1KLN

DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Work: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of DNA polymerase I Klenow fragment bound to duplex DNA.

Beese, L.S.Derbyshire, V.Steitz, T.A.

(1993) Science 260: 352-355

  • DOI: 10.1126/science.8469987
  • Primary Citation of Related Structures:  
    1KLN

  • PubMed Abstract: 
  • Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5' exonuclease domain ...

    Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5' exonuclease domain. When the fragment bound DNA, a region previously referred to as the "disordered domain" became more ordered and moved along with two helices toward the 3' to 5' exonuclease domain to form the binding groove. A single-stranded, 3' extension of three nucleotides bound to the 3' to 5' exonuclease active site. Although this cocrystal structure appears to be an editing complex, it suggests that the primer strand approaches the catalytic site of the polymerase from the direction of the 3' to 5' exonuclease domain and that the duplex DNA product may bend to enter the cleft that contains the polymerase catalytic site.


    Related Citations: 
    • Structural Basis for the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I: A Two Metal Ion Mechanism
      Beese, L.S., Steitz, T.A.
      (1991) EMBO J 10: 25
    • Co-Crystal Structure of an Editing Complex of Klenow Fragment with DNA
      Freemont, P.S., Friedman, J.M., Beese, L.S., Steitz, T.A.
      (1988) Proc Natl Acad Sci U S A 85: 8924
    • Structure of Large Fragment of Escherichia Coli DNA Polymerase I Complexed with dTMP
      Ollis, D.L., Brick, P., Hamlin, R., Xuong, N.G., Steitz, T.A.
      (1985) Nature 313: 762

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7))C [auth A]605Escherichia coliMutation(s): 1 
EC: 2.7.7.7
UniProt
Find proteins for P00582 (Escherichia coli (strain K12))
Explore P00582 
Go to UniProtKB:  P00582
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3')A [auth B]13N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*CP*GP*CP*GP*AP*GP*GP*C)-3')B [auth C]10N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      D [auth B]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.20 Å
      • R-Value Work: 0.230 
      • Space Group: P 43
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 104.3α = 90
      b = 104.3β = 90
      c = 86γ = 90
      Software Package:
      Software NamePurpose
      X-PLORrefinement

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1994-11-30
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance