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Information on EC 5.4.3.2 - lysine 2,3-aminomutase and Organism(s) Clostridium subterminale and UniProt Accession Q9XBQ8

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EC Tree
     5 Isomerases
         5.4 Intramolecular transferases
             5.4.3 Transferring amino groups
                5.4.3.2 lysine 2,3-aminomutase
IUBMB Comments
This enzyme is a member of the 'AdoMet radical' (radical SAM) family. It contains pyridoxal phosphate and a [4Fe-4S] cluster and binds an exchangeable S-adenosyl-L-methionine molecule. Activity in vitro requires a strong reductant such as dithionite and strictly anaerobic conditions. A 5'-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of S-adenosyl-L-methionine, mediated by the iron-sulfur cluster. S-adenosyl-L-methionine is regenerated at the end of the reaction.
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This record set is specific for:
Clostridium subterminale
UNIPROT: Q9XBQ8
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Word Map
The taxonomic range for the selected organisms is: Clostridium subterminale
The enzyme appears in selected viruses and cellular organisms
Synonyms
lysine 2,3-aminomutase, lysine-2,3-aminomutase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Aminomutase, lysine 2,3-
-
-
-
-
L-Lysine-2,3-aminomutase
-
-
-
-
lysine 2,3-aminomutase
-
-
Mutase, lysine 2,3-amino-
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-lysine = (3S)-3,6-diaminohexanoate
show the reaction diagram
L-lysine = (3S)-3,6-diaminohexanoate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
L-lysine 2,3-aminomutase
This enzyme is a member of the 'AdoMet radical' (radical SAM) family. It contains pyridoxal phosphate and a [4Fe-4S] cluster and binds an exchangeable S-adenosyl-L-methionine molecule. Activity in vitro requires a strong reductant such as dithionite and strictly anaerobic conditions. A 5'-deoxyadenosyl radical is generated during the reaction cycle by reductive cleavage of S-adenosyl-L-methionine, mediated by the iron-sulfur cluster. S-adenosyl-L-methionine is regenerated at the end of the reaction.
CAS REGISTRY NUMBER
COMMENTARY hide
9075-20-1
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
L-lysine
(3S)-3,6-diaminohexanoate
show the reaction diagram
-
-
-
?
L-lysine
(3S)-3,6-diaminohexanoic acid
show the reaction diagram
-
-
-
r
L-lysine
L-beta-lysine
show the reaction diagram
-
-
-
r
S-adenosylmethionine
5'-deoxyadenosylmethionine
show the reaction diagram
-
-
-
r
(S)-lysine
(S)-beta-lysine
show the reaction diagram
-
-
-
-
r
L-2-aminobutyrate
L-3-aminobutyrate
show the reaction diagram
-
very low activity
-
-
?
L-alanine
beta-alanine
show the reaction diagram
-
very low activity
-
-
?
L-Lys
(3S)-3,6-diaminohexanoic acid
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
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-lysine
(3S)-3,6-diaminohexanoate
show the reaction diagram
-
-
-
?
