CRYSTAL-STRUCTURE OF GLYCINE N-METHYLTRANSFERASE FROM RAT-LIVER

Glycine N-methyltransferase (GNMT) from rat liver is a tetrameric enzy me with 292 amino acid residues in each identical subunit and catalyze s the S-adenosylmethionine (AdoMet) dependent methylation of glycine t o form sarcosine. The crystal structure of GNMT complexed with AdoMet and acetate, a competitive inhibitor of glycine, has been determined a t 2.2 Angstrom resolution. The subunit of GNMT forms a spherical shape with an extended N-terminal region which corks the entrance of active site of the adjacent subunit. The active site is located in the near center of the spherical subunit. As a result, the AdoMet and acetate i n the active site are completely surrounded by amino acid residues. Ca reful examination of the structure reveals several characteristics of GNMT. (1) Although the structure of the AdoMet binding domain of the G NMT is very similar to those of other methyltransferases recently dete rmined by X-ray diffraction method, an additional domain found only in GNMT encloses the active site to form a molecular basket, and consequ ently the structure of GNMT looks quite different from those of other methyltransferases. (2) This unique molecular structure can explain wh y GNMT can capture folate and polycyclic aromatic hydrocarbons. (3) Th e unique N-terminal conformation and the subunit structure can explain why GNMT exhibits positive cooperativity in binding AdoMet. From the structural features of GNMT, we propose that the enzyme might be able to capture yet unidentified molecules in the cytosol and thus particip ates in various biological processes including detoxification of polyc yclic aromatic hydrocarbons. In the active site, acetate binds near th e S-CH3 moiety of AdoMet. Simple modeling indicates that the amino gro up of the substrate glycine can be placed close to the methyl group of AdoMet within 3.0 Angstrom and form a hydrogen bond with the carboxyl group of Glu(15) of the adjacent subunit. On the basis of the ternary complex structure, the mechanism of the methyl transfer in GNMT has b een proposed.