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Literature summary for 2.6.1.62 extracted from

  • 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 (2004), Biochemistry, 43, 1213-1222.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
overexpression of wild-type and mutant enzymes Escherichia coli

Crystallization (Commentary)

Crystallization (Comment) Organism
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 Escherichia coli

Protein Variants

Protein Variants Comment Organism
D147N site-directed mutagenesis, mutation of an active site residue, inactive mutant Escherichia coli
R253A site-directed mutagenesis, altered kinetics, highly increased Km for S-adenosyl-L-methionine compared to the wild-type enzyme Escherichia coli
R253K site-directed mutagenesis, altered kinetics compared to the wild-type enzyme Escherichia coli
R253M site-directed mutagenesis, altered kinetics compared to the wild-type enzyme Escherichia coli
R253Q site-directed mutagenesis, altered kinetics compared to the wild-type enzyme Escherichia coli
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 Escherichia coli
Y17F site-directed mutagenesis, mutation of an active site residue, highly reduced activity compared to the wild-type enzyme Escherichia coli

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information single turnover reactions, stopped-flow, wild-type and mutant enzymes Escherichia coli
0.0006
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253M Escherichia coli
0.0008
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253K Escherichia coli
0.001
-
8-Amino-7-oxononanoate pH 9.0, recombinant wild-type enzyme Escherichia coli
0.0014
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253Q Escherichia coli
0.0022
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253A Escherichia coli
0.01
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant R253K Escherichia coli
0.011
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant R253Q Escherichia coli
0.02
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant Y17F Escherichia coli
0.063
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant Y17F Escherichia coli
0.1
-
S-adenosyl-(5')-3-methylthiopropylamine pH 9.0, recombinant mutant R253K Escherichia coli
0.15
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant Y144F Escherichia coli
0.3
-
S-adenosyl-L-methionine pH 9.0, recombinant wild-type enzyme Escherichia coli
0.75
-
S-adenosyl-(5')-3-methylthiopropylamine pH 9.0, recombinant wild-type enzyme Escherichia coli
1
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant R253A Escherichia coli
3
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant Y144F Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
S-adenosyl-L-methionine + 8-amino-7-oxononanoate Escherichia coli second of 4 steps in the biosynthesis of vitamin H, i.e. biotin S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
-
r

Organism

Organism UniProt Comment Textmining
Escherichia coli P12995
-
-

Reaction

Reaction Comment Organism Reaction ID
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-(methylsulfanyl)-2-oxobutanoate + 7,8-diaminononanoate reaction mechanism, substrate binding structure, detailed reversible aminotransferase half-reaction, overview, residues Tyr17, Asp147, and conserved Tyr144 and Arg253 are important for catalysis Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
S-adenosyl-(5')-3-methylthiopropylamine + 8-amino-7-oxononanoate decarboxylated S-adenosyl-L-methionine is as reactive as S-adenosyl-L-methionine Escherichia coli ? + (7S,8R)-diaminononanoate
-
r
S-adenosyl-L-methionine + 8-amino-7-oxononanoate second of 4 steps in the biosynthesis of vitamin H, i.e. biotin Escherichia coli S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
-
r
S-adenosyl-L-methionine + 8-amino-7-oxononanoate the aminotransferase half-reaction is reversible, substrate binding structure Escherichia coli S-adenosyl-4-methylthio-2-oxobutanoate + (7S,8R)-diaminononanoate
-
r

Synonyms

Synonyms Comment Organism
7,8-diaminopelargonic acid synthase
-
Escherichia coli
DAPA synthase
-
Escherichia coli

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
additional information
-
additional information single turnover reactions Escherichia coli
0.001
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant R253A Escherichia coli
0.0035
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant Y17F Escherichia coli
0.009
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant R253K Escherichia coli
0.01
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant R253M Escherichia coli
0.012
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant Y17F Escherichia coli
0.016
-
S-adenosyl-L-methionine pH 9.0, recombinant wild-type enzyme Escherichia coli
0.016
-
S-adenosyl-(5')-3-methylthiopropylamine pH 9.0, recombinant wild-type enzyme and mutant R253K Escherichia coli
0.04
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant Y144F Escherichia coli
0.06
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant Y144F Escherichia coli
0.074
-
S-adenosyl-L-methionine pH 9.0, recombinant mutant R253Q Escherichia coli
0.67
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253M Escherichia coli
0.79
-
8-Amino-7-oxononanoate pH 9.0, recombinant wild-type enzyme Escherichia coli
1.3
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253A Escherichia coli
1.3
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253K Escherichia coli
1.7
-
8-Amino-7-oxononanoate pH 9.0, recombinant mutant R253Q Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
9
-
assay at Escherichia coli

Cofactor

Cofactor Comment Organism Structure
pyridoxal 5'-phosphate i.e. vitamin B6, dependent on Escherichia coli