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Literature summary extracted from

  • Uda, N.; Matoba, Y.; Oda, K.; Kumagai, T.; Sugiyama, M.
    The structural and mutational analyses of O-ureido-L-serine synthase necessary for D-cycloserine biosynthesis (2015), FEBS J., 282, 3929-3944.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.5.1.47 expression in Escherichia coli Streptomyces lavendulae
2.6.99.3 expression in Escherichia coli Streptomyces lavendulae

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.5.1.47 wild-type and mutant K43A, to 2.25 and 1.9 A resolution, respectively. Each monomer of DcsD takes a typical fold of type II pyridoxal 5'-phosphate enzymes with the cofactor pyridoxal 5'-phosphate covalently bound to invariant Lys residue (Lys43) at the active site. The pyridine ring of pyridoxal 5'-phoshate makes hydrogen bonds with invariant Asn73 and Ser265 residues. Its phosphate group makes hydrogen bonds with Gly177, Thr178, Thr179 and Thr181 residues Streptomyces lavendulae
2.6.99.3 wild-type and mutant K43A, to 2.25 and 1.9 A resolution, respectively. Each monomer of DcsD takes a typical fold of type II pyridoxal 5'-phosphate enzymes with the cofactor pyridoxal 5'-phosphate covalently bound to invariant Lys residue (Lys43) at the active site. The pyridine ring of pyridoxal 5'-phoshate makes hydrogen bonds with invariant Asn73 and Ser265 residues. Its phosphate group makes hydrogen bonds with Gly177, Thr178, Thr179 and Thr181 residues Streptomyces lavendulae

Protein Variants

EC Number Protein Variants Comment Organism
2.5.1.47 K43A mutation in invariant Lys43 residue, inactive. Mutant forms an external aldimine adduct upon addition of L-methionine or O-ureido-L-serine Streptomyces lavendulae
2.5.1.47 S121A decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.5.1.47 S121M decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.5.1.47 V74T decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.5.1.47 Y97F decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.5.1.47 Y97M decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.6.99.3 K43A mutation in invariant Lys43 residue, inactive. Mutant forms an external aldimine adduct upon addition of L-methionine or O-ureido-L-serine Streptomyces lavendulae
2.6.99.3 S121A decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.6.99.3 S121M decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.6.99.3 V74T decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.6.99.3 Y97F decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae
2.6.99.3 Y97M decreased activity for synthesis of ureido-L-serine, increased activity for synthesis of L-cysteine Streptomyces lavendulae

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.5.1.47 0.073
-
 H2S mutant Y97F, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 0.084
-
 H2S mutant Y97M, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 0.095
-
 H2S mutant S121A, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 0.12
-
 H2S wild-type, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 0.14
-
 H2S mutant V74T, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 0.2
-
 H2S mutant S121M, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 9
-
 Hydroxyurea wild-type, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 18
-
 Hydroxyurea mutant Y97F, pH 8.0, 30°C Streptomyces lavendulae

Organism

EC Number Organism UniProt Comment Textmining
2.5.1.47 Streptomyces lavendulae D2Z027
-
-
2.5.1.47 Streptomyces lavendulae ATCC 11924 D2Z027
-
-
2.6.99.3 Streptomyces lavendulae D2Z027
-
-
2.6.99.3 Streptomyces lavendulae ATCC 11924 D2Z027
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.5.1.47 additional information enzyme additionally catalyzes the formation of O-ureido-L-serine from O-acetyl-L-serine and hydroxyurea, reaction of EC 2.6.99.3. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis Streptomyces lavendulae ?
-
 ?
2.5.1.47 additional information enzyme additionally catalyzes the formation of O-ureido-L-serine from O-acetyl-L-serine and hydroxyurea, reaction of EC 2.6.99.3. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis Streptomyces lavendulae ATCC 11924 ?
-
 ?
2.5.1.47 O-acetyl-L-serine
-
 Streptomyces lavendulae L-cysteine + acetate
-
 ?
2.5.1.47 O-acetyl-L-serine
-
 Streptomyces lavendulae ATCC 11924 L-cysteine + acetate
-
 ?
2.6.99.3 additional information enzyme additionally catalyzes the formation of L-cysteine from O-acetyl-L-serine and H2S, reaction of EC 2.5.1.47. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis Streptomyces lavendulae ?
-
 ?
2.6.99.3 additional information enzyme additionally catalyzes the formation of L-cysteine from O-acetyl-L-serine and H2S, reaction of EC 2.5.1.47. The kcat/Km value of DcsD for L-cysteine synthesis is 80fold higher than that for O-ureido-L-serine synthesis Streptomyces lavendulae ATCC 11924 ?
-
 ?
2.6.99.3 O-acetyl-L-serine + hydroxyurea
-
 Streptomyces lavendulae O-ureido-L-serine + acetate
-
 ?
2.6.99.3 O-acetyl-L-serine + hydroxyurea
-
 Streptomyces lavendulae ATCC 11924 O-ureido-L-serine + acetate
-
 ?

Subunits

EC Number Subunits Comment Organism
2.5.1.47 tetramer both in solution and in a crystalline state, crystallization data Streptomyces lavendulae
2.6.99.3 tetramer both in solution and in a crystalline state, crystallization data Streptomyces lavendulae

Synonyms

EC Number Synonyms Comment Organism
2.5.1.47 DcsD
-
 Streptomyces lavendulae
2.6.99.3 DcsD
-
 Streptomyces lavendulae

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.5.1.47 10
-
 H2S mutant Y97F, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 12
-
 H2S wild-type, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 15
-
 H2S mutant S121A, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 22
-
 H2S mutant Y97M, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 26
-
 H2S mutant V74T, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 44
-
 H2S mutant S121M, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 4.6
-
 Hydroxyurea mutant Y97F, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 11
-
 Hydroxyurea wild-type, pH 8.0, 30°C Streptomyces lavendulae

Cofactor

EC Number Cofactor Comment Organism Structure
2.5.1.47 pyridoxal 5'-phosphate
-
 Streptomyces lavendulae
2.6.99.3 pyridoxal 5'-phosphate
-
 Streptomyces lavendulae

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2.5.1.47 100
-
 H2S wild-type, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 140
-
 H2S mutant Y97F, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 160
-
 H2S mutant S121A, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 190
-
 H2S mutant V74T, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 220
-
 H2S mutant S121M, pH 8.0, 30°C Streptomyces lavendulae
2.5.1.47 260
-
 H2S mutant Y97M, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 0.002
-
 Hydroxyurea mutant S121M, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 0.088
-
 Hydroxyurea mutant Y97M, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 0.094
-
 Hydroxyurea mutant S121A, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 0.22
-
 Hydroxyurea mutant V74T, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 0.25
-
 Hydroxyurea mutant Y97F, pH 8.0, 30°C Streptomyces lavendulae
2.6.99.3 1.2
-
 Hydroxyurea wild-type, pH 8.0, 30°C Streptomyces lavendulae