4c5l Summary

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Structure of the pyridoxal kinase from Staphylococcus aureus in complex with pyridoxal

The structure was published by Nodwell, M.B., Koch, M.F., Alte, F., Schneider, S., and Sieber, S.A., in 2014 in a paper entitled "A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.85 Å and deposited in 2013.

The experimental data on which the structure is based was also deposited.

This PDB entry contains multiple copies of the structure of PHOSPHOMETHYLPYRIMIDINE KINASE.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A PHOSPHOMETHYLPYRIMIDINE KINASE Q99W31 (2-276) (Q99W31_STAAM)search Staphylococcus aureus subsp. aureus Mu50search 100% 276 98%
B PHOSPHOMETHYLPYRIMIDINE KINASE Q99W31 (2-276) (Q99W31_STAAM)search Staphylococcus aureus subsp. aureus Mu50search 100% 276 98%
C PHOSPHOMETHYLPYRIMIDINE KINASE Q99W31 (2-276) (Q99W31_STAAM)search Staphylococcus aureus subsp. aureus Mu50search 100% 276 98%
D PHOSPHOMETHYLPYRIMIDINE KINASE Q99W31 (2-276) (Q99W31_STAAM)search Staphylococcus aureus subsp. aureus Mu50search 100% 276 98%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q99W31 (2 - 276) PHOSPHOMETHYLPYRIMIDINE KINASE Staphylococcus aureus subsp. aureus Mu50

Chain Sequence family (Pfam)
A, B, C, D (Q99W31) PF08543: Phosphomethylpyrimidine kinasesearch

Chain ID Molecular function (GO) Biological process (GO)
A, B, C, D (Q99W31) phosphomethylpyrimidine kinase activitysearch nucleotide bindingsearch kinase activitysearch ATP bindingsearch transferase activitysearch thiamine biosynthetic processsearch phosphorylationsearch

Chain InterPro annotation
A, B, C, D Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinasesearch Pyridoxamine kinase/Phosphomethylpyrimidine kinasesearch Ribokinase-likesearch