Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase

Thymidine phosphorylase (TP) is a dual substrate enzyme with two domains. E ach domain binds a substrate. In the crystal structure of Escherichia coli TP, the two domains are arranged so that the two substrate binding sites ar e too far away for the two substrates to directly react. Molecular dynamics simulations reveal a different structure of the enzyme in which the two do mains have moved to place the two substrates in close contact. This structu re has a root-mean-square deviation from the crystal structure of 4.1 Angst rom. Quantum mechanical calculations-using this structure find that the rea ction can proceed by a direct nucleophilic attack with a low barrier. This mechanism is not feasible in the crystal structure environment and is consi stent with the mechanism observed for other N-glycosidic enzymes, Important catalytic roles are found for the three highly conserved residues His 85, Arg 171, and Lys 190. Proteins 1999;37:242-252. (C) 1999 Wiley-Liss, Inc.