Divalent metal ions (manganese) bound to T5 5'-exonuclease

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.252 

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This is version 1.3 of the entry. See complete history


Roles of Divalent Metal Ions in Flap Endonuclease-Substrate Interactions

Feng, M.Patel, D.Dervan, J.Ceska, T.A.Suck, D.Haq, I.Sayers, J.R.

(2004) Nat Struct Mol Biol 11: 450

  • DOI: https://doi.org/10.1038/nsmb754
  • Primary Citation of Related Structures:  
    1UT5, 1UT8

  • PubMed Abstract: 

    Flap endonucleases (FENs) have essential roles in DNA processing. They catalyze exonucleolytic and structure-specific endonucleolytic DNA cleavage reactions. Divalent metal ions are essential cofactors in both reactions. The crystal structure of FEN shows that the protein has two conserved metal-binding sites. Mutations in site I caused complete loss of catalytic activity. Mutation of crucial aspartates in site II abolished exonuclease action, but caused enzymes to retain structure-specific (flap endonuclease) activity. Isothermal titration calorimetry revealed that site I has a 30-fold higher affinity for cofactor than site II. Structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity site, whereas exonuclease activity requires that both the high- and low-affinity sites be occupied by divalent cofactor. The data suggest that a novel two-metal mechanism operates in the FEN-catalyzed exonucleolytic reaction. These results raise the possibility that local concentrations of free cofactor could influence the endo- or exonucleolytic pathway in vivo.

  • Organizational Affiliation

    University of Sheffield School of Medicine and Biomedical Science, Division of Genomic Medicine, Beech Hill Road, Sheffield, S10 2RX, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
291Tequintavirus T5Mutation(s): 0 
Find proteins for P06229 (Escherichia phage T5)
Explore P06229 
Go to UniProtKB:  P06229
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06229
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.252 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.6α = 90
b = 77.6β = 90
c = 134.61γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description