3ODC

Human PARP-1 zinc finger 2 (Zn2) bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY.

Langelier, M.F.Planck, J.L.Roy, S.Pascal, J.M.

(2011) J Biol Chem 286: 10690-10701

  • DOI: 10.1074/jbc.M110.202507
  • Primary Citation of Related Structures:  
    3ODA, 3ODC, 3ODE, 3OD8

  • PubMed Abstract: 
  • Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural bas ...

    Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1AB111Homo sapiensMutation(s): 0 
Gene Names: ADPRTPARP1PPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
NIH Common Fund Data Resources
PHAROS  P09874
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'C, E8N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'D, F8N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download CCD File 
      A, B
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.240 
      • R-Value Work: 0.193 
      • R-Value Observed: 0.195 
      • Space Group: P 31 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 63.731α = 90
      b = 63.731β = 90
      c = 192.405γ = 120
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      CBASSdata collection
      HKL-2000data reduction
      SOLVEphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2011-01-12
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2017-11-08
        Changes: Refinement description