1RZT

Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology.

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

(2004) Mol Cell 13: 561-572

  • DOI: 10.1016/s1097-2765(04)00061-9
  • Primary Citation of Related Structures:  
    1RZT

  • PubMed Abstract: 
  • Human DNA polymerase lambda (Pol lambda) is a family X member with low frameshift fidelity that has been suggested to perform gap-filling DNA synthesis during base excision repair and during repair of broken ends with limited homology. Here, we prese ...

    Human DNA polymerase lambda (Pol lambda) is a family X member with low frameshift fidelity that has been suggested to perform gap-filling DNA synthesis during base excision repair and during repair of broken ends with limited homology. Here, we present a 2.1 A crystal structure of the catalytic core of Pol lambda in complex with DNA containing a two nucleotide gap. Pol lambda makes limited contacts with the template strand at the polymerase active site, and superimposition with Pol beta in a ternary complex suggests a shift in the position of the DNA at the active site that is reminiscent of a deletion intermediate. Surprisingly, Pol lambda can adopt a closed conformation, even in the absence of dNTP binding. These observations have implications for the catalytic mechanism and putative DNA repair functions of Pol lambda.


    Organizational Affiliation

    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaAEIM331Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
NIH Common Fund Data Resources
PHAROS  Q9UGP5
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*GP*CP*AP*AP*CP*GP*CP*AP*C)-3'B, F, J, N11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*TP*GP*CP*G)-3'C, G, K, O5N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*CP*CP*G)-3'D, H, L, P4N/A
        Small Molecules
        Ligands 2 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        EDO
        Query on EDO

        Download CCD File 
        M
        1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

        Download CCD File 
        A, B, E, F, I, J, M
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.10 Å
        • R-Value Free: 0.260 
        • R-Value Work: 0.227 
        • R-Value Observed: 0.227 
        • Space Group: P 21 21 2
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 191.321α = 90
        b = 99.034β = 90
        c = 104.838γ = 90
        Software Package:
        Software NamePurpose
        CNSrefinement
        SCALEPACKdata scaling
        MOLREPphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2004-03-02
          Type: Initial release
        • Version 1.1: 2008-04-29
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance
        • Version 1.3: 2017-10-11
          Changes: Refinement description