Crystal Structure of Mj1640/DUF358 Protein Reveals a Putative SPOUT-Class RNA Methyltransferase

摘要

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 Methonocoldococcus jonnoschli DUF358/Mj1640 in complex with S-adenosyl-L-methionine(SAM)at 1.4 (A) resolution.The structure reveals a single domain structure consisting of eight-stranded -sheets sandwiched by six -helices at both sides.Similar to other SPOUT-class members,Mjl640 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 -helices oriented almost perpendicular to each othen.Although Mj1640 shares close structural similarity with Nepl.the significant differences in N-terminal extension domain and the overall surface charge distribution stronly suggest that Mi1640 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.