RlmD (formerly RumA) methylates the conserved U1939 in a loose hairpin ‘70’ located between conserved hairpins 69 and 71 in domain IV the large subunit rRNA. Recombinant E.coli RlmD was shown to be active in vitro on a small 40 nucleotides long fragment of 23S rRNA encompassing U1939. It displays a N-terminal TRAM domain, a five-stranded beta barrel architecture characteristic of an oligosaccharide/ oligonucleotide binding fold and a central domain contains a [Fe(4)S(4)] cluster coordinated by four conserved cysteine residues. The C-terminal domain displays the typical SAM-dependent methyltransferase fold. AdoMet is the methyl group donor. The paralog enzyme in B. subtilis (RlmCD) is multisite specific, while in Archaea, no RlmD paralog has been identified. The presence of m5U1939 methylation in 23S rRNA is not essential but helps to improve ribosome performance.