5J0T

Binary complex crystal structure of DNA polymerase Beta with G:A mismatch at the primer terminus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.201 

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This is version 1.1 of the entry. See complete history. 


Literature

Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.

Batra, V.K., Beard, W.A., Pedersen, L.C., Wilson, S.H.

(2016) Structure 24: 1863-1875

  • DOI: 10.1016/j.str.2016.08.006
  • Primary Citation of Related Structures:  
    5TZV, 5J0T, 5J0S, 5J0U, 5J0X, 5J0W, 5J0Y, 5J0P, 5J0O, 5J0R

  • PubMed Abstract: 

    • High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic s ...

    High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis.

    Organizational Affiliation: 

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709-12233, USA. Electronic address: wilson5@niehs.nih.gov.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
NIH Common Fund Data Resources
PHAROS  P06746
GTEx  ENSG00000070501
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    Template StrandT16synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      Primer StrandP10synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        Downstream Primer StrandD5synthetic construct
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.00 Å
        • R-Value Free: 0.258 
        • R-Value Work: 0.201 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.4α = 90
        b = 79.2β = 106.1
        c = 54.7γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data collection
        CNSrefinement
        PDB_EXTRACTdata extraction
        HKL-2000data reduction
        HKL-2000data scaling
        CNSphasing

        Structure Validation

        View Full Validation Report


        View more in-depth experimental data

        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2016-10-26
          Type: Initial release
        • Version 1.1: 2016-11-09
          Changes: Database references