3HKM

Crystal Structure of rice(Oryza sativa) Rrp46


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9845 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation

Yang, C.-C.Wang, Y.-T.Hsiao, Y.-Y.Doudeva, L.G.Kuo, P.-H.Chow, S.Y.Yuan, H.S.

(2010) Rna 16: 1748-1759

  • DOI: 10.1261/rna.2180810
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rrp46 was first identified as a protein component of the eukaryotic exosome, a protein complex involved in 3' processing of RNA during RNA turnover and surveillance. The Rrp46 homolog, CRN-5, was subsequently characterized as a cell death-related nuc ...

    Rrp46 was first identified as a protein component of the eukaryotic exosome, a protein complex involved in 3' processing of RNA during RNA turnover and surveillance. The Rrp46 homolog, CRN-5, was subsequently characterized as a cell death-related nuclease, participating in DNA fragmentation during apoptosis in Caenorhabditis elegans. Here we report the crystal structures of CRN-5 and rice Rrp46 (oRrp46) at a resolution of 3.9 A and 2.0 A, respectively. We found that recombinant human Rrp46 (hRrp46), oRrp46, and CRN-5 are homodimers, and that endogenous hRrp46 and oRrp46 also form homodimers in a cellular environment, in addition to their association with a protein complex. Dimeric oRrp46 had both phosphorolytic RNase and hydrolytic DNase activities, whereas hRrp46 and CRN-5 bound to DNA without detectable nuclease activity. Site-directed mutagenesis in oRrp46 abolished either its DNase (E160Q) or RNase (K75E/Q76E) activities, confirming the critical importance of these residues in catalysis or substrate binding. Moreover, CRN-5 directly interacted with the apoptotic nuclease CRN-4 and enhanced the DNase activity of CRN-4, suggesting that CRN-5 cooperates with CRN-4 in apoptotic DNA degradation. Taken together all these results strongly suggest that Rrp46 forms a homodimer separately from exosome complexes and, depending on species, is either a structural or catalytic component of the machinery that cleaves DNA during apoptosis.


    Organizational Affiliation

    Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, 10617 Taiwan, Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Os03g0854200 protein
A, B, C
246Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: RRP46
EC: 3.1.13.-
Find proteins for Q84T68 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q84T68
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9845 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.169 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 111.607α = 90.00
b = 111.607β = 90.00
c = 57.702γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance