4KAZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1371/journal.pbio.1001803
  • Primary Citation of Related Structures:  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 critic ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease T
A
235Escherichia coli (strain K12)Gene Names: rnt
EC: 3.1.13.-
Find proteins for P30014 (Escherichia coli (strain K12))
Go to UniProtKB:  P30014
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')B20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 60.675α = 90.00
b = 90.580β = 90.00
c = 46.621γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Database references