The ycdX gene of Escherichia coli encodes the protein of 27 kDa molecular weight that belongs to the PHP superfamily of proteins that have diverse functions. This superfamily includes several types of DNA polymerases (namely the a-subunit of bacterial DNA polymerase III, eukaryotic DNA polymerase b, and family X DNA polymerase), histidinol phosphatases, and a number of uncharacterized protein families. In common for all PHP proteins are the presence of four conserved sequence motifs that contain invariant histidine and aspartate residues implicated in metal ion coordination. As part of DNA polymerases, the PHP domain was suggested to hydrolyse pyrophosphate to shift the reaction equilibrium towards nucleotide polymerization. It cannot be ruled out however that the PHP domain possesses a nuclease activity, particularly in repair polymerases of the X-family. No functional information is available for stand-alone proteins that belong to the PHP superfamily. The YcdX protein is one of them. The crystal structure determination of YcdX, a member of the PHP superfamily, was undertaken as part of a structural genomics effort (http://s2f.carb.nist.gov
) in order to assist with the functional assignment of the protein. The YcdX protein from Escherichia coli was cloned, expressed, and the crystal structure determined at 1.6- resolution. YcdX has an unusual topology of a b7a7 barrel as compared to the more common b8a8 (TIM) barrel. All b-strands are parallel, and their order is consecutive. The deep cleft at the C-terminal side of the barrel contains three metal binding sites ligated to the imidazole and carboxylate groups of the protein. Only four proteins with known structures have a trinuclear zinc catalytic site. All four (nuclease P1, endonuclease IV, alkaline phosphatase, and phospholipase C) hydrolyze the phosphoester bond. This suggests a similar activity for YcdX. Furthermore, endonuclease IV is structurally similar to YcdX since it has a TIM-barrel topology.