Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase A
Synonym: KsgA, Dim1, MJ1029
GI: 15669218
COG: COG0030
UniProt: Q58435
Structures: | 3FYD | 3FYC | 3GRR | 3GRU | 3GRV | 3GRY |
Enzyme type: methyltransferase

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

The enzymes of the KsgA/Dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. The well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal course of ribosome maturation, and the structures of KsgA from Escherichia coli and Dim1 from Homo sapiens and Plasmodium falciparum have been determined. To this point, no examples of archaeal structures have been reported. Here, we report the structure of Dim1 from the thermophilic archaeon Methanocaldococcus jannaschii. While it shares obvious similarities with the bacterial and eukaryotic orthologs, notable structural differences exist among the three members, particularly in the C-terminal domain. Previous work showed that eukaryotic and archaeal Dim1 were able to robustly complement for KsgA in E. coli. Here, we repeated similar experiments to test for complementarity of archaeal Dim1 and bacterial KsgA in Saccharomyces cerevisiae. However, neither the bacterial nor the archaeal ortholog could complement for the eukaryotic Dim1. This might be related to the secondary, non-methyltransferase function that Dim1 is known to play in eukaryotic ribosomal maturation. To further delineate regions of the eukaryotic Dim1 critical to its function, we created and tested KsgA/Dim1 chimeras. Of the chimeras, only one constructed with the N-terminal domain from eukaryotic Dim1 and the C-terminal domain from archaeal Dim1 was able to complement, suggesting that eukaryotic-specific Dim1 function resides in the N-terminal domain also, where few structural differences are observed between members of the KsgA/Dim1 family. Future work is required to identify those determinants directly responsible for Dim1 function in ribosome biogenesis. Finally, we have conclusively established that none of the methyl groups are critically important to growth in yeast under standard conditions at a variety of temperatures.

Download RCSB-PDB Structures:

Pdb Files   3FYC.pdb   3FYD.pdb   3GRR.pdb   3GRU.pdb   3GRV.pdb   3GRY.pdb  
Pdbx/mmCIF Files   3FYC.cif   3FYD.cif   3GRR.cif   3GRU.cif   3GRV.cif   3GRY.cif  

Protein sequence:



Archaeal RsmA belongs to the bacterial KsgA/eukaryal Dim1 super family of methyltransferases. It dimethylates two very conserved adjacent adenosines (positions 1518 and 1519 in E.coli numbering) in the loop of a conserved hairpin near the 3'-end of small subunit rRNA. AdoMet is the methyl group donor. Identity of the target nucleotides was identified by using a heterologous rRNA substrate.


Title Authors Journal Details PubMed Id DOI
Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution. O'Farrell HC, Pulicherla N, Desai PM, Rife JP RNA [details] 16540698 -
Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. Pulicherla N, Pogorzala LA, Xu Z, O Farrell HC, Musayev FN, Scarsdale JN, Sia EA, Culver GM, Rife JP J Mol Biol [details] 19520088 -
Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design. O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP Biochemistry [details] 20163168 -