A Three Dimensional Model of Human Thiopurine Methyltransferase; Ligand Interactions and Structural Consequences of Naturally Occurring Mutations

Abstract

The three-dimensional model of human thiopurine methyltransferase (hTPMT) was constructed by molecular modeling. A multiple alignment of AdoMet dependent methyltransferases based on a structural superposition of the AdoMet binding domain of Hhai, TaqI and rCOMT was used in the modeling procedure. The reliability of the model was examined by comparing its conformation and packing properties with those of Hhai, TaqI and rCOMT and structures in the PDB-database. The examined criteria indicated a reliable model structure. The model gave insight into the structural effects of naturally occurring mutations of the hTPMT allele, and was used to characterize the ligand interactions of the protein. The residues Gln42 and Glu91 were predicted to participate in AdoMet binding through H-bond interactions whereas Phe146 participates through Van der Waal interaction. The cationic methyl-sulphonium group of AdoMet was located close to the aromatic residue Phe40. The model also indicated that substrates interact with hTPMT situated in a pocket consisting of the hydrophobic residues Phe40, Met148, Val184, Val220 and the charged residues Lys145, Glu218, Lys219. These residues were also included in a predictive explanation for the inhibitor/substrate preference of the enzyme. The most frequent of naturally occurring mutations was predicted to cause alterations on the surface of the protein with minor/none structural consequences. The mutation Ala80-Pro seemed directly to cause an inactive enzyme by disrupting the structure of the binding site of AdoMet.