3AIA

Crystal structure of DUF358 reveals a putative SPOUT-class methltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

Chen, H.Y.Yuan, Y.A.

(2010) J Mol Cell Biol 2: 366-374

  • DOI: https://doi.org/10.1093/jmcb/mjq034
  • Primary Citation of Related Structures:  
    3AI9, 3AIA

  • 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.


  • Organizational Affiliation

    Mechanobiology Institute, National University of Singapore, T-lab Building, 5A Engineering Drive 1, Singapore 117411, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0217 protein MJ1640
A, B
211Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ1640
EC: 2.1.1.257
UniProt
Find proteins for Q59034 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q59034 
Go to UniProtKB:  Q59034
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59034
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.862α = 90
b = 93.869β = 100.14
c = 53.837γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description