2PFN

Na in the active site of DNA Polymerase lambda

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.213 

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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(by identity cutoff)  |  Structure
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
GTEx  ENSG00000166169
Protein Feature View
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  • Reference Sequence
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    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    TemplateT11N/A
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      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      PrimerP6N/A
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        • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        Downstream PrimerD4N/A
        Small Molecules
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.90 Å
        • R-Value Free: 0.232 
        • R-Value Work: 0.213 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 55.082α = 90
        b = 61.557β = 90
        c = 140.532γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        CNSrefinement
        PDB_EXTRACTdata extraction
        StructureStudiodata collection
        HKL-2000data reduction
        HKL-2000data scaling
        MOLREPphasing

        Structure Validation

        View Full Validation Report


        View more in-depth experimental data

        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