4KAZ

Crystal structure of RNase T in complex with a Y structured DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways.

Hsiao, Y.Y.Fang, W.H.Lee, C.C.Chen, Y.P.Yuan, H.S.

(2014) PLoS Biol 12: e1001803-e1001803

  • DOI: https://doi.org/10.1371/journal.pbio.1001803
  • Primary Citation of Related Structures:  
    4KAZ, 4KB0, 4KB1

  • PubMed Abstract: 

    DNA repair mechanisms are essential for preservation of genome integrity. However, it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways. Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-damaging agents and UV radiation. RNase T specifically trims the 3' end of structured DNA, including bulge, bubble, and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3' end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3' overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V-dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DnaQ-like exonucleases in DNA 3'-end processing.


  • Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease T235Escherichia coli K-12Mutation(s): 0 
Gene Names: b1652JW1644rnt
EC: 3.1.13
UniProt
Find proteins for P30014 (Escherichia coli (strain K12))
Explore P30014 
Go to UniProtKB:  P30014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30014
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')20N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.675α = 90
b = 90.58β = 90
c = 46.621γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description