2C4R

Catalytic domain of E. coli RNase E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.319 
  • R-Value Observed: 0.320 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover

Callaghan, A.J.Marcaida, M.J.Stead, J.A.McDowall, K.J.Scott, W.G.Luisi, B.F.

(2005) Nature 437: 1187

  • DOI: 10.1038/nature04084
  • Primary Citation of Related Structures:  
    2C0B, 2C4R, 2BX2

  • PubMed Abstract: 
  • The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability, in which the targeted destruction of subsets of tran ...

    The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability, in which the targeted destruction of subsets of transcripts generates the potential for cross-regulating metabolic pathways. In Escherichia coli, the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors. RNase E cleaves RNA internally, but its catalytic power is determined by the 5' terminus of the substrate, even if this lies at a distance from the cutting site. Here we report crystal structures of the catalytic domain of RNase E as trapped allosteric intermediates with RNA substrates. Four subunits of RNase E catalytic domain associate into an interwoven quaternary structure, explaining why the subunit organization is required for catalytic activity. The subdomain encompassing the active site is structurally congruent to a deoxyribonuclease, making an unexpected link in the evolutionary history of RNA and DNA nucleases. The structure explains how the recognition of the 5' terminus of the substrate may trigger catalysis and also sheds light on the question of how RNase E might selectively process, rather than destroy, specific RNA precursors.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE EL517Escherichia coliMutation(s): 0 
EC: 3.1.4 (PDB Primary Data), 3.1.26.12 (UniProt)
Find proteins for P21513 (Escherichia coli (strain K12))
Explore P21513 
Go to UniProtKB:  P21513
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    SSRNA MOLECULE: 5'-R(*AP*CP*AP*GP*UP*AP*UP*UP*UP*GP)-3'R10Escherichia coli
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    L
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.60 Å
    • R-Value Free: 0.347 
    • R-Value Work: 0.319 
    • R-Value Observed: 0.320 
    • Space Group: P 62 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 196.586α = 90
    b = 196.586β = 90
    c = 140.766γ = 120
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2005-10-25
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Advisory, Refinement description, Version format compliance
    • Version 1.2: 2018-04-04
      Changes: Data collection, Database references