2A1R

Crystal structure of PARN nuclease domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insight into poly(A) binding and catalytic mechanism of human PARN

Wu, M.Reuter, M.Lilie, H.Liu, Y.Wahle, E.Song, H.

(2005) EMBO J 24: 4082-4093

  • DOI: 10.1038/sj.emboj.7600869
  • Primary Citation of Related Structures:  
    2A1S, 2A1R

  • PubMed Abstract: 
  • Poly(A)-specific ribonuclease (PARN) is a processive, poly(A)-specific 3' exoribonuclease. The crystal structure of C-terminal truncated human PARN determined in two states (free and RNA-bound forms) reveals that PARNn is folded into two domains, an ...

    Poly(A)-specific ribonuclease (PARN) is a processive, poly(A)-specific 3' exoribonuclease. The crystal structure of C-terminal truncated human PARN determined in two states (free and RNA-bound forms) reveals that PARNn is folded into two domains, an R3H domain and a nuclease domain similar to those of Pop2p and epsilon186. The high similarity of the active site structures of PARNn and epsilon186 suggests that they may have a similar catalytic mechanism. PARNn forms a tight homodimer, with the R3H domain of one subunit partially enclosing the active site of the other subunit and poly(A) bound in a deep cavity of its nuclease domain in a sequence-nonspecific manner. The R3H domain and, possibly, the cap-binding domain are involved in poly(A) binding but these domains alone do not appear to contribute to poly(A) specificity. Mutations disrupting dimerization abolish both the enzymatic and RNA-binding activities, suggesting that the PARN dimer is a structural and functional unit. The cap-binding domain may act in concert with the R3H domain to amplify the processivity of PARN.


    Organizational Affiliation

    Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, Proteos, Singapore.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(A)-specific ribonuclease PARNAB430Homo sapiensMutation(s): 0 
Gene Names: PARNDAN
EC: 3.1.13.4
Find proteins for O95453 (Homo sapiens)
Explore O95453 
Go to UniProtKB:  O95453
NIH Common Fund Data Resources
PHAROS  O95453
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*AP*A)-3'C, D3N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.236 
    • R-Value Work: 0.218 
    • R-Value Observed: 0.219 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 72.778α = 90
    b = 92.401β = 90
    c = 159.642γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    MOSFLMdata reduction
    CCP4data scaling
    SnBphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2005-06-21 
    • Released Date: 2005-12-20 
    • Deposition Author(s): Wu, M., Song, H.

    Revision History 

    • Version 1.0: 2005-12-20
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Advisory, Version format compliance
    • Version 1.3: 2017-10-11
      Changes: Refinement description