{PDOC50916}
{PS50916; RABBD}
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* