{PDOC50819}
{PS50819; INTEIN_ENDONUCLEASE}
{BEGIN}
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* Intein DOD-type homing endonuclease domain profile *
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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
alpha/beta motifs  related  by  pseudo two-fold symmetry (see <PDB:1DFA>). The
two alpha-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].

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: May 2002 / First entry.

[ 1] Liu X.-Q.
     "Protein-splicing intein: Genetic mobility, origin, and evolution."
     Annu. Rev. Genet. 34:61-76(2000).
     PubMed=11092822; DOI=10.1146/annurev.genet.34.1.61
[ 2] Perler F.B., Olsen G.J., Adam E.
     "Compilation and analysis of intein sequences."
     Nucleic Acids Res. 25:1087-1093(1997).
     PubMed=9092614
[ 3] Perler F.B.
     "InBase, the Intein Database."
     Nucleic Acids Res. 28:344-345(2000).
     PubMed=10592269
[ 4] Belfort M., Roberts R.J.
     "Homing endonucleases: keeping the house in order."
     Nucleic Acids Res. 25:3379-3388(1997).
     PubMed=9254693
[ 5] Jurica M.S., Stoddard B.L.
     "Homing endonucleases: structure, function and evolution."
     Cell. Mol. Life Sci. 55:1304-1326(1999).
     PubMed=10487208
[E1] http://tools.neb.com/inbase/

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