3AI9: Crystal Structure Of Duf358 Protein Reveals A Putative Spout-Class Rrna Methyltransferase

The proteins in DUF358 family are all bacterial proteins, which are approximately 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 A resolution. The structure reveals a single domain structure consisting of eight-stranded beta-sheets sandwiched by six alpha-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 alpha-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.
PDB ID: 3AI9Download
MMDB ID: 89498
PDB Deposition Date: 2010/5/11
Updated in MMDB: 2011/05
Experimental Method:
x-ray diffraction
Resolution: 1.55  Å
Source Organism:
Similar Structures:
Biological Unit for 3AI9: dimeric; determined by author and by software (PISA)
Molecular Components in 3AI9
Label Count Molecule
Proteins (2 molecules)
Upf0217 Protein Mj1640(Gene symbol: MJ_RS08730)
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB