3T3N

Molecular basis for the recognition and cleavage of RNA (UUCCGU) by the bifunctional 5'-3' exo/endoribonuclease RNase J


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J.

Dorleans, A.Li de la Sierra-Gallay, I.Piton, J.Zig, L.Gilet, L.Putzer, H.Condon, C.

(2011) Structure 19: 1252-1261

  • DOI: https://doi.org/10.1016/j.str.2011.06.018
  • Primary Citation of Related Structures:  
    3T3N, 3T3O

  • PubMed Abstract: 

    RNase J is a key member of the β-CASP family of metallo-β-lactamases involved in the maturation and turnover of RNAs in prokaryotes. The B. subtilis enzyme possesses both 5'-3' exoribonucleolytic and endonucleolytic activity, an unusual property for a ribonuclease. Here, we present the crystal structure of T. thermophilus RNase J bound to a 4 nucleotide RNA. The structure reveals an RNA-binding channel that illustrates how the enzyme functions in 5'-3' exoribonucleolytic mode and how it can function as an endonuclease. A second, negatively charged tunnel leads from the active site, and is ideally located to evacuate the cleaved nucleotide in 5'-3' exonucleolytic mode. We show that B. subtilis RNase J1, which shows processive behavior on long RNAs, behaves distributively for substrates less than 5 nucleotides in length. We propose a model involving the binding of the RNA to the surface of the β-CASP domain to explain the enzyme's processive action.


  • Organizational Affiliation

    FRC550, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metal dependent hydrolase562Thermus thermophilus HB27Mutation(s): 1 
Gene Names: ttc0775TT_C0775
EC: 3
UniProt
Find proteins for Q72JJ7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72JJ7 
Go to UniProtKB:  Q72JJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72JJ7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
O2'methyl-RNA6N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.207 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.95α = 90
b = 116.78β = 90
c = 231.28γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSCONVdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Derived calculations
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description