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

Structure. 2010 Jun 9;18(6):734-43. doi: 10.1016/j.str.2010.03.009.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Catalytic Domain / genetics
  • DNA Restriction Enzymes / genetics
  • DNA Restriction Enzymes / metabolism*
  • DNA* / chemistry
  • DNA* / genetics
  • DNA* / metabolism
  • Deoxyribonucleases, Type II Site-Specific
  • Metals / chemistry
  • Protein Structure, Tertiary / genetics


  • Metals
  • DNA
  • DNA Restriction Enzymes
  • Deoxyribonucleases, Type II Site-Specific
  • endodeoxyribonuclease PacI