The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is present as bound to tRNA and to a 3'-end fragment of 16 S rRNA.

The enzyme tRNA-(m5U54)-methyltransferase (EC 2.1.1.35) of Escherichia coli catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to uridine in position 54 of the T psi-loop of all E. coli tRNA species, forming 5-methyluridine (m5U). In vivo, this enzyme is present both as a native polypeptide of 42 kDa and as a TrmA.RNA complex. The TrmA.RNA complex is not dissociated during strong denaturing conditions such as boiling in 8 M urea or 6 M guanidine HCl, consisting with that the RNA is covalently bound to the protein. After sequencing and Southern blot analyses, the RNA was identified to be a subset of undermodified tRNA species as well as the 3' terminus of 16 S rRNA. However, the complex is not associated with the ribosome and the covalently bound RNA does not affect the tRNA methylating activity of the enzyme.