1Y97

The human TREX2 3' exonuclease structure suggests a mechanism for efficient non-processive DNA catalysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Human TREX2 3' -> 5'-Exonuclease Structure Suggests a Mechanism for Efficient Nonprocessive DNA Catalysis.

Perrino, F.W.Harvey, S.McMillin, S.Hollis, T.

(2005) J.Biol.Chem. 280: 15212-15218

  • DOI: 10.1074/jbc.M500108200

  • PubMed Abstract: 
  • The 3' --> 5'-exonucleases process DNA ends in many DNA repair pathways of human cells. Determination of the human TREX2 structure is the first of a dimeric 3'-deoxyribonuclease and indicates how this highly efficient nonprocessive enzyme removes nuc ...

    The 3' --> 5'-exonucleases process DNA ends in many DNA repair pathways of human cells. Determination of the human TREX2 structure is the first of a dimeric 3'-deoxyribonuclease and indicates how this highly efficient nonprocessive enzyme removes nucleotides at DNA 3' termini. Symmetry in the TREX2 dimer positions the active sites at opposite outer edges providing open access for the DNA. Adjacent to each active site is a flexible region containing three arginines positioned appropriately to bind DNA and to control its entry into the active site. Mutation of these three arginines to alanines reduces the DNA binding capacity by approximately 100-fold with no effect on catalysis. The human TREX2 catalytic residues overlay with the bacterial DnaQ family of 3'-exonucleases confirming the structural conservation of the catalytic sites despite limited sequence identity, and mutations of these residues decrease the still measurable activity by approximately 10(5)-fold, confirming their catalytic role.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Three prime repair exonuclease 2
A, B
238Homo sapiensMutation(s): 0 
Gene Names: TREX2
EC: 3.1.11.2
Find proteins for Q9BQ50 (Homo sapiens)
Go to Gene View: TREX2
Go to UniProtKB:  Q9BQ50
Small Molecules
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: 2.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.500α = 90.00
b = 77.200β = 90.00
c = 101.700γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance