3AI9

Crystal structure of DUF358 protein reveals a putative SPOUT-class rRNA methyltransferase

Summary for 3AI9

• Entry DOI: 10.2210/pdb3ai9/pdb
• Related: 3AIA
• Descriptor: UPF0217 protein MJ1640, S-ADENOSYLMETHIONINE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: mjduf358, rrna methyltransferase, spout-class fold, transferase
• Biological source: Methanocaldococcus jannaschii (Methanococcus jannaschii)
• Total number of polymer chains: 1
• Total formula weight: 25094.54

Authors

Yuan, Y.A.,Chen, H.Y. (deposition date: 2010-05-11, release date: 2011-03-30, Last modification date: 2024-10-16)

Primary citation

Chen, H.Y.,Yuan, Y.A.
Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase
J Mol Cell Biol, 2:366-374, 2010

PubMed 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.

PubMed: 21098051
DOI: 10.1093/jmcb/mjq034

Experimental method

X-RAY DIFFRACTION (1.55 Å)