4RO1

An 3'-5'-exoribonuclease that specifically recognizes RNAs.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural analysis of Dis3l2, an exosome-independent exonuclease from Schizosaccharomyces pombe.

Lv, H., Zhu, Y., Qiu, Y., Niu, L., Teng, M., Li, X.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1284-1294

  • DOI: 10.1107/S1399004715005805
  • Primary Citation of Related Structures:  
    4RO1

  • PubMed Abstract: 

    • After deadenylation and decapping, cytoplasmic mRNA can be digested in two opposite directions: in the 5'-3' direction by Xrn1 or in the 3'-5' direction by the exosome complex. Recently, a novel 3'-5' RNA-decay pathway involving Dis3l2 has been described that differs from degradation by Xrn1 and the exosome ...

    After deadenylation and decapping, cytoplasmic mRNA can be digested in two opposite directions: in the 5'-3' direction by Xrn1 or in the 3'-5' direction by the exosome complex. Recently, a novel 3'-5' RNA-decay pathway involving Dis3l2 has been described that differs from degradation by Xrn1 and the exosome. The product of the Schizosaccharomyces pombe gene SPAC2C4.07c was identified as a homologue of human Dis3l2. In this work, the 2.8 Å resolution X-ray crystal structure of S. pombe Dis3l2 (SpDis3l2) is reported, the conformation of which is obviously different from that in the homologous mouse Dis3l2-RNA complex. Fluorescence polarization assay experiments showed that RNB and S1 are the primary RNA-binding domains and that the CSDs (CSD1 and CSD2) play an indispensable role in the RNA-binding process of SpDis3l2. Taking the structure comparison and mutagenic experiments together, it can be inferred that the RNA-recognition pattern of SpDis3l2 resembles that of its mouse homologue rather than that of the Escherichia coli RNase II-RNA complex. Furthermore, a drastic conformation change could occur following the binding of the RNA substrate to SpDis3l2.

    Organizational Affiliation: 

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIS3-like exonuclease 2B [auth A],
A [auth B]		764Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: dis32, dis3l2, SPAC2C4.07c
EC: 3.1.13
UniProt
Find proteins for O14040 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O14040 
Go to UniProtKB:  O14040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14040
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.966α = 90
b = 54.201β = 107.09
c = 127.217γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AutoSolphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-10-27 
  • Released Date: 2015-06-10 
    • Deposition Author(s): Lv, H., Zhu, Y., Teng, M.

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references