4YNQ

TREX1-dsDNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Exonuclease TREX1 degrades double-stranded DNA to prevent spontaneous lupus-like inflammatory disease.

Grieves, J.L.Fye, J.M.Harvey, S.Grayson, J.M.Hollis, T.Perrino, F.W.

(2015) Proc.Natl.Acad.Sci.USA 112: 5117-5122

  • DOI: 10.1073/pnas.1423804112

  • PubMed Abstract: 
  • The TREX1 gene encodes a potent DNA exonuclease, and mutations in TREX1 cause a spectrum of lupus-like autoimmune diseases. Most lupus patients develop autoantibodies to double-stranded DNA (dsDNA), but the source of DNA antigen is unknown. The TREX1 ...

    The TREX1 gene encodes a potent DNA exonuclease, and mutations in TREX1 cause a spectrum of lupus-like autoimmune diseases. Most lupus patients develop autoantibodies to double-stranded DNA (dsDNA), but the source of DNA antigen is unknown. The TREX1 D18N mutation causes a monogenic, cutaneous form of lupus called familial chilblain lupus, and the TREX1 D18N enzyme exhibits dysfunctional dsDNA-degrading activity, providing a link between dsDNA degradation and nucleic acid-mediated autoimmune disease. We determined the structure of the TREX1 D18N protein in complex with dsDNA, revealing how this exonuclease uses a novel DNA-unwinding mechanism to separate the polynucleotide strands for single-stranded DNA (ssDNA) loading into the active site. The TREX1 D18N dsDNA interactions coupled with catalytic deficiency explain how this mutant nuclease prevents dsDNA degradation. We tested the effects of TREX1 D18N in vivo by replacing the TREX1 WT gene in mice with the TREX1 D18N allele. The TREX1 D18N mice exhibit systemic inflammation, lymphoid hyperplasia, vasculitis, and kidney disease. The observed lupus-like inflammatory disease is associated with immune activation, production of autoantibodies to dsDNA, and deposition of immune complexes in the kidney. Thus, dysfunctional dsDNA degradation by TREX1 D18N induces disease in mice that recapitulates many characteristics of human lupus. Failure to clear DNA has long been linked to lupus in humans, and these data point to dsDNA as a key substrate for TREX1 and a major antigen source in mice with dysfunctional TREX1 enzyme.


    Organizational Affiliation

    Department of Biochemistry.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Three-prime repair exonuclease 1
A, B, C, D
235Mus musculusMutation(s): 1 
Gene Names: Trex1
EC: 3.1.11.2
Find proteins for Q91XB0 (Mus musculus)
Go to UniProtKB:  Q91XB0
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (24-MER)E,G21synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')F,H20synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DT
Query on DT

Download SDF File 
Download CCD File 
H
THYMIDINE-5'-MONOPHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.142α = 90.00
b = 84.457β = 102.15
c = 103.000γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing
d*TREKdata reduction
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release