha-carboxylate groups of substrate
D330N
no catalytic activity, 1.0 mol iron and 0.63 mol sulfur per mol of subunit
D96N
less than 1% of wild-type activity, 1.2 mol iron and 0.95 mol sulfur per mol of subunit
E236Q
about 1% of wild-type activity, 0.7 mol iron and 0.5 mol sulfur per mol of subunit
E86Q
about 20% of wild-type activity, 0.5 mol iron and 0.4 mol sulfur per mol of subunit
R130K
no catalytic activity, 0.2 mol iron and 0.3 mol sulfur per mol of subunit
R130Q
no catalytic activity, 0.42 mol iron and 0.2 mol sulfur per mol of subunit
R134K
no catalytic activity, 1.5 mol iron and 1.5 mol sulfur per mol of subunit
R134Q
no catalytic activity, 2.8 mol iron and 2.7 mol sulfur per mol of subunit. Involved in binding of epsilon-aminium and alpha-carboxylate groups of substrate
R135K
about 16% of wild-type activity, 2.4 mol iron and 1.6 mol sulfur per mol of subunit
R135Q
about 1.5% of wild-type activity, 1.8 mol iron and 1.5 mol sulfur per mol of subunit
R136Q
about 1.2% of wild-type activity, 0.48 mol iron and 0.35 mol sulfur per mol of subunit
DELTAabl::pac
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deletion mutant, loss of the ability to synthesise Nepsilon-acetyl-beta-lysine
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
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