1UOC

X-ray structure of the RNase domain of the yeast Pop2 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Structure and Activity of the Yeast Pop2 Protein: A Nuclease Subunit of the Mrna Deadenylase Complex

Thore, S.Mauxion, F.Seraphin, B.Suck, D.

(2003) Embo Rep. 4: 1150

  • DOI: 10.1038/sj.embor.7400020

  • PubMed Abstract: 
  • In Saccharomyces cerevisiae, a large complex, known as the Ccr4-Not complex, containing two nucleases, is responsible for mRNA deadenylation. One of these nucleases is called Pop2 and has been identified by similarity with PARN, a human poly(A) nucle ...

    In Saccharomyces cerevisiae, a large complex, known as the Ccr4-Not complex, containing two nucleases, is responsible for mRNA deadenylation. One of these nucleases is called Pop2 and has been identified by similarity with PARN, a human poly(A) nuclease. Here, we present the crystal structure of the nuclease domain of Pop2 at 2.3 A resolution. The domain has the fold of the DnaQ family and represents the first structure of an RNase from the DEDD superfamily. Despite the presence of two non-canonical residues in the active site, the domain displays RNase activity on a broad range of RNA substrates. Site-directed mutagenesis of active-site residues demonstrates the intrinsic ability of the Pop2 RNase D domain to digest RNA. This first structure of a nuclease involved in the 3'-5' deadenylation of mRNA in yeast provides information for the understanding of the mechanism by which the Ccr4-Not complex achieves its functions.


    Organizational Affiliation

    European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POP2
A, B
289Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: POP2 (CAF1)
EC: 3.1.13.4
Find proteins for P39008 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39008
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
XE
Query on XE

Download SDF File 
Download CCD File 
A, B
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.582α = 90.00
b = 79.440β = 90.00
c = 101.324γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SOLVE/RESOLVEphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance