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: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

Starting Model: experimental
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This is version 1.2 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 U S A 110: E3071-E3080

  • DOI: https://doi.org/10.1073/pnas.1305281110
  • Primary Citation of Related Structures:  
    4K1G

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endonuclease 4
A, B
285Escherichia coli K-12Mutation(s): 1 
Gene Names: nfob2159JW2146
EC: 3.1.21.2
UniProt
Find proteins for P0A6C1 (Escherichia coli (strain K12))
Explore P0A6C1 
Go to UniProtKB:  P0A6C1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6C1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')C [auth E],
F [auth M]
6N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')D [auth F],
G [auth N]
15N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')E [auth H],
H [auth O]
9N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.95α = 90
b = 136.66β = 90
c = 112.46γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description