1NKB

A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report



Literature

Structures of mismatch replication errors observed in a DNA polymerase.

Johnson, S.J.Beese, L.S.

(2004) Cell 116: 803-816

  • DOI: 10.1016/s0092-8674(04)00252-1
  • Primary Citation of Related Structures:  
    1NKE, 1NKC, 1NKB, 1NK5, 1NK4, 1NK0, 1NJZ, 1NJY, 1NJX, 1NK9

  • PubMed Abstract: 
  • Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereb ...

    Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.


    Related Citations: 
    • Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
      Johnson, S.J., Taylor, J.S., Beese, L.S.
      (2003) Proc Natl Acad Sci U S A 100: 3895
    • Visualizing DNA Replication in a Catalytically Active Bacillus DNA Polymerase Crystal
      Kiefer, J.R., Mao, C., Braman, J.C., Beese, L.S.
      (1998) Nature 391: 304
    • Crystal Structure of a Thermostable Bacillus DNA Polymerase I Large Fragment at 2.1 A Resolution
      Kiefer, J.R., Mao, C., Hansen, C.J., Basehore, S.L., Hogrefe, H.H., Braman, J.C., Beese, L.S.
      (1997) Structure 5: 95

    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASE IA580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polApol
EC: 2.7.7.7
Find proteins for P52026 (Geobacillus stearothermophilus)
Explore P52026 
Go to UniProtKB:  P52026
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA PRIMER STRANDB13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA TEMPLATE STRANDC15N/A
      Oligosaccharides

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      Entity ID: 4
      MoleculeChainsChain Length2D Diagram Glycosylation
      beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
      D, E
      2 N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download CCD File 
      A
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Biologically Interesting Molecules (External Reference) 1 Unique
      Entity ID: 4
      IDChainsNameType/Class2D Diagram3D Interactions
      PRD_900003
      Query on PRD_900003
      D, EsucroseOligosaccharide /  Nutrient

      --

      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.00 Å
      • R-Value Free: 0.244 
      • R-Value Work: 0.205 
      • R-Value Observed: 0.224 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 88.239α = 90
      b = 93.698β = 90
      c = 105.444γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-03-30
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 2.0: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary