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* Ubiquitin family signature *
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Ubiquitin [1,2,3] is a protein  of  seventy  six amino acid residues, found in
all eukaryotic  cells  and  whose  sequence   is extremely well conserved from
protozoan to  vertebrates.  It  plays  a  key  role  in  a variety of cellular
processes, such as ATP-dependent  selective  degradation of cellular proteins,
maintenance of  chromatin  structure,  regulation  of  gene expression, stress
response and ribosome biogenesis.

In most  species,  there are many genes coding for ubiquitin. However they can
be classified  into  two  classes.  The  first  class  produces  polyubiquitin
molecules consisting of exact head to tail repeats of ubiquitin. The number of
repeats  is  variable (up  to  twelve in a Xenopus gene).  In  the majority of
polyubiquitin precursors, there is a  final amino-acid  after the last repeat.
The second  class  of genes produces precursor proteins consisting of a single
copy of ubiquitin fused to a C-terminal extension protein (CEP). There are two
types of CEP proteins and both seem to be ribosomal proteins.

Ubiquitin is a globular protein, the  last  four C-terminal residues (Leu-Arg-
Gly-Gly) extending  from the compact structure to form a 'tail', important for
its function.  The latter is mediated by the covalent conjugation of ubiquitin
to target  proteins,  by  an isopeptide linkage between the C-terminal glycine
and the epsilon amino group of lysine residues in the target proteins.

There are a number of proteins which are evolutionary related to ubiquitin:

 - Ubiquitin-like  proteins from  baculoviruses as well as in  some strains of
   bovine viral diarrhea viruses (BVDV).  These proteins are highly similar to
   their eukaryotic counterparts.
 - Mammalian  protein  GDX [4].  GDX is composed  of two domains, a N-terminal
   ubiquitin-like domain of 74 residues and a C-terminal domain of 83 residues
   with some similarity with the thyroglobulin hormonogenic site.
 - Mammalian  protein  FAU  [5].   FAU is a  fusion protein which consist of a
   N-terminal ubiquitin-like protein of 74 residues fused to ribosomal protein
   S30.
 - Mouse protein NEDD-8 [6]. The complete sequence of NEDD-8 is not yet known;
   but it  contains  a  ubiquitin-like domain that ends 30 residues before the
   C-terminal extremity of the protein.

To identify ubiquitin and related proteins  we  have developed a pattern based
on conserved positions in the central section of the sequence.

-Consensus pattern: K-x(2)-[LIVM]-x-[DES]-x(3)-[LIVM]-[PA]-x(3)-Q-x-[LIVM](2)-
                    [LIVMFY]-x-G-x(4)-[DE]-x(4)-[SAG]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in SWISS-PROT: NONE.
-Last update: June 1994 / Pattern and text revised.

[ 1] Jentsch S., Seufert W., Hauser H.-P.
     Biochim. Biophys. Acta 1089:127-139(1991).
[ 2] Monia B.P., Ecker D.J., Croke S.T.
     Bio/Technology 8:209-215(1990).
[ 3] Finley D., Varshavsky A.
     Trends Biochem. Sci. 10:343-347(1985).
[ 4] Filippi M., Tribioli C., Toniolo D.
     Genomics 7:453-457(1990).
[ 5] Olvera J., Wool I.G.
     J. Biol. Chem. 268:17967-17974(1993).
[ 6] Kumar S., Tomooka Y., Noda M.
     Biochem. Biophys. Res. Commun. 185:1155-1161(1992).