2NUE

Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 2.9-Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A stepwise model for double-stranded RNA processing by ribonuclease III.

Gan, J.Shaw, G.Tropea, J.E.Waugh, D.S.Court, D.L.Ji, X.

(2007) Mol.Microbiol. 67: 143-154

  • DOI: 10.1111/j.1365-2958.2007.06032.x
  • Primary Citation of Related Structures:  2NUF, 2NUG

  • PubMed Abstract: 
  • RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a v ...

    RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a valuable model system for the family. Previously, we have shown that RNase III uses two catalytic sites to create the 2-nucleotide (nt) 3' overhangs in its products. Here, we present three crystal structures of RNase III in complex with double-stranded RNA, demonstrating how Mg(2+) is essential for the formation of a catalytically competent protein-RNA complex, how the use of two Mg(2+) ions can drive the hydrolysis of each phosphodiester bond, and how conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover, we have modelled a protein-substrate complex and a protein-reaction intermediate (transition state) complex on the basis of the crystal structures. Together, the crystal structures and the models suggest a stepwise mechanism for RNase III to execute the phosphoryl transfer reaction.


    Organizational Affiliation

    Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease III
A, B
221Aquifex aeolicus (strain VF5)Gene Names: rnc
EC: 3.1.26.3
Find proteins for O67082 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67082
Entity ID: 1
MoleculeChainsLengthOrganism
46-MERC46N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.596α = 90.00
b = 101.657β = 103.69
c = 67.082γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MAR345data collection
HKL-2000data scaling
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description