L-lysine
L-beta-lysine
show the reaction diagram
-
-
-
r
L-lysine
(3S)-3,6-diaminohexanoate
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
S-adenosyl-L-methionine
[4Fe-4S] cluster
pyridoxal 5'-phosphate
S-adenosyl-L-methionine
-
-
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe
contains traces of iron, and activity is enhanced by addition of ferrous ions
Iron
[4Fe-4S] cluster, 2.7 mol of iron per mol of subunit
Co2+
-
enzyme contains Co2+, required
Zn2+
-
KAM contains 1 Zn2+ per subunit
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4,5-dehydro-(S)-lysine
-
suicide inactivator
4-thia-L-lysine
-
substrate analogue, generates a stable analogues of the alpha-Lys radical
trans-4,5-dehydro-L-lysine
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Dithionite
activity absolutely depends on the addition of dithionite
S-adenosylmethionine
activity absolutely depends on the addition of S-adenosylmethionine
ethylamine
-
saturating ethylamine accelerates the L-alanine reaction 70fold
methylamine
-
saturating methylamine accelerates the L-2-aminobutyrate reaction 47fold
S-adenosylmethionine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
83
L-Lys
-
pH 8.0, 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8
L-lysine
-
at pH 8.0, 37°C, in 0.2 M Na-EPPS buffer
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
62
recombinant wild-type with His-tag
88
wild-type, Fe-S centers reconstituted
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
physiological function
lysine 2,3-aminomutase (LAM) utilizes the radical-SAM machinery to isomerize L-alpha-lysine to L-beta-lysine
additional information
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
KAMA_CLOSU
416
0
47102
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
259000
-
calculation from sedimentation and diffusion coefficient
47000
-
6 * 47000, SDS-PAGE
48000
-
6 * 48000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
homodimer
-
2 * 000, SDS-PAGE
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
PROTEIN VARIANTS
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
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is extremely sensitive to oxidation by air and is active under anaerobic conditions
-
714347
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)pLysS by nickel affinity chromatography, ultrafiltration, and dialysis
recombinant protein, purification under anaerobic conditions
-
Sephacryl S200 gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene kamA, recombinant expression of C-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3)pLysS
expressed in Escherichia coli
-
expression in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Aberhart, D.J.; Gould, S.J.; Lin, H.J.; Thiruvengadam, T.K.; Weiller, B.H.
Stereochemistry of lysine 2,3-aminomutase isolated from Clostridium subterminale strain SB4
J. Am. Chem. Soc.
105
5461-5470
1983
Clostridium subterminale, Clostridium subterminale SB4
-
Manually annotated by BRENDA team
Song, K.B.; Frey, P.A.
Molecular properties of lysine-2,3-aminomutase
J. Biol. Chem.
266
7651-7655
1991
Clostridium subterminale, Clostridium subterminale SB4
Manually annotated by BRENDA team
Aberhart, D.J.
Studies of the mechanism of lysine 2,3-aminomutase
J. Chem. Soc. Perkin Trans. I
1988
343-350
1988
Clostridium subterminale, Clostridium subterminale SB4
-
Manually annotated by BRENDA team
Aberhart, D.J.; Cotting, J.A.
Mechanistic studies on lysine 2,3-aminomutase: carbon-13-deuterium crossover experiments
J. Chem. Soc. Perkin Trans. I
1988
2119-2122
1988
Clostridium subterminale
-
Manually annotated by BRENDA team
Lieder, K.W.; Booker, S.; Ruzicka, F.J.; Beinert, H.; Reed, G.H.; Frey, P.A.
S-Adenosylmethionine-dependent reduction of lysine 2,3-aminomutase and observation of the catalytically functional iron-sulfur centers by electron paramagnetic resonance
Biochemistry
37
2578-2585
1998
Clostridium subterminale
Manually annotated by BRENDA team
Frey, P.A.
Lysine 2,3-aminomutase: is adenosylmethionine a poor man's adenosylcobalamin?
FASEB J.
7
662-670
1993
Clostridium subterminale
Manually annotated by BRENDA team
Cosper, N.J.; Booker, S.J.; Ruzicka, F.; Frey, P.A.; Scott, R.A.
Direct FeS cluster involvement in generation of a radical in lysine 2,3-aminomutase
Biochemistry
39
15668-15673
2000
Clostridium subterminale
Manually annotated by BRENDA team
Wu, W.; Booker, S.; Lieder, K.W.; Bandarian, V.; Reed, G.H.; Frey, P.A.
Lysine 2,3-aminomutase and trans-4,5-dehydrolysine: characterization of an allylic analogue of a substrate-based radical in the catalytic mechanism
Biochemistry
39
9561-9570
2000
Clostridium subterminale
Manually annotated by BRENDA team
Chen, D.; Walsby, C.; Hoffman, B.M.; Frey, P.A.
Coordination and mechanism of reversible cleavage of S-adenosylmethionine by the [4Fe-4S] center in lysine 2,3-aminomutase
J. Am. Chem. Soc.
125
11788-11789
2003
Clostridium subterminale
Manually annotated by BRENDA team
Lepore, B.W.; Ruzicka, F.J.; Frey, P.A.; Ringe, D.
