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Literature summary for 2.7.1.35 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)

Cloned (Comment) Organism
-
Staphylococcus aureus

Crystallization (Commentary)

Crystallization (Comment) Organism
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

Protein Variants Comment Organism
C110A residue C110 is mandatory for pyridoxal, but not for pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine turnover Staphylococcus aureus
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

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

KM Value [mM]

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

Organism

Organism UniProt Comment Textmining
Staphylococcus aureus A0A0H3JTP0
-
-
Staphylococcus aureus ATCC 700699 A0A0H3JTP0
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine reaction of EC 2.7.1.49 Staphylococcus aureus ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
-
?
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
-
?
ATP + pyridoxal
-
Staphylococcus aureus ADP + pyridoxal 5'-phosphate
-
?
ATP + pyridoxal
-
Staphylococcus aureus ATCC 700699 ADP + pyridoxal 5'-phosphate
-
?
ATP + pyridoxine
-
Staphylococcus aureus ADP + pyridoxine 5'-phosphate
-
?
ATP + pyridoxine
-
Staphylococcus aureus ATCC 700699 ADP + pyridoxine 5'-phosphate
-
?
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 ?
-
?
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 ?
-
?

Synonyms

Synonyms Comment Organism
SAV0580
-
Staphylococcus aureus

Turnover Number [1/s]

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