Methyltransferases (methylases) use S-adenosylmethione (SAM) as a cofactor for tRNA methylation reactions. All five known classes of methyltransferases of the TrmD and SpoU families have a distinct alpha/beta topology and considered to be structurally different enzymes. In the structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus (Staph), two domains, N-terminal SAM-binding domain and C-terminal RNA-binding domain, of the protein are interconnected with a long partially unfolded loop region. The core of the N-terminal domain made up of six parallel beta-strands resembling structural fold of the class IV methylases of the SpoU family. Six strands are flanked by helices with the final three strands are folded into a rare deep trefoil knot, which provides the binding site for the cofactor. TrmD is believed to function as a dimer that is formed in parallel fashion by symmetry operation in the P4332 space group of the Staph protein. Such quaternary architecture localized two active sites in a close proximity to each other. The disordered inter-domain linker is a characteristic feature of the apo-methyltransferases. Based on literature data, the flexible loop between two domains appears to possibly cover the SAM-active site upon binding of the cognate tRNA and providing a candidate for the catalytic base. The C-terminal domain has a lower average B-factor than the catalytic domain and shows structural similarity to DNA-binding domains of trp and tet repressors. Co-crystallization of the Staph TrmD with its cofactor can help in understanding the mechanism and inhibition of the methylation reaction.