2IX0

RNase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Unravelling the Dynamics of RNA Degradation by Ribonuclease II and its RNA-Bound Complex

Frazao, C.Mcvey, C.E.Amblar, M.Barbas, A.Vonrhein, C.Arraiano, C.M.Carrondo, M.A.

(2006) Nature 7: 443

  • DOI: 10.1038/nature05080
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RNA degradation is a determining factor in the control of gene expression. The maturation, turnover and quality control of RNA is performed by many different classes of ribonucleases. Ribonuclease II (RNase II) is a major exoribonuclease that interve ...

    RNA degradation is a determining factor in the control of gene expression. The maturation, turnover and quality control of RNA is performed by many different classes of ribonucleases. Ribonuclease II (RNase II) is a major exoribonuclease that intervenes in all of these fundamental processes; it can act independently or as a component of the exosome, an essential RNA-degrading multiprotein complex. RNase II-like enzymes are found in all three kingdoms of life, but there are no structural data for any of the proteins of this family. Here we report the X-ray crystallographic structures of both the ligand-free (at 2.44 A resolution) and RNA-bound (at 2.74 A resolution) forms of Escherichia coli RNase II. In contrast to sequence predictions, the structures show that RNase II is organized into four domains: two cold-shock domains, one RNB catalytic domain, which has an unprecedented alphabeta-fold, and one S1 domain. The enzyme establishes contacts with RNA in two distinct regions, the 'anchor' and the 'catalytic' regions, which act synergistically to provide catalysis. The active site is buried within the RNB catalytic domain, in a pocket formed by four conserved sequence motifs. The structure shows that the catalytic pocket is only accessible to single-stranded RNA, and explains the specificity for RNA versus DNA cleavage. It also explains the dynamic mechanism of RNA degradation by providing the structural basis for RNA translocation and enzyme processivity. We propose a reaction mechanism for exonucleolytic RNA degradation involving key conserved residues. Our three-dimensional model corroborates all existing biochemical data for RNase II, and elucidates the general basis for RNA degradation. Moreover, it reveals important structural features that can be extrapolated to other members of this family.


    Related Citations: 
    • Expression, Purification, Crystallization and Preliminary Diffraction Data Characterization of Escherichia Coli Ribonuclease II (Rnase II)
      Mcvey, C.E.,Amblar, M.,Barbas, A.,Cairrao, F.,Coelho, R.,Romao, C.,Arraiano, C.M.,Carrondo, M.A.,Frazao, C.
      (2006) Acta Crystallogr.,Sect.F 62: 684
    • DNA Sequencing and Expression of the Gene Rnb Encoding Escherichia Coli Ribonuclease II
      Zilhao, R.,Camelo, L.,Arraiano, C.M.
      (1993) Mol.Microbiol. 8: 43
    • Characterization of the Functional Domains of Escherichia Coli Rnase II.
      Amblar, M.,Barbas, A.,Fialho, A.M.,Arraiano, C.M.
      (2006) J.Mol.Biol. 360: 921


    Organizational Affiliation

    Division of Biological Chemistry, ITQB-Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apt. 127, 2781-901 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXORIBONUCLEASE 2
A
663Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rnb
EC: 3.1.13.1
Find proteins for P30850 (Escherichia coli (strain K12))
Go to UniProtKB:  P30850
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
C5P
Query on C5P

Download SDF File 
Download CCD File 
A
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.836α = 90.00
b = 125.719β = 111.91
c = 66.244γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation