2VOA

Structure of an AP Endonuclease from Archaeoglobus fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure and Function of the Abasic Site Specificity Pocket of an Ap Endonuclease from Archaeoglobus Fulgidus.

Schmiedel, R.Kuettner, E.B.Keim, A.Strater, N.Greiner-Stoffele, T.

(2009) DNA Repair (Amst) 8: 219

  • DOI: 10.1016/j.dnarep.2008.10.009
  • Primary Citation of Related Structures:  
    2VOA

  • PubMed Abstract: 
  • The major AP endonuclease in Escherichia coli Exonuclease III (ExoIII) is frequently used in gene technology due to its strong exonucleolytic activity. A thermostabilized variant of ExoIII or a homologous enzyme from thermophilic organisms could be most useful for further applications ...

    The major AP endonuclease in Escherichia coli Exonuclease III (ExoIII) is frequently used in gene technology due to its strong exonucleolytic activity. A thermostabilized variant of ExoIII or a homologous enzyme from thermophilic organisms could be most useful for further applications. For this purpose we characterized a nuclease from the hyperthermophilic archaeon Archaeoglobus fulgidus (Af_Exo), which shares 33% overall sequence identity and 55% similarity to ExoIII. The gene coding for this thermostable enzyme was cloned and expressed in E. coli. The purified protein shows a strong Mg(2+)-dependent nicking activity at AP-sites, nicking of undamaged double-stranded (ds) DNA and a weak exonucleolytic activity. A V217G variant of the enzyme was crystallized with decamer ds-DNA molecule, and the three-dimensional structure was determined to 1.7A resolution. Besides our goal to find or produce a thermostable exonuclease, the structural and catalytic data of Af_Exo and a series of mutant proteins, based on the crystal structure, provide new insight into the mechanism of abasic site recognition and repair. Each of the hydrophobic residues Phe 200, Trp 215 and Val 217, forming a binding pocket for the abasic deoxyribose in Af_Exo, were mutated to glycine or serine. By expanding the size of the binding pocket the unspecific endonucleolytic activity is increased. Thus, size and flexibility of the mostly hydrophobic binding pocket have a significant influence on AP-site specificity. We suggest that its tight fitting to the flipped-out deoxyribose allows for a preferred competent binding of abasic sites. In a larger or more flexible pocket however, intact nucleotides more easily bind in a catalytically competent conformation, resulting in loss of specificity. Moreover, with mutations of Phe 200 and Trp 215 we induced a strong exonucleolytic activity on undamaged DNA.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Characterization of Two Thermostable DNA Nucleases
      Kuettner, E.B., Pfeifer, S., Keim, A., Greiner-Stoffele, T., Strater, N.
      (2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1290

    Organizational Affiliation

    Institute of Biochemistry, Faculty of Biology, Pharmacy and Psychology, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXODEOXYRIBONUCLEASE IIIA, B257Archaeoglobus fulgidusMutation(s): 1 
EC: 4.2.99.18
UniProt
Find proteins for O29675 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29675 
Go to UniProtKB:  O29675
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*GP*GP*TP*AP*GP*CP*CP*GP)-3'C10synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*GP*GP*CP*TP*AP*CP*CP*GP*CP)-3'D10synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      OCS
      Query on OCS
      A, BL-PEPTIDE LINKINGC3 H7 N O5 SCYS
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.230 
      • R-Value Work: 0.198 
      • R-Value Observed: 0.198 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 67.786α = 90
      b = 60.817β = 91.22
      c = 72.349γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2008-12-09
        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: 2019-05-08
        Changes: Data collection, Derived calculations, Experimental preparation, Other, Source and taxonomy
      • Version 1.4: 2019-05-29
        Changes: Data collection, Experimental preparation
      • Version 1.5: 2021-09-01
        Changes: Database references, Derived calculations, Other