Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine

Sci Rep. 2017 Apr 20;7(1):969. doi: 10.1038/s41598-017-01186-5.


Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site. One monomer provides the SAM-binding site, whereas the conserved C-terminal tail of the second monomer provides residues essential for catalysis. Our findings elucidate the mechanism by which a small protein dimer assembles a functionally asymmetric architecture.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine / analogs & derivatives
  • Adenosine / metabolism
  • Binding Sites
  • Catalytic Domain
  • Escherichia coli / chemistry
  • Escherichia coli / enzymology*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Methylation
  • Methyltransferases / chemistry*
  • Methyltransferases / genetics
  • Methyltransferases / metabolism*
  • Models, Molecular
  • Mutation
  • Protein Binding
  • Protein Multimerization
  • Protein Structure, Secondary
  • Pseudouridine / metabolism
  • RNA, Ribosomal, 23S / chemistry*
  • S-Adenosylmethionine / metabolism*
  • Substrate Specificity


  • Escherichia coli Proteins
  • RNA, Ribosomal, 23S
  • Pseudouridine
  • S-Adenosylmethionine
  • Methyltransferases
  • RlmH protein, E coli
  • Adenosine
  • sinefungin