Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA

Abstract

Poly(ADP-ribose) polymerase-1 (PARP-1) has two homolo- gous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activ- ity 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 involve- ment in DNA repair and transcription. Here, we have deter- mined crystal structures for the individual Zn1 and Zn2 domains in complex with aDNAdouble strand break, providing the first views ofPARP-1 zinc fingers bound to DNA. The Zn1- DNAand Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a con- tinuous region of the phosphodiester backbone and the hydro- phobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains per- form 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.