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: https://doi.org/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 2277Saccharolobus 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
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UniProt GroupQ9UXC0
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1250Saccharolobus 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
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UniProt GroupQ9UXC2
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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))
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Go to UniProtKB:  Q9UXC4
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UniProt GroupQ9UXC4
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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
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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
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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