Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3′-azido-2′-fluoro-2′,3′-dideoxyuridine

Abstract

The threedimensional structures of thymidine phosphorylase from E. coli containing the bound sulfate ion in the phosphatebinding site and of the co mplex of thymidine phosphorylase with sulfate in the phosphatebinding site and the inhibitor 3'�azido�2'�fluoro�2',3'�dideoxyuridine ( N3FddU ) in the nucleo� sidebinding site were determined at 1.55 and 1.50 A resolution, respectively. The aminoacid residues involved in the ligand binding and the hydrogenbond network in the active site occupied by a large number of bound water molecules are described. A comparison of the structure of thymidine phosphorylase in com� plex with N3 FddU with the structure of pyrimidine nucleoside phosphorylase from St. Aureus in complex with the natural substrate thymidine (PDB_ID: 3H5Q) shows that the substrate and the inhibitor in the nucleosidebinding pocket have different orientations. It is suggested that the position of N3FddU can be influenced by the presence of the azido group, which prefers a hydrophobic environment. In both structures, the active sites of the subunits are in the open conformation.