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Journal of Bacteriology, December 2004, p. 8074-8082, Vol. 186, No. 23
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.23.8074-8082.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Crystal Structure of the PdxY Protein from Escherichia coli

Department of Medicinal Chemistry,¹ Department of Biochemistry,² Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia,³ Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Università La Sapienza, Rome, Italy⁴

Received 1 June 2004/ Accepted 25 August 2004

The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-Å 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.

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