Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.

Publication Type:

Journal Article


Structure (London, England : 1993), Volume 18, Issue 6, p.734-43 (2010)


2010, Base Pairing, Base Sequence, Basic Sciences Division, CATALYTIC DOMAIN, Center-Authored Paper, Deoxyribonucleases, Type II Site-Specific, DNA, DNA Restriction Enzymes, Metals, Protein Structure, Tertiary


The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight-base-pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 A resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a betabetaalpha-metal catalytic site. The latter is unusual in that a tyrosine residue likely initiates strand cleavage. PacI dramatically distorts its target sequence from Watson-Crick duplex DNA base pairing, with every base separated from its original partner. Two bases on each strand are unpaired, four are engaged in noncanonical A:A and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners. This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and implies that initial recognition of the target site might involve significantly different contacts from those visualized in the DNA-bound cocrystal structures.