Abstract of the PDB Structure's related Publication:
RlmJ catalyzes the m(6)A2030 methylation of 23S rRNA during ribosome biogenesis in Escherichia coli. Here, we present crystal structures of RlmJ in apo form, in complex with the cofactor S-adenosyl-methionine and in complex with S-adenosyl-homocysteine plus the substrate analogue adenosine monophosphate (AMP). RlmJ displays a variant of the Rossmann-like methyltransferase (MTase) fold with an inserted helical subdomain. Binding of cofactor and substrate induces a large shift of the N-terminal motif X tail to make it cover the cofactor binding site and trigger active-site changes in motifs IV and VIII. Adenosine monophosphate binds in a partly accommodated state with the target N6 atom 7 Å away from the sulphur of AdoHcy. The active site of RlmJ with motif IV sequence 164DPPY167 is more similar to DNA m(6)A MTases than to RNA m(6)2A MTases, and structural comparison suggests that RlmJ binds its substrate base similarly to DNA MTases T4Dam and M.TaqI. RlmJ methylates in vitro transcribed 23S rRNA, as well as a minimal substrate corresponding to helix 72, demonstrating independence of previous modifications and tertiary interactions in the RNA substrate. RlmJ displays specificity for adenosine, and mutagenesis experiments demonstrate the critical roles of residues Y4, H6, K18 and D164 in methyl transfer.
SAM-dependent MTase. The enzyme is neither essential for ribosome assembly nor for function. The substrate preference in vitro is deproteinized 23S rRNA. Modified residue m6A2030 is located in helix 72, close the peptidyltransferase center of Domain IV and the elongation factor binding site of Domain II in the folded 3D architecture of the ribosome. Orthologs are found mostly in proteobacteria. A possible role is stabilization of local tertiary structure of the ribosome. M6A exist also at position 1618 where it is introduced by a related MTase RlmF(UbiN) and of course at the conserved m6,2A1518, 1519 of 16S rRNA (introduced by RsmA/KsgA).
The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA.