Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase

J Mol Cell Biol. 2010 Dec;2(6):366-74. doi: 10.1093/jmcb/mjq034.

Abstract

The proteins in DUF358 family are all bacterial proteins, which are ∼200 amino acids long with unknown function. Bioinformatics analysis suggests that these proteins contain several conserved arginines and aspartates that might adopt SPOUT-class fold. Here we report crystal structure of Methanocaldococcus jannaschii DUF358/Mj1640 in complex with S-adenosyl-L-methionine (SAM) at 1.4 Å resolution. The structure reveals a single domain structure consisting of eight-stranded β-sheets sandwiched by six α-helices at both sides. Similar to other SPOUT-class members, Mj1640 contains a typical deep trefoil knot at its C-terminus to accommodate the SAM cofactor. However, Mj1640 has limited structural extension at its N-terminus, which is unique to this family member. Mj1640 forms a dimer, which is mediated by two parallel pairs of α-helices oriented almost perpendicular to each other. Although Mj1640 shares close structural similarity with Nep1, the significant differences in N-terminal extension domain and the overall surface charge distribution strongly suggest that Mj1640 might target a different RNA sequence. Detailed structural analysis of the SAM-binding pocket reveals that Asp157 or Glu183 from its own monomer or Ser43 from the associate monomer probably plays the catalytic role for RNA methylation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaeal Proteins / chemistry*
  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • Methanococcales / enzymology*
  • Methyltransferases / chemistry*
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • RNA / chemistry
  • S-Adenosylmethionine / chemistry
  • Sequence Alignment
  • Sequence Homology, Amino Acid

Substances

  • Archaeal Proteins
  • RNA
  • S-Adenosylmethionine
  • Methyltransferases

Associated data

  • PDB/3AI9
  • PDB/3AIA