2IOC

The crystal structure of TREX1 explains the 3' nucleotide specificity and reveals a polyproline II helix for protein partenring

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals a Polyproline II Helix for Protein Partnering.

de Silva, U., Choudhury, S., Bailey, S.L., Harvey, S., Perrino, F.W., Hollis, T.

(2007) J.Biol.Chem. 282: 10537-10543

  • DOI: 10.1074/jbc.M700039200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The TREX1 enzyme processes DNA ends as the major 3' --> 5' exonuclease activity in human cells. Mutations in the TREX1 gene are an underlying cause of the neurological brain disease Aicardi-Goutières syndrome implicating TREX1 dysfunction in an aberr ...

    The TREX1 enzyme processes DNA ends as the major 3' --> 5' exonuclease activity in human cells. Mutations in the TREX1 gene are an underlying cause of the neurological brain disease Aicardi-Goutières syndrome implicating TREX1 dysfunction in an aberrant immune response. TREX1 action during apoptosis likely prevents autoimmune reaction to DNA that would otherwise persist. To understand the impact of TREX1 mutations identified in patients with Aicardi-Goutières syndrome on structure and activity we determined the x-ray crystal structure of the dimeric mouse TREX1 protein in substrate and product complexes containing single-stranded DNA and deoxyadenosine monophosphate, respectively. The structures show the specific interactions between the bound nucleotides and the residues lining the binding pocket of the 3' terminal nucleotide within the enzyme active site that account for specificity, and provide the molecular basis for understanding mutations that lead to disease. Three mutant forms of TREX1 protein identified in patients with Aicardi-Goutières syndrome were prepared and the measured activities show that these specific mutations reduce enzyme activity by 4-35,000-fold. The structure also reveals an 8-amino acid polyproline II helix within the TREX1 enzyme that suggests a mechanism for interactions of this exonuclease with other protein complexes.

    Organizational Affiliation: 

    Department of Biochemistry, Center for Structural Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Three prime repair exonuclease 1
B, A
242Mus musculusMutation(s): 0 
Gene Names: Trex1
EC: 3.1.11.2
Find proteins for Q91XB0 (Mus musculus)
Go to UniProtKB:  Q91XB0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
D5M
Query on D5M
Download SDF File 
Download CCD File 
A, B
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 119.700α = 90.00
b = 119.700β = 90.00
c = 83.300γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-14
    Type: Experimental preparation