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Information on EC 2.6.1.62 - adenosylmethionine-8-amino-7-oxononanoate transaminase and Organism(s) Escherichia coli and UniProt Accession P12995

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IUBMB Comments
A pyridoxal 5'-phosphate enzyme. S-adenosylhomocysteine can also act as donor.
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This record set is specific for:
Escherichia coli
UNIPROT: P12995
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
7,8-diaminopelargonic acid synthase, bio3-bio1, dapa aminotransferase, 7,8-diaminopelargonic acid transaminase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7,8-diaminopelargonic acid synthase
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DAPA synthase
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7,8-diaminononanoate transaminase
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7,8-diaminopelargonate synthase
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7,8-diaminopelargonic acid aminotransferase
7,8-diaminopelargonic acid synthase
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7-keto-8-aminopelargonic acid aminotransferase
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-
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7-keto-8-aminopelargonic acid-7,8-diaminopelargonic acid aminotransferase
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-
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DAPA aminotransferase
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-
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DAPA AT
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DAPA synthase
DAPA transaminase
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-
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diaminopelargonate synthase
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-
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synthase, diaminopelargonate
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-
-
-
additional information
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the enzyme is a member of fold type I PLP enzyme group, aminotransferase subclass II
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-(methylsulfanyl)-2-oxobutanoate + 7,8-diaminononanoate
show the reaction diagram
reaction mechanism, substrate binding structure, detailed reversible aminotransferase half-reaction, overview, residues Tyr17, Asp147, and conserved Tyr144 and Arg253 are important for catalysis
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-(methylsulfanyl)-2-oxobutanoate + 7,8-diaminononanoate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
amino group transfer
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-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:8-amino-7-oxononanoate aminotransferase
A pyridoxal 5'-phosphate enzyme. S-adenosylhomocysteine can also act as donor.
CAS REGISTRY NUMBER
COMMENTARY hide
37259-71-5
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-(5')-3-methylthiopropylamine + 8-amino-7-oxononanoate
? + (7S,8R)-diaminononanoate
show the reaction diagram
decarboxylated S-adenosyl-L-methionine is as reactive as S-adenosyl-L-methionine
-
-
r
S-adenosyl-L-methionine + 8-amino-7-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
show the reaction diagram
(S,S)-S-adenosyl-L-methionine + 8-amino-7-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
show the reaction diagram
-
first half-reaction is reversible, the second one is irreversible, enzyme does not react with the (R,S)-diastereomer of S-adenosyl-L-methionine
i.e. 7,8-diaminopelargonic acid
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?
S-adenosyl-L-methionine + 7,8-diketopelargonic acid
S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
show the reaction diagram
S-adenosyl-L-methionine + 7-amino-8-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
show the reaction diagram
S-adenosyl-L-methionine + 8-amino-7-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
show the reaction diagram
S-adenosyl-L-methionine + 8-amino-7-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
show the reaction diagram
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
S-adenosyl-L-methionine + 8-amino-7-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
show the reaction diagram
second of 4 steps in the biosynthesis of vitamin H, i.e. biotin
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-
r
S-adenosyl-L-methionine + 8-amino-7-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
show the reaction diagram
S-adenosyl-L-methionine + 8-amino-7-oxononanoate
S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
show the reaction diagram
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biotin synthesis
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
i.e. vitamin B6, dependent on
pyridoxal 5'-phosphate
pyridoxamine 5'-phosphate
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7-amino-8-oxononanoate
7-Keto-8-aminopelargonic acid
8-Amino-7-oxononanoate
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adenine
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8 mM
adenosine
amiclenomycin
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cis-amiclenomycin
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and analogues, overview, irreversible inactivation, kinact. 0.4 min-1, little or no inhibition by the trans-compound, overview
S-Adenosyl-L-(2-hydroxy-4-methylthio)butyric acid
S-adenosyl-L-ethionine
S-adenosyl-L-homocysteine
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5 mM
S-Inosyl-L-(2-hydroxy-4-methylthio)butyric acid
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2 mM
additional information
-
no inhibition by the (R,S)-diastereomer of S-adenosyl-L-methionine
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0006 - 0.15
8-Amino-7-oxononanoate
0.1 - 0.75
S-adenosyl-(5')-3-methylthiopropylamine
0.01 - 3
S-adenosyl-L-methionine
0.001
7-amino-8-oxononanoate
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pH 8.5, 37°C
0.0012 - 0.23
8-Amino-7-oxononanoate
0.032
pyridoxal 5'-phosphate
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pH 8.5, 37°C
0.021
pyridoxamine 5'-phosphate
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pH 8.5, 37°C
0.0002 - 0.2
S-adenosyl-L-methionine
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.012 - 1.7
8-Amino-7-oxononanoate
0.016
S-adenosyl-(5')-3-methylthiopropylamine
pH 9.0, recombinant wild-type enzyme and mutant R253K
0.001 - 0.074
S-adenosyl-L-methionine
0.0021 - 0.8
8-Amino-7-oxononanoate
0.02 - 0.13
S-adenosyl-L-methionine
additional information
additional information
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.025 - 2
7-Keto-8-aminopelargonic acid
0.025
8-Amino-7-oxononanoate
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native enzyme
0.002
amiclenomycin
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native enzyme
additional information
additional information
-
inactivation kinetics
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
47000
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2 * 47000, SDS-PAGE
94000
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gel filtration, sucrose density gradient sedimentation
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant mutant enzymes Y17F, Y144F, D147N, R253A, and R253K, hanging drop method, 20°C, 10 mg/ml protein in solution mixed with equal volume of well solution containing 26-28% PEG 4000, 9-12% methylpentanediol, 100 mM HEPES, pH 7.5, microseeding, 2 days, X-ray diffraction structure determination and analysis at 1.7-2.4 A resolution, modeling
complex of holoenzyme and 7-keto-8-aminopelargonic acid
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hanging drop vapor diffusion method
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D147N
site-directed mutagenesis, mutation of an active site residue, inactive mutant
R253A
site-directed mutagenesis, altered kinetics, highly increased Km for S-adenosyl-L-methionine compared to the wild-type enzyme
R253K
site-directed mutagenesis, altered kinetics compared to the wild-type enzyme
R253M
site-directed mutagenesis, altered kinetics compared to the wild-type enzyme
R253Q
site-directed mutagenesis, altered kinetics compared to the wild-type enzyme
Y144F
site-directed mutagenesis, mutation of an active site residue, highly increased Km for S-adenosyl-L-methionine, highly reduced activity compared to the wild-type enzyme
Y17F
site-directed mutagenesis, mutation of an active site residue, highly reduced activity compared to the wild-type enzyme
R391A
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increased Km for 7,8-diaminopelargonic acid, no significantly altered crystal structure
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 20% glycerol, stable for 1 year
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from strain BL21(DE3)
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpression of wild-type and mutant enzymes
cloning from strain JM101, overexpression in strain BL21(DE3)
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wild-type and R391A mutant
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Stoner, G.L.; Eisenberg, M.A.
