2PFO

DNA Polymerase lambda in complex with DNA and dUPNPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Role of the catalytic metal during polymerization by DNA polymerase lambda.

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

(2007) DNA Repair (Amst) 6: 1333-1340

  • DOI: 10.1016/j.dnarep.2007.03.005
  • Primary Citation of Related Structures:  
    2PFO, 2PFN, 2PFQ, 2PFP

  • PubMed Abstract: 
  • The incorporation of dNMPs into DNA by polymerases involves a phosphoryl transfer reaction hypothesized to require two divalent metal ions. Here we investigate this hypothesis using as a model human DNA polymerase lambda (Pol lambda), an enzyme sugge ...

    The incorporation of dNMPs into DNA by polymerases involves a phosphoryl transfer reaction hypothesized to require two divalent metal ions. Here we investigate this hypothesis using as a model human DNA polymerase lambda (Pol lambda), an enzyme suggested to be activated in vivo by manganese. We report the crystal structures of four complexes of human Pol lambda. In a 1.9 A structure of Pol lambda containing a 3'-OH and the non-hydrolyzable analog dUpnpp, a non-catalytic Na+ ion occupies the site for metal A and the ribose of the primer-terminal nucleotide is found in a conformation that positions the acceptor 3'-OH out of line with the alpha-phosphate and the bridging oxygen of the pyrophosphate leaving group. Soaking this crystal in MnCl2 yielded a 2.0 A structure with Mn2+ occupying the site for metal A. In the presence of Mn2+, the conformation of the ribose is C3'-endo and the 3'-oxygen is in line with the leaving oxygen, at a distance from the phosphorus atom of the alpha-phosphate (3.69 A) consistent with and supporting a catalytic mechanism involving two divalent metal ions. Finally, soaking with MnCl2 converted a pre-catalytic Pol lambda/Na+ complex with unreacted dCTP in the active site into a product complex via catalysis in the crystal. These data provide pre- and post-transition state information and outline in a single crystal the pathway for the phosphoryl transfer reaction carried out by DNA polymerases.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaA335Homo sapiensMutation(s): 1 
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
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    TemplateT11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      PrimerP6N/A
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      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        Downstream PrimerD4N/A
        Small Molecules
        Ligands 5 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        DUP
        Query on DUP

        Download CCD File 
        A
        2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
        C9 H16 N3 O13 P3
        XZLLMTSKYYYJLH-SHYZEUOFSA-N
         Ligand Interaction
        EDO
        Query on EDO

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        A
        1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        MN
        Query on MN

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        A
        MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N
         Ligand Interaction
        MG
        Query on MG

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        A
        MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

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        A
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.00 Å
        • R-Value Free: 0.242 
        • R-Value Work: 0.217 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 56.094α = 90
        b = 61.411β = 90
        c = 140.314γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        CNSrefinement
        PDB_EXTRACTdata extraction
        StructureStudiodata collection
        HKL-2000data reduction
        MOLREPphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2007-05-15
          Type: Initial release
        • Version 1.1: 2008-05-01
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance
        • Version 1.3: 2017-10-18
          Changes: Refinement description