Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase
Classification:
TRANSFERASE
Technique:
X-Ray Diffraction
Resolution:
1.95
R value free:
0.227
R value observed:
R value work:
0.186
Abstract of the PDB Structure's related Publication:
RumA catalyzes transfer of a methyl group from S-adenosylmethionine (SAM) specifically to uridine 1939 of 23S ribosomal RNA in Escherichia coli to yield 5-methyluridine. We determined the crystal structure of RumA at 1.95 A resolution. The protein is organized into three structural domains: The N-terminal domain contains sequence homology to the conserved TRAM motif and displays a five-stranded beta barrel architecture characteristic of an oligosaccharide/oligonucleotide binding fold. The 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. The catalytic nucleophile Cys389 lies in a motif different from that in DNA 5-methylcytosine methyltransferases. The electrostatic potential surface reveals a predominately positively charged area that covers the concave surface of the first two domains and suggests an RNA binding mode. The iron-sulfur cluster may be involved in the correct folding of the protein or may have a role in RNA binding.
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.