3MDC

DNA polymerase lambda in complex with dFdCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interaction between DNA Polymerase lambda and anticancer nucleoside analogs.

Garcia-Diaz, M.Murray, M.S.Kunkel, T.A.Chou, K.M.

(2010) J Biol Chem 285: 16874-16879

  • DOI: 10.1074/jbc.M109.094391
  • Primary Citation of Related Structures:  
    3MDC, 3MDA

  • PubMed Abstract: 
  • The anticancer activity of cytarabine (AraC) and gemcitabine (dFdC) is thought to result from chain termination after incorporation into DNA. To investigate their incorporation into DNA at atomic level resolution, we present crystal structures of hum ...

    The anticancer activity of cytarabine (AraC) and gemcitabine (dFdC) is thought to result from chain termination after incorporation into DNA. To investigate their incorporation into DNA at atomic level resolution, we present crystal structures of human DNA polymerase lambda (Pol lambda) bound to gapped DNA and containing either AraC or dFdC paired opposite template dG. These structures reveal that AraC and dFdC can bind within the nascent base pair binding pocket of Pol lambda. Although the conformation of the ribose of AraCTP is similar to that of normal dCTP, the conformation of dFdCTP is significantly different. Consistent with these structures, Pol lambda efficiently incorporates AraCTP but not dFdCTP. The data are consistent with the possibility that Pol lambda could modulate the cytotoxic effect of AraC.


    Organizational Affiliation

    Laboratory of Structural Biology and Laboratory of Molecular Genetics, Department of Health and Human Services, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaA325Homo 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: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3')T11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')P6N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*CP*CP*G)-3')D4N/A
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        GTF
        Query on GTF

        Download Ideal Coordinates CCD File 
        A
        2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)
        C9 H14 F2 N3 O13 P3
        YMOXEIOKAJSRQX-QPPQHZFASA-N
         Ligand Interaction
        MG
        Query on MG

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

        Download Ideal Coordinates CCD File 
        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: 0.266 
        • R-Value Work: 0.216 
        • R-Value Observed: 0.219 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 55.206α = 90
        b = 59.773β = 90
        c = 142.008γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        MOLREPphasing
        PHENIXrefinement
        PDB_EXTRACTdata extraction

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2010-04-28
          Type: Initial release
        • Version 1.1: 2011-07-13
          Changes: Version format compliance
        • Version 1.2: 2017-11-08
          Changes: Refinement description