5YWT

Crystal structure of TREX1 in complex with a duplex DNA with 3' overhang


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: https://doi.org/10.1371/journal.pbio.2005653
  • Primary Citation of Related Structures:  
    5YWS, 5YWT, 5YWU, 5YWV

  • 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 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

    Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, ROC.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Three-prime repair exonuclease 1
A, B
276Mus musculusMutation(s): 0 
Gene Names: Trex1
EC: 3.1.11.2
UniProt
Find proteins for Q91XB0 (Mus musculus)
Explore Q91XB0 
Go to UniProtKB:  Q91XB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XB0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')C [auth D],
D [auth C]
19Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.17α = 90
b = 80.35β = 90
c = 85.22γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • 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  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description