3JWH

Crystal structure analysis of the methyltransferase domain of bacterial-AvHen1-C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and biochemical insights into 2'-O-methylation at the 3'-terminal nucleotide of RNA by Hen1.

Mui Chan, C.Zhou, C.Brunzelle, J.S.Huang, R.H.

(2009) Proc.Natl.Acad.Sci.USA 106: 17699-17704

  • DOI: 10.1073/pnas.0907540106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small RNAs of approximately 20-30 nt have diverse and important biological roles in eukaryotic organisms. After being generated by Dicer or Piwi proteins, all small RNAs in plants and a subset of small RNAs in animals are further modified at their 3' ...

    Small RNAs of approximately 20-30 nt have diverse and important biological roles in eukaryotic organisms. After being generated by Dicer or Piwi proteins, all small RNAs in plants and a subset of small RNAs in animals are further modified at their 3'-terminal nucleotides via 2'-O-methylation, carried out by the S-adenosylmethionine-dependent methyltransferase (MTase) Hen1. Methylation at the 3' terminus is vital for biological functions of these small RNAs. Here, we report four crystal structures of the MTase domain of a bacterial homolog of Hen1 from Clostridium thermocellum and Anabaena variabilis, which are enzymatically indistinguishable from the eukaryotic Hen1 in their ability to methylate small single-stranded RNAs. The structures reveal that, in addition to the core fold of the MTase domain shared by other RNA and DNA MTases, the MTase domain of Hen1 possesses a motif and a domain that are highly conserved and are unique to Hen1. The unique motif and domain are likely to be involved in RNA substrate recognition and catalysis. The structures allowed us to construct a docking model of an RNA substrate bound to the MTase domain of bacterial Hen1, which is likely similar to that of the eukaryotic counterpart. The model, supported by mutational studies, provides insight into RNA substrate specificity and catalytic mechanism of Hen1.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hen1
A, B
217Anabaena variabilis (strain ATCC 29413 / PCC 7937)Mutation(s): 0 
Find proteins for Q3MCR9 (Anabaena variabilis (strain ATCC 29413 / PCC 7937))
Go to UniProtKB:  Q3MCR9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.519α = 90.00
b = 49.772β = 101.36
c = 90.433γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
CNSrefinement
PHASESphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Structure summary