2A1R

Crystal structure of PARN nuclease domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 

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:  

  • 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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Poly(A)-specific ribonuclease PARN
A, B
430Homo sapiensMutation(s): 0 
Gene Names: PARN (DAN)
EC: 3.1.13.4
Find proteins for O95453 (Homo sapiens)
Go to Gene View: PARN
Go to UniProtKB:  O95453
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*AP*AP*A)-3'C,D3N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.778α = 90.00
b = 92.401β = 90.00
c = 159.642γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction
SnBphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description