High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI

Nucleic Acids Res. 2002 Sep 15;30(18):3962-71. doi: 10.1093/nar/gkf523.


The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the approximately 35 bp recognition sequence. At 1.35 A resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75 degrees bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Endodeoxyribonucleases / chemistry*
  • Endodeoxyribonucleases / genetics
  • Fungal Proteins / chemistry
  • Fungal Proteins / genetics
  • Models, Molecular
  • Protein Conformation
  • Protein Splicing
  • Protein Structure, Tertiary
  • Proton-Translocating ATPases*
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae Proteins*


  • Fungal Proteins
  • Saccharomyces cerevisiae Proteins
  • Endodeoxyribonucleases
  • Proton-Translocating ATPases
  • VMA1 protein, S cerevisiae

Associated data

  • PDB/1BP7
  • PDB/1DFA
  • PDB/1EF0
  • PDB/1GPP
  • PDB/1JVA
  • PDB/1VDE