4BA2

Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction.

Lorentzen, E.Conti, E.

(2012) Archaea 2012: 21869

  • DOI: 10.1155/2012/721869
  • Primary Citation of Related Structures:  
    4BA1, 4BA2

  • PubMed Abstract: 
  • The RNA exosome is an important protein complex that functions in the 3' processing and degradation of RNA in archaeal and eukaryotic organisms. The archaeal exosome is functionally similar to bacterial polynucleotide phosphorylase (PNPase) and RNase PH enzymes as it uses inorganic phosphate (Pi) to processively cleave RNA substrates releasing nucleoside diphosphates ...

    The RNA exosome is an important protein complex that functions in the 3' processing and degradation of RNA in archaeal and eukaryotic organisms. The archaeal exosome is functionally similar to bacterial polynucleotide phosphorylase (PNPase) and RNase PH enzymes as it uses inorganic phosphate (Pi) to processively cleave RNA substrates releasing nucleoside diphosphates. To shed light on the mechanism of catalysis, we have determined the crystal structures of mutant archaeal exosome in complex with either Pi or with both RNA and Pi at resolutions of 1.8 Å and 2.5 Å, respectively. These structures represent views of precatalytic states of the enzyme and allow the accurate determination of the substrate binding geometries. In the structure with both Pi and RNA bound, the Pi closely approaches the phosphate of the 3'-end nucleotide of the RNA and is in a perfect position to perform a nucleophilic attack. The presence of negative charge resulting from the close contacts between the phosphates appears to be neutralized by conserved positively charged residues in the active site of the archaeal exosome. The high degree of structural conservation between the archaeal exosome and the PNPase including the requirement for divalent metal ions for catalysis is discussed.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2A277Saccharolobus solfataricusMutation(s): 0 
UniProt
Find proteins for Q9UXC0 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Go to UniProtKB:  Q9UXC0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1B250Saccharolobus solfataricusMutation(s): 1 
EC: 3.1.13
UniProt
Find proteins for Q9UXC2 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Go to UniProtKB:  Q9UXC2
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1C [auth I]251Saccharolobus solfataricusMutation(s): 0 
UniProt
Find proteins for Q9UXC4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UXC4 
Go to UniProtKB:  Q9UXC4
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*AP*AP*AP)-3'D [auth R]4Saccharolobus solfataricus
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    1PE
    Query on 1PE

    Download Ideal Coordinates CCD File 
    E [auth A]PENTAETHYLENE GLYCOL
    C10 H22 O6
    JLFNLZLINWHATN-UHFFFAOYSA-N
     Ligand Interaction
    PO4
    Query on PO4

    Download Ideal Coordinates CCD File 
    F [auth B], H [auth I]PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    G [auth B]SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.259 
    • R-Value Work: 0.185 
    • R-Value Observed: 0.189 
    • Space Group: P 21 3
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 134.83α = 90
    b = 134.83β = 90
    c = 134.83γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XDSdata scaling

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2012-10-03
      Type: Initial release
    • Version 1.1: 2013-01-30
      Changes: Database references
    • Version 1.2: 2014-01-15
      Changes: Database references