4FZZ

Exonuclease X in complex with 5' overhanging duplex DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease

Wang, T.Sun, H.L.Cheng, F.Zhang, X.E.Bi, L.Jiang, T.

(2013) Nucleic Acids Res. 41: 7556-7565

  • DOI: 10.1093/nar/gkt495
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Members of the DnaQ superfamily are major 3'-5' exonucleases that degrade either only single-stranded DNA (ssDNA) or both ssDNA and double-stranded DNA (dsDNA). However, the mechanism by which dsDNA is recognized and digested remains unclear. Exonucl ...

    Members of the DnaQ superfamily are major 3'-5' exonucleases that degrade either only single-stranded DNA (ssDNA) or both ssDNA and double-stranded DNA (dsDNA). However, the mechanism by which dsDNA is recognized and digested remains unclear. Exonuclease X (ExoX) is a distributive DnaQ exonuclease that cleaves both ssDNA and dsDNA substrates. Here, we report the crystal structures of Escherichia coli ExoX in complex with three different dsDNA substrates: 3' overhanging dsDNA, blunt-ended dsDNA and 3' recessed mismatch-containing dsDNA. In these structures, ExoX binds to dsDNA via both a conserved substrate strand-interacting site and a previously uncharacterized complementary strand-interacting motif. When ExoX complexes with blunt-ended dsDNA or 5' overhanging dsDNA, a 'wedge' composed of Leu12 and Gln13 penetrates between the first two base pairs to break the 3' terminal base pair and facilitates precise feeding of the 3' terminus of the substrate strand into the ExoX cleavage active site. Site-directed mutagenesis showed that the complementary strand-binding site and the wedge of ExoX are dsDNA specific. Together with the results of structural comparisons, our data support a mechanism by which normal and mismatched dsDNA are recognized and digested by E. coli ExoX. The crystal structures also provide insight into the structural framework of the different substrate specificities of the DnaQ family members.


    Organizational Affiliation

    National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China, Graduate School of Chinese Academy of Sciences, Beijing 100039, China and State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exodeoxyribonuclease 10
A, B
175Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: exoX (yobC)
EC: 3.1.11.-
Find proteins for P0AEK0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEK0
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*AP*TP*TP*GP*TP*GP*GP*AP*TP*CP*CP*GP*AP*G)-3')D,C17N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.192α = 90.00
b = 79.009β = 90.00
c = 156.012γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references