2GWS

Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Promiscuous mismatch extension by human DNA polymerase lambda.

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

(2006) Nucleic Acids Res 34: 3259-3266

  • DOI: 10.1093/nar/gkl377
  • Primary Citation of Related Structures:  
    2GWS

  • PubMed Abstract: 
  • DNA polymerase lambda (Pol lambda) is one of several DNA polymerases suggested to participate in base excision repair (BER), in repair of broken DNA ends and in translesion synthesis. It has been proposed that the nature of the DNA intermediates partly d ...

    DNA polymerase lambda (Pol lambda) is one of several DNA polymerases suggested to participate in base excision repair (BER), in repair of broken DNA ends and in translesion synthesis. It has been proposed that the nature of the DNA intermediates partly determines which polymerase is used for a particular repair reaction. To test this hypothesis, here we examine the ability of human Pol lambda to extend mismatched primer-termini, either on 'open' template-primer substrates, or on its preferred substrate, a 1 nt gapped-DNA molecule having a 5'-phosphate. Interestingly, Pol lambda extended mismatches with an average efficiency of approximately 10(-2) relative to matched base pairs. The match and mismatch extension catalytic efficiencies obtained on gapped molecules were approximately 260-fold higher than on template-primer molecules. A crystal structure of Pol lambda in complex with a single-nucleotide gap containing a dG.dGMP mismatch at the primer-terminus (2.40 A) suggests that, at least for certain mispairs, Pol lambda is unable to differentiate between matched and mismatched termini during the DNA binding step, thus accounting for the relatively high efficiency of mismatch extension. This property of Pol lambda suggests a potential role as a 'mismatch extender' during non-homologous end joining (NHEJ), and possibly during translesion synthesis.


    Organizational Affiliation

    Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, 28049 Madrid, Spain.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambda AEIM335Homo 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: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'F, J, N, T11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*TP*GP*CP*GP*G)-3'G, K, P, R6N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*CP*CP*G)-3'D, H, L, Q4N/A
        Small Molecules
        Ligands 5 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        CAC
        Query on CAC

        Download Ideal Coordinates CCD File 
        D, H, J
        CACODYLATE ION
        C2 H6 As O2
        OGGXGZAMXPVRFZ-UHFFFAOYSA-M
         Ligand Interaction
        EDO
        Query on EDO

        Download Ideal Coordinates CCD File 
        E, N
        1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        CL
        Query on CL

        Download Ideal Coordinates CCD File 
        A
        CHLORIDE ION
        Cl
        VEXZGXHMUGYJMC-UHFFFAOYSA-M
         Ligand Interaction
        MG
        Query on MG

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

        Download Ideal Coordinates CCD File 
        A, E, I, M, P, Q, T
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.40 Å
        • R-Value Free: 0.253 
        • R-Value Work: 0.209 
        • Space Group: P 21 21 2
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 192.374α = 90
        b = 98.268β = 90
        c = 104.96γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        CNSrefinement
        PDB_EXTRACTdata extraction

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2006-09-05
          Type: Initial release
        • Version 1.1: 2008-05-01
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Non-polymer description, Version format compliance
        • Version 1.3: 2017-10-18
          Changes: Refinement description