Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase A
Synonym: KsgA, TTHA0083
GI: 55980052
COG: COG0030
UniProt: Q5SM60
Structures: | 3FUT | 3FUU | 3FUW | 3FUV | 3FUX |
Enzyme type: methyltransferase
Position of modification - modification: s:1491(1518) - m6,6A
s:1492(1519) - m6,6A

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

Posttranscriptional modification of ribosomal RNA (rRNA) occurs in all kingdoms of life. The S-adenosyl-L-methionine-dependent methyltransferase KsgA introduces the most highly conserved rRNA modification, the dimethylation of A1518 and A1519 of 16S rRNA. Loss of this dimethylation confers resistance to the antibiotic kasugamycin. Here, we report biochemical studies and high-resolution crystal structures of KsgA from Thermus thermophilus. Methylation of 30S ribosomal subunits by T. thermophilus KsgA is more efficient at low concentrations of magnesium ions, suggesting that partially unfolded RNA is the preferred substrate. The overall structure is similar to that of other methyltransferases but contains an additional alpha-helix in a novel N-terminal extension. Comparison of the apoenzyme with complex structures with 5'-methylthioadenosine or adenosine bound in the cofactor-binding site reveals novel features when compared with related enzymes. Several mobile loop regions that restrict access to the cofactor-binding site are observed. In addition, the orientation of residues in the substrate-binding site indicates that conformational changes are required for binding two adjacent residues of the substrate rRNA.

Download RCSB-PDB Structures:

Pdb Files   3FUT.pdb   3FUU.pdb   3FUV.pdb   3FUW.pdb   3FUX.pdb  
Pdbx/mmCIF Files   3FUT.cif   3FUU.cif   3FUV.cif   3FUW.cif   3FUX.cif  

Protein sequence:



Thermophilic RsmA belongs to the bacterial KsgA/eukaryal-archaeal 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.

Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m6A RNA rRNA 1492 SSU-16S Prokaryotic Cytosol 19285505   
m6A:m6,6A RNA rRNA 1492 16S-SSU Prokaryotic Cytosol 19285505   
A:m6A RNA rRNA 1493 16S-SSU Prokaryotic Cytosol 19285505   
m6A:m6,6A RNA rRNA 1493 SSU-16S Prokaryotic Cytosol 19285505   


Title Authors Journal Details PubMed Id DOI
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. Demirci H, Belardinelli R, Seri E, Gregory ST, Gualerzi C, Dahlberg AE, Jogl G J Mol Biol [details] 19285505 -