5A0T

Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.283 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J

Pei, X.Y.Bralley, P.Jones, G.H.Luisi, B.F.

(2015) Nucleic Acids Res. 43: 8066

  • DOI: 10.1093/nar/gkv732
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with ...

    In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 Å and 2.80 Å resolution, respectively. These structures reveal snapshots of the enzyme cleaving substrate directionally and sequentially from the 5' terminus. In the pre-cleavage state, a water molecule is coordinated to a zinc ion pair in the active site but is imperfectly oriented to launch a nucleophilic attack on the phosphate backbone. A conformational switch is envisaged that enables the in-line positioning of the attacking water and may be facilitated by magnesium ions. Adjacent to the scissile bond, four bases are stacked in a tightly sandwiching pocket, and mutagenesis results indicate that this organization helps to drive processive exo-ribonucleolytic cleavage. Like its numerous homologues, S. coelicolor RNase J can also cleave some RNA internally, and the structural data suggest how the preference for exo- versus endo-cleavage mode is linked with recognition of the chemical status of the substrate's 5' end.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE J
A, B
561Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Mutation(s): 0 
Gene Names: rnj
EC: 3.1.-.-
Find proteins for O86842 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  O86842
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*CP*GP*CP*CP*UP)-3'E,F6Escherichia coli BL21(DE3)
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.283 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 186.187α = 90.00
b = 186.187β = 90.00
c = 113.382γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
SHELXphasing
PHENIXphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references