3C5F

Structure of a binary complex of the R517A Pol lambda mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.

Bebenek, K.Garcia-Diaz, M.Foley, M.C.Pedersen, L.C.Schlick, T.Kunkel, T.A.

(2008) EMBO Rep 9: 459-464

  • DOI: 10.1038/embor.2008.33
  • Primary Citation of Related Structures:  
    3C5F, 3C5G

  • PubMed Abstract: 
  • The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerative diseases ...

    The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerative diseases. The classical idea is that simple deletions arise by strand slippage. A prime opportunity for slippage occurs during DNA synthesis, but it remains unclear how slippage is controlled during a polymerization cycle. Here, we report crystal structures and molecular dynamics simulations of mutant derivatives of DNA polymerase lambda bound to a primer-template during strand slippage. Relative to the primer strand, the template strand is in multiple conformations, indicating intermediates on the pathway to deletion mutagenesis. Consistent with these intermediates, the mutant polymerases generate single-base deletions at high rates. The results indicate that dNTP-induced template strand repositioning during conformational rearrangements in the catalytic cycle is crucial to controlling the rate of strand slippage.


    Organizational Affiliation

    Laboratory of Structural Biology and Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaG [auth A], H [auth B]335Homo sapiensMutation(s): 1 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3')A [auth T], D [auth U]11N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')B [auth P], E [auth Q]6N/A
      Protein Feature View
      Expand
      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*DGP*DCP*DCP*DG)-3')C [auth D], F [auth E]4N/A
        Protein Feature View
        Expand
        • Reference Sequence
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.25 Å
        • R-Value Free: 0.263 
        • R-Value Work: 0.224 
        • Space Group: P 21 21 2
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 94.237α = 90
        b = 151.884β = 90
        c = 85.635γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        CNSrefinement
        PDB_EXTRACTdata extraction
        HKL-2000data collection
        CNSphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2008-09-02
          Type: Initial release
        • Version 1.1: 2011-07-13
          Changes: Version format compliance
        • Version 1.2: 2017-10-25
          Changes: Refinement description