1NK6

CYTOSINE-CYTOSINE MISMATCH AT THE POLYMERASE ACTIVE SITE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


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, 1NJW, 1NK8, 1NK7, 1NK6

  • 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, thereby favoring subsequent mismatch excision ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASE IC [auth A]580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA, pol
EC: 2.7.7.7
UniProt
Find proteins for P52026 (Geobacillus stearothermophilus)
Explore P52026 
Go to UniProtKB:  P52026
Protein Feature View
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  • Reference Sequence
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    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA PRIMER STRANDA [auth B]9N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA TEMPLATE STRANDB [auth C]15N/A
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      • Reference Sequence
      Oligosaccharides

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      Entity ID: 4
      MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
      beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseD, E2N/A Oligosaccharides Interaction
      Glycosylation Resources
      GlyTouCan:  G05551OP
      GlyCosmos:  G05551OP
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4
      Download Ideal Coordinates CCD File 
      		 F [auth A], G [auth A], H [auth A]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L      		 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 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.10 Å
      • R-Value Free: 0.252 
      • R-Value Work: 0.213 
      • R-Value Observed: 0.241 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 87.863α = 90
      b = 93.682β = 90
      c = 105.452γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      CNSphasing

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • 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