4AV1

Crystal structure of the human PARP-1 DNA binding domain in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

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This is version 1.1 of the entry. See complete history


Literature

The Zinc-Finger Domains of Parp1 Cooperate to Recognise DNA Strand-Breaks

Ali, A.A.E.Timinszky, G.Arribas-Bosacoma, R.Kozlowski, M.Hassa, P.O.Hassler, M.Ladurner, A.G.Pearl, L.H.Oliver, A.W.

(2012) Nat Struct Mol Biol 19: 685

  • DOI: 10.1038/nsmb.2335
  • Primary Citation of Related Structures:  
    4AV1

  • PubMed Abstract: 
  • Poly(ADP-ribose) polymerase 1 (PARP1) is a primary DNA damage sensor whose (ADP-ribose) polymerase activity is acutely regulated by interaction with DNA breaks. Upon activation at sites of DNA damage, PARP1 modifies itself and other proteins by covalent addition of long, branched polymers of ADP-ribose, which in turn recruit downstream DNA repair and chromatin remodeling factors ...

    Poly(ADP-ribose) polymerase 1 (PARP1) is a primary DNA damage sensor whose (ADP-ribose) polymerase activity is acutely regulated by interaction with DNA breaks. Upon activation at sites of DNA damage, PARP1 modifies itself and other proteins by covalent addition of long, branched polymers of ADP-ribose, which in turn recruit downstream DNA repair and chromatin remodeling factors. PARP1 recognizes DNA damage through its N-terminal DNA-binding domain (DBD), which consists of a tandem repeat of an unusual zinc-finger (ZnF) domain. We have determined the crystal structure of the human PARP1-DBD bound to a DNA break. Along with functional analysis of PARP1 recruitment to sites of DNA damage in vivo, the structure reveals a dimeric assembly whereby ZnF1 and ZnF2 domains from separate PARP1 molecules form a strand-break recognition module that helps activate PARP1 by facilitating its dimerization and consequent trans-automodification.


    Organizational Affiliation

    Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN7 9QR, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLY [ADP-RIBOSE] POLYMERASE 1A, B, C, D223Homo sapiensMutation(s): 0 
Gene Names: PARP1ADPRTPPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
PHAROS:  P09874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*AP*GP*TP*GP*TP*TP*GP*CP*AP*TP*TP)-3'E [auth X]12synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*AP*TP*GP*CP*AP*AP*CP*AP*CP*TP)-3'F [auth Y]12synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.978α = 90
b = 59.504β = 101.18
c = 61.582γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Other