1td2 | pdb_00001td2
Crystal Structure of the PdxY Protein from Escherichia coli
Structural highlights
FunctionPDXY_ECOLI Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxamine, but has negligible activity toward pyridoxal and pyridoxine as substrates.[HAMAP-Rule:MF_01639] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme. Crystal structure of the PdxY Protein from Escherichia coli.,Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V J Bacteriol. 2004 Dec;186(23):8074-82. PMID:15547280[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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