5YWU

Crystal structure of TREX1 in complex with a inosine contained dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1

Huang, K.W.Liu, T.C.Liang, R.Y.Chu, L.Y.Cheng, H.L.Chu, J.W.Hsiao, Y.Y.

(2018) PLoS Biol. 16: e2005653-e2005653

  • DOI: 10.1371/journal.pbio.2005653
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Three prime repair exonuclease 1 (TREX1) is an essential exonuclease in mammalian cells, and numerous in vivo and in vitro data evidenced its participation in immunity regulation and in genotoxicity remediation. In these very complicated cellular fun ...

    Three prime repair exonuclease 1 (TREX1) is an essential exonuclease in mammalian cells, and numerous in vivo and in vitro data evidenced its participation in immunity regulation and in genotoxicity remediation. In these very complicated cellular functions, the molecular mechanisms by which duplex DNA substrates are processed are mostly elusive because of the lack of structure information. Here, we report multiple crystal structures of TREX1 complexed with various substrates to provide the structure basis for overhang excision and terminal unwinding of DNA duplexes. The substrates were designed to mimic the intermediate structural DNAs involved in various repair pathways. The results showed that the Leu24-Pro25-Ser26 cluster of TREX1 served to cap the nonscissile 5'-end of the DNA for precise removal of the short 3'-overhang in L- and Y-structural DNA or to wedge into the double-stranded region for further digestion along the duplex. Biochemical assays were also conducted to demonstrate that TREX1 can indeed degrade double-stranded DNA (dsDNA) to a full extent. Overall, this study provided unprecedented knowledge at the molecular level on the enzymatic substrate processing involved in prevention of immune activation and in responses to genotoxic stresses. For example, Arg128, whose mutation in TREX1 was linked to a disease state, were shown to exhibit consistent interaction patterns with the nonscissile strand in all of the structures we solved. Such structure basis is expected to play an indispensable role in elucidating the functional activities of TREX1 at the cellular level and in vivo.


    Organizational Affiliation

    Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan, ROC.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Nankang, Taipei, Taiwan, ROC.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, ROC.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, ROC.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Three-prime repair exonuclease 1
A, B
259Mus musculusMutation(s): 0 
Gene Names: Trex1
EC: 3.1.11.2
Find proteins for Q91XB0 (Mus musculus)
Go to UniProtKB:  Q91XB0
Entity ID: 2
MoleculeChainsLengthOrganism
INOSINE CONTAINED DSDNASC,D23Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 133.180α = 90.00
b = 133.180β = 90.00
c = 76.282γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-30 
  • Released Date: 2018-05-23 
  • Deposition Author(s): Hsiao, Y.Y.

Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwanMOST103-2311-B-009-001-MY3

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release