title: Crystal structure of the PdxY Protein from Escherichia coli.
abstract: The 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.
authors.affiliation: Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA . msafo@mail2.vcu.edu
authors.forename: Martin K
authors.initials: MK
authors.lastname: Safo
authors.forename: Faik N
authors.initials: FN
authors.lastname: Musayev
authors.forename: Sharyn
authors.initials: S
authors.lastname: Hunt
authors.forename: Martino L
authors.initials: ML
authors.lastname: di Salvo
authors.forename: Neel
authors.initials: N
authors.lastname: Scarsdale
authors.forename: Verne
authors.initials: V
authors.lastname: Schirch
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites; D003460:Crystallization; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000145:classification; D011730:Pyridoxal / Q000378:metabolism; D011731:Pyridoxal Kinase / Q000737:chemistry* / Q000502:physiology
chemical_list: D029968:Escherichia coli Proteins; D011730:Pyridoxal; D000255:Adenosine Triphosphate; D017853:Phosphotransferases (Alcohol Group Acceptor); C022534:ribokinase; D011731:Pyridoxal Kinase