Inteins are protein-splicing elements, most of which contain conserved sequence blocks that define a family of homing endonucleases. Like group I introns that encode such endonucleases, inteins are mobile genetic elements. Recent crystallography and computer modeling studies suggest that inteins consist of two structural domains that correspond to the endonuclease and the protein-splicing elements. like group I introns, mobile inteins arose by an endonuclease gene invading a sequence encoding a small, functional splicing element.

(Victoria Derbyshire, David W. Wood, , Wei Wu, John T. Dansereau, Jacob Z. Dalgaard , and Marlene Belfort: Genetic definition of a protein-splicing domain: Functional mini-inteins support structure predictions and a model for intein evolution: Vol. 94, pp. 11466-11471, October 1997.)

Protein splicing is so rapid that the precursor protein is rarely observed in native systems. The intein plus the first C-extein residue contain sufficient information for splicing in foreign proteins. However, exteins may affect splicing rates or efficiency. Splicing in foreign protein contexts often results in an increase in dead-end cleavage reaction products.
Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues. The intein penultimate His in Block G assists in Asn cyclization and C-terminal cleavage by hydrogen bonding to the Asn carbonyl oxygen, making this peptide bond more labile. The Thr and His in Block B assist in the initial acyl rearrangement at the N-terminal splice junction by hydrogen bonding to main chain atoms and holding the residue preceding the intein in a non-standard cis conformation or in a strained conformation. Any residue that can form similar hydrogen bonds can substitute for these conserved facilitating residues in Blocks B and G. The mechanism of protein splicing has recently been reviewed in Noren 2000, Paulus 2000, Perler 1997C, Shao 1997 and Perler 1998. Several previous reviews contain mechanisms now known to be incorrect.

(Perler, F. B. (2002). InBase, the Intein Database. Nucleic Acids Res. 30, 383-384)

Step 1:
The first step in protein splicing is a reversible transition of the peptide bond between the amino end of the intein and its amino terminal flank (N-extein) into an ester or thioester bond. This transition depends on a nucleophilic attack of the bond by the side-chain of the Ser or Cys residues at the amino terminal end of the intein (-OH or -SH respectively). This reaction is termed N-O when the attacking atom is an Oxygen and N-S when this atom is Sulfur. This scheme shows the reaction with a Cys in the intein amino end. All inteins begin with either Ser or Cys residues,except for the two klbA inteins in M.jannaschii and Pyrococcus horikoshii OT3. These start with an Ala and if they are active it cannot be through this step since the Ala side-chain is a methyl group (CH3) not capable of nucleophilic attack.

Step 2:
In the next step the side-chain of the residue C-terminal to the intein (the first residue of the Carboxy (C) extein) attacks the ester (or thioester) bond at the amino end of the intein. Here too the attack is by a polar side chain of a Ser, Thr (both OH) or Cys (SH).This leads to a transesterification and formation of a branched intermediate with two amino ends, one of the N-extein and one of the intein. The intein is joined by peptide bond to the C-extein and the two exteins are joined by a thio/ester bond. This reaction is also reversible. All known inteins indeed have Ser, Thr or Cys directly following their C-end. This scheme shows the reaction with a Ser following the intein carboxy end.

Step 3:
The branched intermediate is resolved by the cyclization of the C-terminal intein residue. The intein is now fully excised from the N and C exteins that are yet linked to each other by the thio/ester bond. This step is ireversible driving the reaction forward. Almost all inteins have Asn as their carboxy end and its cyclization results in a succinimide ring. Two known inteins have Gln in their carboxy end and a variation of this step has been proposed to account for this. In brief, the reaction proceeds through Gln cyclization into a glutarimide ring.

Step 4:
The final steps consist of spontaneous shift of the thio/ester bond linking the exteins into a peptide bond (S/O-N acyl rearrangement) and probably some hydrolysis of the succinimide (or glutarimide) ring at the intein carboxy end to Asn and iso-Asn. These reactions are ireversible too and form the mature host protein, chemically identical to the product of an intein-less gene. Not much is biochemically known on the fate of the excised intein. In experiments where it is over-produced it seems to be rapidly degraded. However, genetic and phylogenetic analysis show that some inteins are also responsible for the homing of the intein gene into unoccupied intein integration points in homologous genes. This horizontal-transfer gene conversion is mediated by the homing endonuclease protein domain found in the central region of most inteins. The reaction is totally independent of the protein splicing reaction depicted here.

(Pietrokovski S. (2001). Inteins- Protein Introns. http://bioinfo.weizmann.ac.il/~pietro/inteins)

(Ming-Qun Xu and Francine B.Perler: The mechanism of protein splicing and its modulation by mutation: The EMBO Journal vol.15 no.19 pp.5146-5153, 1996.)