2PNZ

Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into the mechanism of progressive RNA degradation by the archaeal exosome.

Navarro, M.V.A.S.Oliveira, C.C.Zanchin, N.I.Guimaraes, B.G.

(2008) J.Biol.Chem. 283: 14120-14131

  • DOI: 10.1074/jbc.M801005200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyroco ...

    Initially identified in yeast, the exosome has emerged as a central component of the RNA maturation and degradation machinery both in Archaea and eukaryotes. Here we describe a series of high-resolution structures of the RNase PH ring from the Pyrococcus abyssi exosome, one of them containing three 10-mer RNA strands within the exosome catalytic chamber, and report additional nucleotide interactions involving positions N5 and N7. Residues from all three Rrp41-Rrp42 heterodimers interact with a single RNA molecule, providing evidence for the functional relevance of exosome ring-like assembly in RNA processivity. Furthermore, an ADP-bound structure showed a rearrangement of nucleotide interactions at site N1, suggesting a rationale for the elimination of nucleoside diphosphate after catalysis. In combination with RNA degradation assays performed with mutants of key amino acid residues, the structural data presented here provide support for a model of exosome-mediated RNA degradation that integrates the events involving catalytic cleavage, product elimination, and RNA translocation. Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation.


    Organizational Affiliation

    Brazilian Synchrotron Light Laboratory, 13083-970 Campinas, SP, Brazil. mn372@cornell.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable exosome complex exonuclease 1
A
249Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: rrp41
EC: 3.1.13.-
Find proteins for Q9V119 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V119
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable exosome complex exonuclease 2
B
277Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: rrp42
Find proteins for Q9V118 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V118
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
5GP
Query on 5GP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.810α = 90.00
b = 93.810β = 90.00
c = 126.260γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
MAR345dtbdata collection
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance