6A4B

Structure of TREX2 in complex with a duplex DNA with 2 nucleotide 3'-overhang


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into the duplex DNA processing of TREX2

Cheng, H.L.Lin, C.T.Huang, K.W.Wang, S.Lin, Y.T.Toh, S.I.Hsiao, Y.Y.

(2018) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gky970
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three prime repair exonuclease 2 (TREX2) is an essential 3'-to-5' exonuclease that functions in cell proliferation, genome integrity and skin homeostasis maintenance. The abnormal expression level of TREX2 can result in broken chromosome, increas ...

    The three prime repair exonuclease 2 (TREX2) is an essential 3'-to-5' exonuclease that functions in cell proliferation, genome integrity and skin homeostasis maintenance. The abnormal expression level of TREX2 can result in broken chromosome, increased susceptibility to skin carcinogenesis and Psoriasis. However, the molecular mechanisms of how TREX2 binds and processes its natural substrates, dsDNA or chromosomal DNA, to maintain genome stability remain unclear. In this study, we present four new crystal structures: apo-TREX2, TREX2 in complex with two different dsDNA substrates, and TREX2 in complex with a processed dsDNA product. Analysis of the structures reveals that TREX2 stacks with the 5'-terminal of dsDNA by a Leu20-Pro21-Asn22 cluster for precisely trimming the 3'-overhang. In addition, TREX2 specifically interacts with the non-scissile strand of dsDNA by an α-helix-loop region. The unique interaction patterns of the TREX2-dsDNA complex highlight the requirement of long double-stranded region for TREX2 binding and provide evidence of the functional role of TREX2 in processing chromosomal DNA. Moreover, the non-processive property of TREX2 is elucidated by the structure of TREX2-product complex. Our work discloses the first structural basis of the molecular interactions between TREX2 and its substrates and unravels the mechanistic actions of TREX2.


    Organizational Affiliation

    Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan 30050, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Three prime repair exonuclease 2
A, B, C, D, E, F
256Mus musculusMutation(s): 0 
Gene Names: Trex2
EC: 3.1.11.2
Find proteins for Q9R1A9 (Mus musculus)
Go to UniProtKB:  Q9R1A9
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')G,H,I,J,K,L18Mus musculus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, I, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.715α = 90.00
b = 87.317β = 90.00
c = 432.941γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-19 
  • Released Date: 2018-11-07 
  • Deposition Author(s): Hsiao, Y.Y.

Funding OrganizationLocationGrant Number
TaiwanMOST 106-2311-B-009-002

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release