5XGU

Escherichia coli. RNase R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.846 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into RNA unwinding and degradation by RNase R.

Chu, L.Y.Hsieh, T.J.Golzarroshan, B.Chen, Y.P.Agrawal, S.Yuan, H.S.

(2017) Nucleic Acids Res. 45: 12015-12024

  • DOI: 10.1093/nar/gkx880

  • PubMed Abstract: 
  • RNase R is a conserved exoribonuclease in the RNase II family that primarily participates in RNA decay in all kingdoms of life. RNase R degrades duplex RNA with a 3' overhang, suggesting that it has RNA unwinding activity in addition to its 3'-to-5' ...

    RNase R is a conserved exoribonuclease in the RNase II family that primarily participates in RNA decay in all kingdoms of life. RNase R degrades duplex RNA with a 3' overhang, suggesting that it has RNA unwinding activity in addition to its 3'-to-5' exoribonuclease activity. However, how RNase R coordinates RNA binding with unwinding to degrade RNA remains elusive. Here, we report the crystal structure of a truncated form of Escherichia coli RNase R (residues 87-725) at a resolution of 1.85 Å. Structural comparisons with other RNase II family proteins reveal two open RNA-binding channels in RNase R and suggest a tri-helix 'wedge' region in the RNB domain that may induce RNA unwinding. We constructed two tri-helix wedge mutants and they indeed lost their RNA unwinding but not RNA binding or degrading activities. Our results suggest that the duplex RNA with an overhang is bound in the two RNA-binding channels in RNase R. The 3' overhang is threaded into the active site and the duplex RNA is unwound upon reaching the wedge region during RNA degradation. Thus, RNase R is a proficient enzyme, capable of concurrently binding, unwinding and degrading structured RNA in a highly processive manner during RNA decay.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease R
B, A
645Escherichia coli DEC6AMutation(s): 1 
Gene Names: rnr
EC: 3.1.13.1
Find proteins for H4USN4 (Escherichia coli DEC6A)
Go to UniProtKB:  H4USN4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.846 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.691α = 90.00
b = 120.863β = 91.61
c = 83.626γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 1.2: 2017-11-29
    Type: Database references