Structural and catalytic roles of the human 18 rRNA methyltransferases DIMT1 in ribosome assembly and translation.

rRNA-modifying enzymes participate in ribosome assembly. However, whether the catalytic activities of these enzymes are important for the ribosome assembly and other cellular processes is not fully understood. Here, we report the crystal structure of WT human dimethyladenosine transferase 1 (DIMT1), an 18 rRNA -dimethyladenosine (mA) methyltransferase, and results obtained with a catalytically inactive DIMT1 variant. We found that heterozygous HEK 293T cells have a significantly decreased 40S fraction and reduced protein synthesis but no major changes in mA levels in 18 rRNA. Expression of a catalytically inactive variant, DIMT1-E85A, in WT and cells significantly decreased mA levels in 18S rRNA, indicating a dominant-negative effect of this variant on mA levels. However, expression of the DIMT1-E85A variant restored the defects in 40S levels. Of note, unlike WT DIMT1, DIMT1-E85A could not revert the defects in protein translation. We found that the differences between this variant and the WT enzyme extended to translation fidelity and gene expression patterns in DNA damage response pathways. These results suggest that the catalytic activity of DIMT1 is involved in protein translation and that the overall protein scaffold of DIMT1, regardless of the catalytic activity on mA in 18 rRNA, is essential for 40S assembly.