1UT5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXODEOXYRIBONUCLEASEA, B291Escherichia virus T5Mutation(s): 0 
Gene Names: D15exo5T5.130T5p128
EC: 3.1.11.3 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P06229 (Escherichia phage T5)
Explore P06229 
Go to UniProtKB:  P06229
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNXrefinement
XDSdata reduction
XDSdata scaling
CCP4phasing

Structure Validation

View Full Validation Report




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