Inteins (for INternal proTEINs) are in frame intervening sequences that
disrupt the coding region of a host gene. They are post-translationally
excised from a protein precursor by a self-catalytic protein splicing process
[1,2,3,E1]. Most inteins are bifunctional proteins mediating both protein
splicing and DNA cleavage. The domain involved in splicing is formed by the
two terminal splicing regions (see <PDOC00687>), which are separated by a
small linker in mini-inteins or a 200- to 250-amino-acid homing endonuclease
in larger inteins [1,3]. Homing endonucleases are rare-cutting enzymes encoded
by inteins and introns. By making a site-specific double-strand break in the
intronless or inteinless alleles, these nucleases create recombinogenic ends
which engage in a gene conversion process that duplicates the intron or intein
[4,5]. There are four families of homing endonucleases classified by conserved
sequence motifs. Homing endonucleases found in inteins generally belong to the
dodecapetide (DOD) family, but an HNH endonuclease is also found.
Endonucleases of the DOD family contain one or two copies of a 10-residue
sequence known as a dodecapeptide or LAGLIDADG motif. They recognize long,
pseudopalindromic homing sites of 14-30 bp in length and cleave their homing
site DNA to generate 4nt, 3' extensions. The DOD endonucleases found in
inteins contain 2 dodecapeptide motifs and are active as monomers. Resolution
of the 3D structure of PI-Sce revealed that the endonuclease domain consist of
α/β motifs related by pseudo two-fold symmetry (see <PDB:1DFA>). The
two α-helices containing the dodecapeptide motifs form the axis of
symmetry [4,5,E1].
The profile we have developed covers the conserved central intein blocks C, D,
E and H. Blocks C and E are the dodecapeptide motifs that are required for
endonuclease activity and each contains an endonuclease active site Asp or Glu
[2,E1].
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