Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA large subunit methyltransferase H
Synonym: YbeA
GI: 67476028
Orf: b0636
COG: COG1576
UniProt: P0A8I8
Structures: | 1NS5 |
Enzyme type: methyltransferase
Position of modification - modification: l:1915(1915) - m3Y

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

Download RCSB-PDB Structures:

Pdb Files   1NS5.pdb  
Pdbx/mmCIF Files   1NS5.cif  

Protein sequence:



RlmH is a S-adenosylmethionine-dependent, homodimeric SPOUT methyltransferase that methylates selectively the N-3 position of pseudouridine 1915 to form m3Y1915 in the loop of helix 69 (Domain IV) of 23S rRNA. RlmH protein is able to methylate pseudouridine in vitro using only 70S ribosomes, but not 50S subunits from the ybeA deletion strain as substrate. It preferentially methylates Y1915 and less efficiently U1915, but not Y at position 1911 or 1917. It docks comfortably into the ribosomal A site without encroaching into the P site. Homologs of E. coli RlmH are present in most bacterial lineages, but are essentially absent in the Archaea and Eukaryota. Formation of Y1915 is dependent on the gene product of rluD.

Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
Y:m3Y RNA rRNA 1915 LSU-23S Prokaryotic Cytosol 18755835   


Title Authors Journal Details PubMed Id DOI
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S RNA [details] 18755835 -
Identification of pseudouridine methyltransferase in Escherichia coli. Ero R, Peil L, Liiv A, Remme J RNA [details] 18755836 -
Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD. Ero R, Leppik M, Liiv A, Remme J RNA [details] 20817755 -