1AKO

EXONUCLEASE III FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and function of the multifunctional DNA-repair enzyme exonuclease III.

Mol, C.D.Kuo, C.F.Thayer, M.M.Cunningham, R.P.Tainer, J.A.

(1995) Nature 374: 381-386

  • DOI: 10.1038/374381a0

  • PubMed Abstract: 
  • The repair of DNA requires the removal of abasic sites, which are constantly generated in vivo both spontaneously and by enzymatic removal of uracil, and of bases damaged by active oxygen species, alkylating agents and ionizing radiation. The major a ...

    The repair of DNA requires the removal of abasic sites, which are constantly generated in vivo both spontaneously and by enzymatic removal of uracil, and of bases damaged by active oxygen species, alkylating agents and ionizing radiation. The major apurinic/apyrimidinic (AP) DNA-repair endonuclease in Escherichia coli is the multifunctional enzyme exonuclease III, which also exhibits 3'-repair diesterase, 3'-->5' exonuclease, 3'-phosphomonoesterase and ribonuclease activities. We report here the 1.7 A resolution crystal structure of exonuclease III which reveals a 2-fold symmetric, four-layered alpha beta fold with similarities to both deoxyribonuclease I and RNase H. In the ternary complex determined at 2.6 A resolution, Mn2+ and dCMP bind to exonuclease III at one end of the alpha beta-sandwich, in a region dominated by positive electrostatic potential. Residues conserved among AP endonucleases from bacteria to man cluster within this active site and appear to participate in phosphate-bond cleavage at AP sites through a nucleophilic attack facilitated by a single bound metal ion.


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXONUCLEASE III
A
268Escherichia coli (strain K12)Gene Names: xthA (xth)
EC: 3.1.11.2
Find proteins for P09030 (Escherichia coli (strain K12))
Go to UniProtKB:  P09030
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.800α = 90.00
b = 107.800β = 90.00
c = 42.800γ = 120.00
Software Package:
Software NamePurpose
XENGENdata reduction
X-PLORrefinement
X-PLORmodel building
PHASESphasing
XENGENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance