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Literature summary extracted from

  • Nodwell, M.B.; Koch, M.F.; Alte, F.; Schneider, S.; Sieber, S.A.
    A subfamily of bacterial ribokinases utilizes a hemithioacetal for pyridoxal phosphate salvage (2014), J. Am. Chem. Soc., 136, 4992-4999.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.7.1.35
-
 Staphylococcus aureus
2.7.1.49
-
 Staphylococcus aureus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.1.35 native protein and in complex with its substrates to 1.4?1.85 A resolution. The protein shows a typical ribokinase fold with a central large beta-sheet consisting of nine strands, flanked by three and five structurally conserved alpha-helices Staphylococcus aureus
2.7.1.49 native protein and in complex with its substrates to 1.4-1.85 A resolution. The protein shows a typical ribokinase fold with a central large beta-sheet consisting of nine strands, flanked by three and five structurally conserved alpha-helices Staphylococcus aureus

Protein Variants

EC Number Protein Variants Comment Organism
2.7.1.35 C110A residue C110 is mandatory for pyridoxal, but not for pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine turnover Staphylococcus aureus
2.7.1.35 C214A mutant does not turn over pyridoxal, pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine. Residue C214 acts as the catalytic base in the phosphorylation reaction Staphylococcus aureus
2.7.1.49 C110A residue C110 is mandatory for pyridoxal, but not for pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine turnover Staphylococcus aureus
2.7.1.49 C214A mutant does not turn over pyridoxal, pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine. Residue C214 acts as the catalytic base in the phosphorylation reaction Staphylococcus aureus

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.7.1.35 rugulactone selectively modifies the enzyme not at the active site cysteine, but on a remote cysteine residue Staphylococcus aureus
2.7.1.49 rugulactone selectively modifies the enzyme not at the active site cysteine, but on a remote cysteine residue Staphylococcus aureus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.7.1.35 0.111
-
 pyridoxal wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 0.26
-
 pyridoxal mutant C214D, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 1.51
-
 pyridoxine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 1.85
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 1.99
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 2.07
-
 pyridoxine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.111
-
 pyridoxal wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.26
-
 pyridoxal mutant C214D, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 1.51
-
 pyridoxine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 1.85
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 1.99
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 2.07
-
 pyridoxine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus

Organism

EC Number Organism UniProt Comment Textmining
2.7.1.35 Staphylococcus aureus A0A0H3JTP0
-
-
2.7.1.35 Staphylococcus aureus ATCC 700699 A0A0H3JTP0
-
-
2.7.1.49 Staphylococcus aureus A0A0H3JTP0
-
-
2.7.1.49 Staphylococcus aureus ATCC 700699 A0A0H3JTP0
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.1.35 ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine reaction of EC 2.7.1.49 Staphylococcus aureus ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
-
 ?
2.7.1.35 ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine reaction of EC 2.7.1.49 Staphylococcus aureus ATCC 700699 ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
-
 ?
2.7.1.35 ATP + pyridoxal
-
 Staphylococcus aureus ADP + pyridoxal 5'-phosphate
-
 ?
2.7.1.35 ATP + pyridoxal
-
 Staphylococcus aureus ATCC 700699 ADP + pyridoxal 5'-phosphate
-
 ?
2.7.1.35 ATP + pyridoxine
-
 Staphylococcus aureus ADP + pyridoxine 5'-phosphate
-
 ?
2.7.1.35 ATP + pyridoxine
-
 Staphylococcus aureus ATCC 700699 ADP + pyridoxine 5'-phosphate
-
 ?
2.7.1.35 additional information the reactive Cys110 residue in the lid region forms a hemithioactetal intermediate with the 4'-aldehyde of pyridoxal. This hemithioacetal, in concert with the catalytic Cys214, increases the nucleophilicity of the pyridoxal 5'-OH group for the inline displacement reaction with the gamma-phosphate of ATP Staphylococcus aureus ?
-
 ?
2.7.1.35 additional information the reactive Cys110 residue in the lid region forms a hemithioactetal intermediate with the 4'-aldehyde of pyridoxal. This hemithioacetal, in concert with the catalytic Cys214, increases the nucleophilicity of the pyridoxal 5'-OH group for the inline displacement reaction with the gamma-phosphate of ATP Staphylococcus aureus ATCC 700699 ?
-
 ?
2.7.1.49 ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
-
 Staphylococcus aureus ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
-
 ?
2.7.1.49 ATP + pyridoxal reaction of EC 2.7.1.35 Staphylococcus aureus ADP + pyridoxal 5'-phosphate
-
 ?
2.7.1.49 ATP + pyridoxal reaction of EC 2.7.1.35 Staphylococcus aureus ATCC 700699 ADP + pyridoxal 5'-phosphate
-
 ?
2.7.1.49 ATP + pyridoxine reaction of EC 2.7.1.35 Staphylococcus aureus ADP + pyridoxine 5'-phosphate
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.7.1.35 SAV0580
-
 Staphylococcus aureus
2.7.1.49 SAV0580
-
 Staphylococcus aureus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.7.1.35 0.015
-
 pyridoxine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 0.016
-
 pyridoxine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 0.044
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 0.045
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 0.165
-
 pyridoxal wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.35 0.328
-
 pyridoxal mutant C214D, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.015
-
 pyridoxine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.016
-
 pyridoxine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.044
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine mutant C110A, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.045
-
 4-Amino-5-hydroxymethyl-2-methylpyrimidine wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.165
-
 pyridoxal wild-type, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus
2.7.1.49 0.328
-
 pyridoxal mutant C214D, pH not specified in the publication, temperature not specified in the publication Staphylococcus aureus