S-adenosylmethionine-dependent methyltransferases (AdoMet-dependent MTases) are a main subfamily of MTases, which play critical roles in diverse methylation reactions in many significant biological processes. AdoMet-dependent MTases catalyze methylation reactions utilizing the methyl donor AdoMet. This thesis describes structure-function studies of several members of this enzyme family which are biomedically important. By combining experimental (X-ray crystallography) and theoretical (molecular dynamics simulation calculations) structural biology techniques with molecular biology and functional studies, the work presented here provides molecular insight into mechanisms of enzyme function and drug response.
The first enzyme studied, thiopurine S-methyltransferase (TPMT), modulates the cytotoxic effects of thiopurine prodrugs such as 6-mercaptopurine (6MP) by methylating them in a reaction using AdoMet as the donor. Patients with TPMT variant allozymes exhibit diminished levels of protein and/or enzyme activity and are at risk for thiopurine drug-induced toxicity. We have determined two crystal structures of wild-type murine TPMT, as a binary complex with the product S-adenosyl-L-homocysteine (AdoHcy) and as a ternary complex with AdoHcy and the substrate 6MP, to 1.8 Å and 2.0 Å resolution, respectively. Comparison of the structures reveals that an active site loop becomes ordered upon 6MP binding. The positions of the two ligands are consistent with the expected SN2 reaction mechanism. Arg147 and Arg221, the only polar amino acids near 6MP, are highlighted as possible participants in substrate deprotonation. Structure-based mutagenesis and enzyme activity assays suggest that either Arg152 or Arg226 may participate in some fashion in the TPMT reaction, with one residue compensating when the other is altered, and that Arg152 may interact with substrate more directly than Arg226, consistent with observations in the murine TPMT crystal structure.
In addition, we have compared the catalytic activity of wild-type and *5 variant TPMTs, and found that the variant's binding affinity for its methyl acceptor and donor substrates are reduced 10-fold and 2-fold, contributing to decreased enzyme activity of murine TPMT*5. We have determined two crystal structures of murine TPMT*5, as a binary complex with AdoHcy and as a ternary complex with AdoHcy and 6MP, respectively. The TPMT*5 crystal structures together with molecular dynamics simulation calculations reveal that the active site loop is more flexible in TPMT*5, which affects the AdoMet and 6MP substrate affinity and results in loss of the enzyme activity. In addition, these TPMT*5 crystal structures and the computational modeling of other TPMT variants using wild-type murine TPMT structures aid our understanding of the molecular consequences of TPMT polymorphisms. Furthermore, crystal structures of TPMT complexes with benzoic acid inhibitors and thiophenol substrate reveal that TPMT possesses a flexible active site which can accommodate both a smaller acceptor substrate such as thiophenol and larger benzoic acid inhibitors. These structures provide insights into the connection between the subtle variation in binding of different acceptor substrate site ligands to TPMT and the different degree of inhibition by these benzoic acid inhibitors. The structural features of the acceptor binding site characterized by the ensemble of TPMT structures reported here may be useful in identifying new small molecule modulators for optimization of thiopurine-based therapy.
Nicotinamide N-methyltransferase (NNMT) catalyzes the N-methylation of nicotinamide, pyridines and other structural analogs using AdoMet as methyl donor. The crystal structure of human NNMT, which plays a significant role in the regulation of metabolic pathways and cancers, was solved as the ternary complex bound to both AdoHcy and nicotinamide. The structure reveals the structural basis for nicotinamide binding, highlights several residues in the active site, which may play roles in nicotinamide recognition and NNMT catalysis, and provides a structural basis for the design of NNMT mutants to further investigate the enzyme's catalytic mechanism. The structure-based mutagenesis of NNMT is being pursued in ongoing studies.
Arsenic methyltransferase (AS3MT) is the third important AdoMet-dependent MTase included in our studies. It is involved in methylation of inorganic arsenic and relevant to public health. To obtain the crystal structure of AS3MT for elucidation of the mechanism of arsenic methylation and to probe the relationship between AS3MT polymorphisms and individual variation in arsenic metabolism, a number of AS3MT constructs have been prepared and characterized, and efforts to crystallize AS3MT are ongoing.