Purification and properties of 7,8-diaminopelargonic acid aminotransferase
J. Biol. Chem.
250
4029-4036
1975
Escherichia coli
Manually annotated by BRENDA team
Izumi, Y.; Sato, K.; Tani, Y.; Ogata, K.
Biosynthesis of biotin by microorganisms. XV. 7,8-Diaminopelargonic acid aminotransferase, an enzyme involved in biotin biosynthesis by microorganisms
Agric. Biol. Chem.
39
175-181
1975
Bacillus roseus, Bacillus roseus IAM 1257, Corynebacterium glutamicum, Corynebacterium glutamicum NRRL 2311, Escherichia coli, Escherichia coli AKV 0015, Kocuria rosea, Salmonella enterica subsp. enterica serovar Typhimurium
-
Manually annotated by BRENDA team
Izumi, Y.; Sato, K.; Tani, Y.; Ogata, K.
7,8-Diaminopelargonic acid aminotransferase, an enzyme involved in biotin biosynthesis by microorganisms
Agric. Biol. Chem.
37
2683-2684
1973
Bacillus roseus, Bacillus roseus IAM 1257, Corynebacterium glutamicum, Escherichia coli, Kocuria rosea, Salmonella enterica subsp. enterica serovar Typhimurium
-
Manually annotated by BRENDA team
Stoner, G.L.; Eisenberg, M.A.
Biosynthesis of 7,8-diaminopelargonic acid from 7-keto-8-aminopelargonic acid and S-adenosyl-L-methionine. The kinetics of the reaction
J. Biol. Chem.
250
4037-4043
1975
Corynebacterium glutamicum, Corynebacterium glutamicum NRRL 2311, Escherichia coli
Manually annotated by BRENDA team
Eisenberg, M.A.; Stoner, G.L.
7,8-Diaminopelargonic acid aminotransferase
Methods Enzymol.
62
342-347
1979
Escherichia coli
Manually annotated by BRENDA team
Eliot, A.C.; Sandmark, J.; Schneider, G.; Kirsch, J.F.
The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation
Biochemistry
41
12582-12589
2002
Escherichia coli
Manually annotated by BRENDA team
Kck, H.; Gibson, K.J.; Gatenby, A.A.; Schneider, G.; Lindqvist, Y.
Purification and preliminary x-ray crystallographic studies of recombinant 7,8-diaminopelargonic acid synthase from Escherichia coli
Acta Crystallogr. Sect. D
54
1397-1398
1998
Escherichia coli
Manually annotated by BRENDA team
Kck, H.; Sandmark, J.; Gibson, K.; Schneider, G.; Lindqvist, Y.
Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes
J. Mol. Biol.
291
857-876
1999
Escherichia coli
Manually annotated by BRENDA team
Eliot, A.C.; Kirsch, J.F.
Avoiding the road less traveled: how the topology of enzyme-substrate complexes can dictate product selection
Acc. Chem. Res.
36
757-765
2003
Escherichia coli
Manually annotated by BRENDA team
Mann, S.; Marquet, A.; Ploux, O.
Inhibition of 7,8-diaminopelargonic acid aminotransferase by amiclenomycin and analogues
Biochem. Soc. Trans.
33
802-805
2005
Escherichia coli, Mycobacterium tuberculosis
Manually annotated by BRENDA team
Sandmark, J.; Eliot, A.C.; Famm, K.; Schneider, G.; Kirsch, J.F.
Conserved and nonconserved residues in the substrate binding site of 7,8-diaminopelargonic acid synthase from Escherichia coli are essential for catalysis
Biochemistry
43
1213-1222
2004
Escherichia coli (P12995), Escherichia coli
Manually annotated by BRENDA team
Breen, R.S.; Campopiano, D.J.; Webster, S.; Brunton, M.; Watt, R.; Baxter, R.L.
The mechanism of 7,8-diaminopelargonate synthase; the role of S-adenosylmethionine as the amino donor
Org. Biomol. Chem.
1
3498-3499
2003
Escherichia coli
Manually annotated by BRENDA team