Protein Name

Intein PI-SceI homing endonuclease / DNA complex


Saccharomyces cerevisiae (Baker's yeast)

Biological Context

DNA is subject to various kinds of chemical damage. Left unfixed, DNA damage would result in incorrect proteins and through its duplication, accumulated genetic defects. To deal with such errors, enzymes called restriction endonucleases are available. They recognize certain DNA sequences and can cut the DNA at these recognition sites. This is the first step in repairing DNA damage. Homing endonucleases are endonucleases that cut at very specific, very rare sites, because the DNA sequence of their recognition sites is much longer than for normal endonucleases. DNA encoding of proteins is not strictly linear. The DNA sequence has stretches called exons which contain code for a protein, separated by stretches of sequence called introns. More than one exon may be needed for a single protein. When an intron gets translated into protein, the result is called an intein. Homing endonucleases like the one seen here are such inteins. They are called homing endonucleases, because they promote introduction of their genetic elements into strands of DNA that do not contain them. The fact that they cut at rather rare sites makes them useful tools for genome analysis.

Structure Description


The homing endonuclease consists of two domains: an endonuclease domain that interacts with DNA and a protein splicing domain which allows it to cut out protein sequences. It uses this last property for a sort of magician trick. The sequence for the endonuclease is actually contained within a sequence encoding an ATPase. The protein cuts itself out of this structure, a process called autocatalytic. Structure PDB:1DFA in the Protein Data Bank shows the first structure of the homing nuclease. The structure here shows the same protein together with DNA. The DNA bound to the protein is 36 base pairs long extending all along the size of the endonuclease. Altogether the DNA contains about 20% of all the atoms in the structure. In the two DNA interacting domains of the protein, binding of DNA causes it to bend significantly, by about 50 degrees in the endonuclease domain and by about half that amount in the splicing domain.

Protein Data Bank (PDB)



  • Moure, C.M. Gimble, F.S. Quiocho, F.A.; "Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence."; Nat.Struct.Biol.; (2002) 9:764-770 PubMed:12219083.


author: Arno Paehler

Japanese version:PDB:1LWS