2BCU

DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp and a T:T mismatch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase

Garcia-Diaz, M.Bebenek, K.Krahn, J.M.Pedersen, L.C.Kunkel, T.A.

(2006) Cell 124: 331-342

  • DOI: 10.1016/j.cell.2005.10.039
  • Primary Citation of Related Structures:  
    2BCR, 2BCQ, 2BCV, 2BCU, 2BCS

  • PubMed Abstract: 
  • Insertions and deletions in coding sequences can alter the reading frame of genes and have profound biological consequences. In 1966, Streisinger proposed that these mutations result from strand slippage, which in repetitive sequences generates misaligned intermediates stabilized by correct base pairing that support polymerization ...

    Insertions and deletions in coding sequences can alter the reading frame of genes and have profound biological consequences. In 1966, Streisinger proposed that these mutations result from strand slippage, which in repetitive sequences generates misaligned intermediates stabilized by correct base pairing that support polymerization. We report here crystal structures of human DNA polymerase lambda, which frequently generates deletion mutations, bound to such intermediates. Each contains an extrahelical template nucleotide upstream of the active site. Surprisingly, the extra nucleotide, even when combined with an adjacent mismatch, does not perturb polymerase active site geometry, which is indistinguishable from that for correctly aligned strands. These structures reveal how pol lambda can polymerize on substrates with minimal homology during repair of double-strand breaks and represent strand-slippage intermediates consistent with Streisinger's classical hypothesis. They are thus relevant to the origin of single-base deletions, a class of mutations that can confer strong biological phenotypes.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaD [auth A]335Homo sapiensMutation(s): 0 
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
    5'-D(P*GP*CP*CP*G)-3'A [auth D]4N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*GP*TP*TP*CP*G)-3'B [auth P]7N/A
      Protein Feature View
      Expand
      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(*CP*GP*GP*CP*CP*GP*AP*TP*AP*CP*TP*G)-3'C [auth T]12N/A
        Protein Feature View
        Expand
        • Reference Sequence
        Small Molecules
        Ligands 2 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        PPV
        Query on PPV

        Download Ideal Coordinates CCD File 
        H [auth A]PYROPHOSPHATE
        H4 O7 P2
        XPPKVPWEQAFLFU-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        E [auth A], F [auth A], G [auth A]SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.20 Å
        • R-Value Free: 0.247 
        • R-Value Work: 0.219 
        • R-Value Observed: 0.219 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 55.998α = 90
        b = 62.667β = 90
        c = 140.494γ = 90
        Software Package:
        Software NamePurpose
        CNSrefinement
        STRUCTUREdata reduction
        SCALEPACKdata scaling
        MOLREPphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2006-03-07
          Type: Initial release
        • Version 1.1: 2008-05-01
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance