{PDOC51157}
{PS51157; ZF_UBR}
{BEGIN}
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* Zinc finger UBR-type profile *
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It  has been observed that the identity of N-terminal residues of a protein is
related  to  the  half  life  of  the protein. This observation yields a rule,
called  the  N-end  rule  [1]. Similar but distinct versions of the N-end rule
operate  in  all  organisms  examined,  from mammals to fungi and bacteria. In
eukaryotes,  the  N-end  rule  pathway  is a part of the ubiquitin degradation
system.  Some  proteins  that  have  a very short half life contain a specific
motif  at  their  N-terminus,  the  N-degron.  It  consists of a destabilizing
N-terminal  residue  and  an  internal Lys, which is the site of poly-Ub chain
[1,2].

The UBR1 protein was shown to bind specifically to proteins bearing N-terminal
residues  that  are  destabilizing  according  to  the  N-end rule, but not to
otherwise identical proteins bearing stabilizing N-terminal residues [3]. UBR1
contain  an  N-terminal  conserved  region (the UBR-type zinc finger) which is
also  found  in  various  proteins  implicated  in  N-degron  recognition. The
UBR-type  zinc finger defines a unique E3 class, most likely N-degron specific
[4].

The profile we developed covers the whole UBR-type zinc finger.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Note: The UBR-type zinc finger is also known as the UBR box motif [4].

-Last update: October 2005 / First entry.

[ 1] Varshavsky A.
     "The N-end rule: functions, mysteries, uses."
     Proc. Natl. Acad. Sci. U.S.A. 93:12142-12149(1996).
     PubMed=8901547
[ 2] Suzuki T., Varshavsky A.
     "Degradation signals in the lysine-asparagine sequence space."
     EMBO J. 18:6017-6026(1999).
     PubMed=10545113; DOI=10.1093/emboj/18.21.6017
[ 3] Xie Y., Varshavsky A.
     "The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger
     of E3 is required for the synthesis of multiubiquitin chain."
     EMBO J. 18:6832-6844(1999).
     PubMed=10581257; DOI=10.1093/emboj/18.23.6832
[ 4] Tasaki T., Mulder L.C., Iwamatsu A., Lee M.J., Davydov I.V.,
     Varshavsky A., Muesing M., Kwon Y.T.
     "A family of mammalian E3 ubiquitin ligases that contain the UBR box
     motif and recognize N-degrons."
     Mol. Cell. Biol. 25:7120-7136(2005).
     PubMed=16055722; DOI=10.1128/MCB.25.16.7120-7136.2005

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