2WNR

The structure of Methanothermobacter thermautotrophicus exosome core assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Methanothermobacter Thermautotrophicus Exosome Rnase Ph Ring

Ng, C.L.Waterman, D.G.Antson, A.A.Ortiz-Lombardia, M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 522

  • DOI: 10.1107/S0907444910002908
  • Primary Citation of Related Structures:  
    2WNR

  • PubMed Abstract: 
  • The core of the exosome, a versatile multisubunit RNA-processing enzyme found in archaea and eukaryotes, includes a ring of six RNase PH subunits. This basic architecture is homologous to those of the bacterial and archaeal RNase PHs and the bacterial polynucleotide phosphorylase (PNPase) ...

    The core of the exosome, a versatile multisubunit RNA-processing enzyme found in archaea and eukaryotes, includes a ring of six RNase PH subunits. This basic architecture is homologous to those of the bacterial and archaeal RNase PHs and the bacterial polynucleotide phosphorylase (PNPase). While all six RNase PH monomers are catalytically active in the homohexameric RNase PH, only half of them are functional in the bacterial PNPase and in the archaeal exosome core and none are functional in the yeast and human exosome cores. Here, the crystal structure of the RNase PH ring from the exosome of the anaerobic methanogenic archaeon Methanothermobacter thermautotrophicus is described at 2.65 A resolution. Free phosphate anions were found for the first time in the active sites of the RNase PH subunits of an exosome structure and provide structural snapshots of a critical intermediate in the phosphorolytic degradation of RNA by the exosome. Furthermore, the present structure highlights the plasticity of the surfaces delineating the polar regions of the RNase PH ring of the exosome, a feature that can facilitate both interaction with the many cofactors involved in exosome function and the processive activity of this enzyme.


    Organizational Affiliation

    York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5YW, England. clng@mrc-lmb.cam.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2A, C, E271Methanothermobacter thermautotrophicusMutation(s): 0 
EC: 3.1.13
Find proteins for O26778 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26778 
Go to UniProtKB:  O26778
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1B, D, F240Methanothermobacter thermautotrophicusMutation(s): 0 
EC: 3.1.13
Find proteins for O26779 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26779 
Go to UniProtKB:  O26779
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth B], H [auth D], I [auth F]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.261α = 90
b = 118.233β = 90
c = 154.708γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-05-30
    Changes: Other