Crystallographic snapshots along a protein-induced DNA-bending pathway

Crystallographic snapshots along a protein-induced DNA-bending pathway

Nancy C. Horton and
John J. Perona*

Department of Chemistry and Biochemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, CA 93106-9510

Edited by Peter H. von Hippel, University of Oregon, Eugene, OR, and approved March 2, 2000 (received for review August 30, 1999)

Abstract

Two new high-resolution cocrystal structures of EcoRV endonuclease bound to DNA show that a large variation in DNA-bending angles is sampled in the ground state binary complex. Together with previous structures, these data reveal a contiguous series of protein conformational states delineating a specific trajectory for the induced-fit pathway. Rotation of the DNA-binding domains, together with movements of two symmetry-related helices binding in the minor groove, causes base unstacking at a key base-pair step and propagates structural changes that assemble the active sites. These structures suggest a complex mechanism for DNA bending that depends on forces generated by interacting protein segments, and on selective neutralization of phosphate charges along the inner face of the bent double helix.

Footnotes

↵ * To whom reprint requests should be addressed. E-mail: perona{at}chem.ucsb.edu.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviation: NS, nonspecific DNA complex.
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID codes 1EOO and 1EOP).
Article published online before print: Proc. Natl. Acad. Sci. USA, 10.1073/pnas.090370797.
Article and publication date are at www.pnas.org/cgi/doi/10.1073/pnas.090370797