3U6F | pdb_00003u6f

Mouse TREX1 D200N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.288 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3U6F

This is version 1.2 of the entry. See complete history

Literature

Defects in DNA degradation revealed in crystal structures of TREX1 exonuclease mutations linked to autoimmune disease.

Bailey, S.L.Harvey, S.Perrino, F.W.Hollis, T.

(2012) DNA Repair (Amst) 11: 65-73

  • DOI: https://doi.org/10.1016/j.dnarep.2011.10.007
  • Primary Citation Related Structures: 
    3U3Y, 3U6F

  • PubMed Abstract: 

    Mutations within the human TREX1 3' exonuclease are associated with Aicardi-Goutières Syndrome (AGS) and familial chilblain lupus (FCL). Both AGS and FCL are autoimmune diseases that result in increased levels of interferon alpha and circulating antibodies to DNA. TREX1 is a member of the endoplasmic reticulum (ER)-associated SET complex and participates in granzyme A-mediated cell death to degrade nicked genomic DNA. The loss of TREX1 activity may result in the accumulation of double-stranded DNA (dsDNA) degradation intermediates that trigger autoimmune activation. The X-ray crystal structures of the TREX1 wt apoprotein, the dominant D200H, D200N and D18N homodimer mutants derived from AGS and FCL patients, as well as the recessive V201D homodimer mutant have been determined. The structures of the D200H and D200N mutant proteins reveal the enzyme has lost coordination of one of the active site metals, and the catalytic histidine (H195) is trapped in a conformation pointing away from the active site. The TREX1 D18N and V201D mutants are able to bind both metals in the active site, but with inter-metal distances that are larger than optimal for catalysis. Additionally, all of the mutant structures reveal a reduced mobility in the catalytic histidine, providing further explanation for the loss of catalytic activity. The structures of the mutant TREX1 proteins provide insight into the dysfunction relating to human disease. Additionally, the TREX1 apoprotein structure together with the previously determined wild type substrate and product structures allow us to propose a distinct mechanism for the TREX1 exonuclease.


  • Organizational Affiliation
    • Department of Biochemistry, Center for Structural Biology, Wake Forest University Health Sciences, Winston-Salem, NC 27157, United States.

Macromolecule Content 

  • Total Structure Weight: 70.08 kDa 
  • Atom Count: 3,701 
  • Modeled Residue Count: 443 
  • Deposited Residue Count: 636 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Three prime repair exonuclease 1A [auth B],
B [auth A]
314Mus musculusMutation(s): 1 
Gene Names: Trex1
EC: 3.1.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q91XB0 (Mus musculus)
Explore Q91XB0 
Go to UniProtKB:  Q91XB0
IMPC:  MGI:1328317
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XB0
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*AP*CP*G)-3'
C, D
4N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.288 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.886α = 90
b = 56.644β = 107.97
c = 68.143γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations