Protein Name

5-methyluridine methyltransferase TrmA


Escherichia coli

Biological Context

RNAs that have been transcribed from the DNA can't express their functions in practice. They must undergo processing or posttranscriptional modifications for becoming mature. For example, mRNAs(messenger RNAs) are translated into proteins after the splicing reaction as intron removal. Functional RNAs such as transfer RNA (tRNA) and ribosomal RNA (rRNA) are reinforced by posttranscriptional modification (methylation, acetylation, or deamination) at a specific base or ribose. Ribose methylation (PDB:1IPA) or pseudouridine isomerization of uridine (PDB:2EY4, PDB:2HVY) are correspond it. In Escherichia coli, the methylation of uridine to 5-methyluridine is found at three conserved positions, U747 or U1939 of rRNA, U54 in the T arm of tRNA. There are three types of enzymes(RumA, RumB, and TrmA) each of which catalyzes methylation of uridine at each site, and they all belong to the same family of AdoMet-dependent m5U MTase (S-Adenosylmethionine-dependent 5-methyluridine methyltransferase).

Family Protein The site of methylation
AdoMet-dependent m5U MTase RumA U1939 of 23S RNA(a subunit of rRNA)
RumB U747 of 23S RNA(a subunit of rRNA)
TrmA U54 in the T arm of tRNA(refer to Fig.1)
(Fig.1) The secondary structure of tRNA

In the presence of AdoMet(S-Adenosylmethionine), these three enzymes can express a common role of transferring a methyl group from the AdoMet to the C-5 carbon of uridine base.

(Fig.2) AdoMet-dependent methyltransferase reaction
AdoMet-dependent m5U Mtase have a role of transferring a methyl group from the cofactor AdoMet to the C-5
carbon of target uridine. AdoMet changes to AdoHcy(S-adenosylhomocysteine) after deprived of its methyl group.

The structure of RumA in complex with a 37-mer fragment of rRNA has already been determined, and revealed a catalytic pocket of the methylation. (refer to Fig.3). However, the way in which m5U MTase recognizes the targeted modification site hasn't been known. To understand the mechanisms, the crystal structure of TrmA complexed with a fragment of RNA T arm was determined and compared with the structure of RumA/23S RNA complex.

(Fig.3) The complex structure of RumA and 23S RNA fragment
In the surface model (right side of the figure), near-U1939-region (yellow) of the RNA fragment
was accommodated in the catalytic pocket (highlight with white) of RumA.

Structure Description


A complex structure of a TrmA and a 19-mer fragment, which derived from the T arm of tRNA, has been determined. (refer to Fig.4). Compared the structure of TrmA(Fig.4 left side) with that of RumA(Fig.3 left side), the secondary structure elements(alpha helices or beta strands) and their topology(the arrangement of secondary structure elements) correspond well. The most interesting finding is that a tRNA region bound to the catalytic pocket of TrmA (purple in Fig.4) and a 23S RNA region bound to the catalytic pocket of RumA (yellow in Fig.3) have a common fold.

(Fig.4) A complex structure of a TrmA and a fragment derived from the T arm of tRNA

As seen in Fig.5, not only the structure but the direction of bases are conserved between the two consensus fold regions. This correspondence happened by accident? At least for isolated-form of tRNA, the conformation of consensus fold region as seen in Fig.6 has not been observed. Furthermore, as seen in Fig.6, the residues along the methyluridine of each protein are also well conserved.

5 6
(Fig.5) Alignment between two consensus fold regions (Fig.6) The conserved residues between TrmA and RumA

The observations obtained this time suggest that the consensus fold region of RNA need to refold into the structure as show in Fig.5 for binding to the catalytic pocket of TrmA or RumA. Further experiments are required to determine what have a major role in RNA refolding.

Protein Data Bank (PDB)



Alian, A. Lee, T.T. Griner, S.L. Stroud, R.M. Finer-Moore, J.; "Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases."; Proc.Natl.Acad.Sci.Usa; (2008) 105:6876-6881 PubMed:18451029.


  • PDB:1MXI: A complex of YibK methyltransferase and AdoHcy(as a inhibitor)

author: Jun-ichi Ito

Japanese version:PDB:3BT7