5J2E

Ternary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.239 

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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:  
    5J2F, 5J2E, 5J2H, 5J2G, 5J2J, 5J2I, 5J2K, 5J2B, 5J2A, 5J2D, 5J2C, 5J0T, 5J0S, 5J0U, 5J0X, 5J0W, 5J0Y, 5J0P, 5J0O, 5J0R, 5J0Q, 5J29, 5TZV

  • 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 structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes ...

    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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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)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    Template StrandB [auth T]16synthetic construct
    Protein Feature View
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      Primer StrandC [auth P]10synthetic construct
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      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        Downstream Primer StrandD5synthetic construct
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        • Reference Sequence
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.10 Å
        • R-Value Free: 0.292 
        • R-Value Work: 0.239 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 50.94α = 90
        b = 79.94β = 107.68
        c = 55.5γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data collection
        CNSrefinement
        PDB_EXTRACTdata extraction
        HKL-2000data reduction
        HKL-2000data scaling
        CNSphasing

        Structure Validation

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        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

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