3PZP

Human DNA polymerase kappa extending opposite a cis-syn thymine dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report



Literature

Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer.

Vasquez-Del Carpio, R.Silverstein, T.D.Lone, S.Johnson, R.E.Prakash, L.Prakash, S.Aggarwal, A.K.

(2011) J Mol Biol 408: 252-261

  • DOI: 10.1016/j.jmb.2011.02.042
  • Primary Citation of Related Structures:  
    3PZP

  • PubMed Abstract: 
  • Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase κ (Polκ), a member of the Y-fa ...

    Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase κ (Polκ), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Polκ in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Polκ in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase kappaA, B517Homo sapiensMutation(s): 0 
Gene Names: POLKDINB1
EC: 2.7.7.7
Find proteins for Q9UBT6 (Homo sapiens)
Explore Q9UBT6 
Go to UniProtKB:  Q9UBT6
NIH Common Fund Data Resources
PHAROS  Q9UBT6
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'P, Q13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'T, U17N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DTP
      Query on DTP

      Download CCD File 
      A, B
      2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      SUYVUBYJARFZHO-RRKCRQDMSA-N
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A, B
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.34 Å
      • R-Value Free: 0.288 
      • R-Value Work: 0.242 
      • R-Value Observed: 0.244 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 117.136α = 90
      b = 154.476β = 90
      c = 217.854γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data collection
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2011-12-28
        Type: Initial release