3PNC

Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Replication infidelity via a mismatch with Watson-Crick geometry.

Bebenek, K.Pedersen, L.C.Kunkel, T.A.

(2011) Proc Natl Acad Sci U S A 108: 1862-1867

  • DOI: 10.1073/pnas.1012825108
  • Primary Citation of Related Structures:  
    3PML, 3PMN, 3PNC

  • PubMed Abstract: 
  • In describing the DNA double helix, Watson and Crick suggested that "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." Indeed, among many mispairing possibilities, either tautomerization or ...

    In describing the DNA double helix, Watson and Crick suggested that "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson-Crick geometry. However, despite substantial progress in understanding the structural basis of error prevention during polymerization, no DNA polymerase has yet been shown to form a natural base-base mismatch with Watson-Crick-like geometry. Here we provide such evidence, in the form of a crystal structure of a human DNA polymerase λ variant poised to misinsert dGTP opposite a template T. All atoms needed for catalysis are present at the active site and in positions that overlay with those for a correct base pair. The mismatch has Watson-Crick geometry consistent with a tautomeric or ionized base pair, with the pH dependence of misinsertion consistent with the latter. The results support the original idea that a base substitution can originate from a mismatch having Watson-Crick geometry, and they suggest a common catalytic mechanism for inserting a correct and an incorrect nucleotide. A second structure indicates that after misinsertion, the now primer-terminal G • T mismatch is also poised for catalysis but in the wobble conformation seen in other studies, indicating the dynamic nature of the pathway required to create a mismatch in fully duplex DNA.


    Organizational Affiliation

    Laboratory of Molecular Genetics, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaA329Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
NIH Common Fund Data Resources
PHAROS  Q9UGP5
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*AP*GP*TP*AP*G)-3'B6N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*GP*GP*CP*CP*TP*TP*AP*CP*TP*G)-3'C11N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(*GP*CP*CP*G)-3'D4N/A
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        1GC
        Query on 1GC

        Download Ideal Coordinates CCD File 
        A
        2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine
        C11 H18 N5 O12 P3
        JTBKCZGNQPBEJY-RRKCRQDMSA-N
         Ligand Interaction
        TRS
        Query on TRS

        Download Ideal Coordinates CCD File 
        A
        2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
        C4 H12 N O3
        LENZDBCJOHFCAS-UHFFFAOYSA-O
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        A
        MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        A, B
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.00 Å
        • R-Value Free: 0.236 
        • R-Value Work: 0.208 
        • R-Value Observed: 0.208 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 56.161α = 90
        b = 62.254β = 90
        c = 139.834γ = 90
        Software Package:
        Software NamePurpose
        CrystalCleardata collection
        MOLREPphasing
        CNSrefinement
        HKL-2000data reduction
        HKL-2000data scaling

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2011-02-02
          Type: Initial release
        • Version 1.1: 2011-07-13
          Changes: Version format compliance