4K1G

Structure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved DNA duplex containing a alphadA:T basepair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases.

Mazouzi, A.Vigouroux, A.Aikeshev, B.Brooks, P.J.Saparbaev, M.K.Morera, S.Ishchenko, A.A.

(2013) Proc.Natl.Acad.Sci.USA 110: E3071-E3080

  • DOI: 10.1073/pnas.1305281110

  • PubMed Abstract: 
  • 8,5'-cyclo-2'-deoxyadenosine (cdA) and 8,5'-cyclo-2'-deoxyguanosine generated in DNA by both endogenous oxidative stress and ionizing radiation are helix-distorting lesions and strong blocks for DNA replication and transcription. In duplex DNA, these ...

    8,5'-cyclo-2'-deoxyadenosine (cdA) and 8,5'-cyclo-2'-deoxyguanosine generated in DNA by both endogenous oxidative stress and ionizing radiation are helix-distorting lesions and strong blocks for DNA replication and transcription. In duplex DNA, these lesions are repaired in the nucleotide excision repair (NER) pathway. However, lesions at DNA strand breaks are most likely poor substrates for NER. Here we report that the apurinic/apyrimidinic (AP) endonucleases--Escherichia coli Xth and human APE1--can remove 5'S cdA (S-cdA) at 3' termini of duplex DNA. In contrast, E. coli Nfo and yeast Apn1 are unable to carry out this reaction. None of these enzymes can remove S-cdA adduct located at 1 or more nt away from the 3' end. To understand the structural basis of 3' repair activity, we determined a high-resolution crystal structure of E. coli Nfo-H69A mutant bound to a duplex DNA containing an α-anomeric 2'-deoxyadenosine:T base pair. Surprisingly, the structure reveals a bound nucleotide incision repair (NIR) product with an abortive 3'-terminal dC close to the scissile position in the enzyme active site, providing insight into the mechanism for Nfo-catalyzed 3'→5' exonuclease function and its inhibition by 3'-terminal S-cdA residue. This structure was used as a template to model 3'-terminal residues in the APE1 active site and to explain biochemical data on APE1-catalyzed 3' repair activities. We propose that Xth and APE1 may act as a complementary repair pathway to NER to remove S-cdA adducts from 3' DNA termini in E. coli and human cells, respectively.


    Organizational Affiliation

    Université Paris-Sud, Laboratoire Stabilité Génétique et Oncogenèse, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 8200, Institut de Cancérologie Gustave-Roussy, F-94805 Villejuif Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endonuclease 4
A, B
285Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: nfo
EC: 3.1.21.2
Find proteins for P0A6C1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6C1
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')E,M6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')F,N15N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')H,O9N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 117.950α = 90.00
b = 136.660β = 90.00
c = 112.460γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
XDSdata reduction
DNAdata collection
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references