2VNU

Crystal structure of Sc Rrp44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Active Subunit of the Yeast Exosome Core, Rrp44: Diverse Modes of Substrate Recruitment in the Rnase II Nuclease Family

Lorentzen, E.Basquin, J.Tomecki, R.Dziembowski, A.Conti, E.

(2008) Mol Cell 29: 717

  • DOI: 10.1016/j.molcel.2008.02.018
  • Primary Citation of Related Structures:  
    2VNU

  • PubMed Abstract: 
  • The eukaryotic exosome is a macromolecular complex essential for RNA processing and decay. It has recently been shown that the RNase activity of the yeast exosome core can be mapped to a single subunit, Rrp44, which processively degrades single-stranded RNAs as well as RNAs containing secondary structures ...

    The eukaryotic exosome is a macromolecular complex essential for RNA processing and decay. It has recently been shown that the RNase activity of the yeast exosome core can be mapped to a single subunit, Rrp44, which processively degrades single-stranded RNAs as well as RNAs containing secondary structures. Here we present the 2.3 A resolution crystal structure of S. cerevisiae Rrp44 in complex with single-stranded RNA. Although Rrp44 has a linear domain organization similar to bacterial RNase II, in three dimensions the domains have a different arrangement. The three domains of the classical nucleic-acid-binding OB fold are positioned on the catalytic domain such that the RNA-binding path observed in RNase II is occluded. Instead, RNA is threaded to the catalytic site via an alternative route suggesting a mechanism for RNA-duplex unwinding. The structure provides a molecular rationale for the observed biochemical properties of the RNase R family of nucleases.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EXOSOME COMPLEX EXONUCLEASE RRP44B [auth D]760Saccharomyces cerevisiaeMutation(s): 1 
EC: 3.1.13 (UniProt), 3.1.26 (UniProt)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08162 
Go to UniProtKB:  Q08162
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP)-3'A [auth B]10Saccharomyces cerevisiae
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    1PE
    Query on 1PE

    Download Ideal Coordinates CCD File 
    E [auth D]PENTAETHYLENE GLYCOL
    C10 H22 O6
    JLFNLZLINWHATN-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    C [auth D]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    DSODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MSE
    Query on MSE
    B [auth D]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.30 Å
    • R-Value Free: 0.278 
    • R-Value Work: 0.217 
    • R-Value Observed: 0.219 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 72.35α = 90
    b = 87.25β = 90
    c = 136.27γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    XDSdata reduction
    XDSdata scaling
    SHELXphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2008-04-08
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Refinement description, Version format compliance