The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale
Proc. Natl. Acad. Sci. USA
102
13819-13824
2005
Clostridium subterminale (Q9XBQ8), Clostridium subterminale
Manually annotated by BRENDA team
Behshad, E.; Ruzicka, F.J.; Mansoorabadi, S.O.; Chen, D.; Reed, G.H.; Frey, P.A.
Enantiomeric free radicals and enzymatic control of stereochemistry in a radical mechanism: the case of lysine 2,3-aminomutases
Biochemistry
45
12639-12646
2006
Clostridium subterminale, Escherichia coli
Manually annotated by BRENDA team
Chen, D.; Frey, P.A.; Lepore, B.W.; Ringe, D.; Ruzicka, F.J.
Identification of structural and catalytic classes of highly conserved amino acid residues in lysine 2,3-aminomutase
Biochemistry
45
12647-12653
2006
Clostridium subterminale (Q9XBQ8), Clostridium subterminale SB4 (Q9XBQ8), Clostridium subterminale SB4
Manually annotated by BRENDA team
Hinckley, G.T.; Frey, P.A.
Cofactor dependence of reduction potentials for [4Fe-4S]2+/1+ in lysine 2,3-aminomutase
Biochemistry
45
3219-3225
2006
Clostridium subterminale, Clostridium subterminale SB4
Manually annotated by BRENDA team
Wang, S.C.; Frey, P.A.
Binding energy in the one-electron reductive cleavage of S-adenosylmethionine in lysine 2,3-aminomutase, a radical SAM enzyme
Biochemistry
46
12889-12895
2007
Clostridium subterminale, Clostridium subterminale SB4
Manually annotated by BRENDA team
Chen, D.; Tanem, J.; Frey, P.A.
Basis for the equilibrium constant in the interconversion of L-lysine and L-beta-lysine by lysine 2,3-aminomutase
Biochim. Biophys. Acta
1774
297-302
2007
Clostridium subterminale, Clostridium subterminale SB4
Manually annotated by BRENDA team
Lees, N.S.; Chen, D.; Walsby, C.J.; Behshad, E.; Frey, P.A.; Hoffman, B.M.
How an enzyme tames reactive intermediates: positioning of the active-site components of lysine 2,3-aminomutase during enzymatic turnover as determined by ENDOR spectroscopy
J. Am. Chem. Soc.
128
10145-10154
2006
Clostridium subterminale, Clostridium subterminale SB4
Manually annotated by BRENDA team
Frey, P.A.; Hegeman, A.D.; Ruzicka, F.J.
The radical SAM superfamily
Crit. Rev. Biochem. Mol. Biol.
43
63-88
2008
Clostridium subterminale (Q9XBQ8)
Manually annotated by BRENDA team
Frey, P.A.; Reed, G.H.
Pyridoxal-5'-phosphate as the catalyst for radical isomerization in reactions of PLP-dependent aminomutases
Biochim. Biophys. Acta
1814
1548-1557
2011
Clostridium subterminale, Clostridium subterminale SB4
Manually annotated by BRENDA team
Ruzicka, F.J.; Frey, P.A.
Kinetic and spectroscopic evidence of negative cooperativity in the action of lysine 2,3-aminomutase
J. Phys. Chem. B
114
16118-16124
2010
Clostridium subterminale, Clostridium subterminale SB4
Manually annotated by BRENDA team
Frey, P.
Travels with carbon-centered radicals. 5'-Deoxyadenosine and 5'-deoxyadenosine-5'-yl in radical enzymology
Acc. Chem. Res.
47
540-549
2014
Clostridium subterminale (Q9XBQ8), Clostridium subterminale SB4 (Q9XBQ8)
Manually annotated by BRENDA team
Horitani, M.; Byer, A.S.; Shisler, K.A.; Chandra, T.; Broderick, J.B.; Hoffman, B.M.
Why nature uses radical SAM enzymes so widely electron nuclear double resonance studies of lysine 2,3-aminomutase show the 5-dAdo? Free radical is never free
J. Am. Chem. Soc.
137
7111-7121
2015
Clostridium subterminale (Q9XBQ8), Clostridium subterminale SB4 (Q9XBQ8), Clostridium subterminale SB4
Manually annotated by BRENDA team