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* Protein splicing signature *
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Protein splicing [1,2,3,4] is a mechanism by which an internal segment (called
intein [5]  or  spacer)  in  a  protein  precursor is excised and the flanking
regions (called  exteins  [5])  are  religated to create a functional protein.
Currently, such a mechanism has been found in the following proteins:

 - Saccharomyces  cerevisiae  and  Candida  tropicalis  vacuolar  ATP synthase
   catalytic subunit A (gene VMA1 or TFP1).
 - Mycobacterium tuberculosis and leprae recA protein.
 - Thermococcus litoralis (an archebacteria) Vent DNA polymerase.

In most  of  these  cases  the intein seems to be an endonuclease. It has been
proposed  that  the splicing initiates at the C-terminal splice junction.  The
beta-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
schematized in the following figures.

 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
      +---------------+  +-------------+           +--------------+

In the  proteins  known to undergo protein splicing, the residues close to the
asparagine involved  in  the nucleophilic attack are conserved and can be used
as a  signature  pattern. We are aware that such a signature is probably going
to evolve  as  soon  as  new examples are discovered, nevertheless, we believe
that it can be useful.

-Consensus pattern: [LIVM](2)-V-H-N-[STC]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in SWISS-PROT: Tomato Golden Mosaic  virus protein
 BR1 and mouse soluble epoxide hydrolase.
-Last update: June 1994 / Text revised.

[ 1] Shub D.A., Goodrich-Blair H.
     Cell 71:183-186(1992).
[ 2] Cooper A.A., Chen Y.-J., Lindorfer M.A., Stevens T.H.
     EMBO J. 12:2575-2583(1993).
[ 3] Cooper A.A., Stevens T.H.
     BioEssays 15:667-674(1993).
[ 4] Hickey D.A.
     Trends Genet. 10:147-149(1994).
[ 5] Perler F.B., Davis E.O., Dean G.E., Gimble F.S., Jack W.E., Neff N.,
     Noren C.J., Thorner J., Belfort M.
     Nucleic Acids Res. 22:1125-1127(1994).