Editing Protein splicing (section)

== Mechanism ==
{{missing information|section|Conserved A, B, F, G blocks |date=November 2023}}
The process for class 1 inteins begins with an N-O or N-S shift when the side chain of the first residue (a [[serine]], [[threonine]], or [[cysteine]]) of the intein portion of the precursor protein [[nucleophile|nucleophilically]] attacks the [[peptide bond]] of the residue immediately upstream (that is, the final residue of the N-extein) to form a linear [[ester]] (or [[thioester]]) intermediate. A [[transesterification]] occurs when the side chain of the first residue of the C-extein attacks the newly formed (thio)ester to free the [[N-terminus|N-terminal]] end of the intein. This forms a branched intermediate in which the N-extein and C-extein are attached, albeit not through a peptide bond. The last residue of the intein is always an [[asparagine]] (Asn), and the [[amide]] nitrogen atom of this side chain cleaves apart the peptide bond between the intein and the C-extein, resulting in a free intein segment with a terminal cyclic [[imide]]. Finally, the free [[amine|amino group]] of the C-extein now attacks the (thio)ester linking the N- and C-exteins together. An O-N or S-N shift produces a peptide bond and the functional, [[Chemical ligation|ligated]] protein.<ref>{{cite journal | vauthors=Noren CJ, Wang J, Perler FB | title=Dissecting the chemistry of protein splicing and its applications| journal=Angew Chem Int Ed Engl| volume=39| issue=3| pages=450–66| year=2000| pmid=10671234| doi=10.1002/(sici)1521-3773(20000204)39:3<450::aid-anie450>3.3.co;2-6}}</ref>

Class 2 inteins have no nucleophilic first side chain, only an alanine. Instead, the reaction starts directly with a nucleophilic displacement, with the first residue of the C-extein atticking the peptide carboxyl on the final residue of the N-extein. The rest proceeds as usual, starting with Asn turning into a cyclic imide.<ref name="pmid33339089"/>

Class 3 inteins have no nucleophilic first side chain, only an alanine, yet they have an internal noncontiguous "WCT" motif. The internal C (cysteine) residue attacks the peptide carboxyl on the final residue of the N-extein (nucleophilic displacement). Transesterification occurs when the first residue of the C-extein attacks the newly formed thioester. The rest proceeds as usual.<ref name=pmid21317331/>

The mechanism for the splicing effect is a naturally occurring analogy to the technique for chemically generating medium-sized proteins called [[native chemical ligation]].