<p>Inteins, or protein introns, are parts of protein sequences that are post-translationally excised, their flanking regions (exteins) being spliced together to yield an additional protein product [<cite idref="PUB00006583"/>,<cite idref="PUB00004447"/>]. This process is believed to be self-catalysed, apparently initiating at the C-terminal splice junction, where a conserved asparagine residue mediates the nucleophilic attack of the peptide bond between it and its neighbouring residue. Most inteins consist of two domains: One is involved in autocatalytic splicing, and the other is an endonucleasethat is important in the spread of inteins [<cite idref="PUB00009828"/>]. </p> <p> Inteins arebetween 134 and 608 amino acids long, and they are found in members of all three domains of life: eukaryotes, bacteria, and archaea, although most frequently in archaea. Inteinsare found in proteins with diverse functions, including metabolic enzymes, DNA and RNA polymerases, proteases, ribonucleotide reductases, and the vacuolar-typeATPase. However, enzymes involved in DNA replication and repair appear to dominate. Inteins are found in conserved regions of conserved proteins and can be regarded as parasitic genetic elements [<cite idref="PUB00009828"/>]. </p> <p>In most cases the intein seems to be an endonuclease which belongs to MEROPS peptidase family C46. It has been proposed that the splicing initiates at the C-terminal splice junction. The delta-nitrogen group of a conserved asparagine residue makes a nucleophilic attack on the peptide bond that links this asparagine to the next residue. The next residue (a Cys, Ser or Thr) is then free to attack the peptide bond at the N-terminal splice junction by a transpeptidation reaction that releases the intein and creates a new peptide bond. Such a mechanism is briefly schematised in the following figures.</p><pre> 1) Primary translation product +---------------+ +-------------+ +--------------+ NH2-| Extein 1 x--y Intein N--z Extein 2 |-COOH +---------------+ +-------------+ +--------------+ 2) Breakage of the peptide bond at the C-terminal splice junction by nucleophilic attack of the asparagine. +---------------+ +-------------+ +--------------+ NH2-| Extein 1 x--y Intein N NH2-z Extein 2 |-COOH +---------------+ +-------------+ +--------------+ 3) Transpeptidation to produce the final products. +---------------+ +-------------+ +--------------+ NH2-| Extein 1 x--z Extein 2 |-COOH NH2-y Intein N +---------------+ +-------------+ +--------------+</pre><p>Inteins are difficult to identify from sequence data because they lie in the same reading frame as the spliced protein and they are characterised by only a few short conserved motifs [<cite idref="PUB00006583"/>]: two of these are similar to the nonapeptide LAGLIDADG, which is diagnostic of certain homing endonucleases (mutation of one such motif causes loss of endonuclease activity, but not of the protein splicing function); another includes the C' splice site, mutations in which disable protein function.</p>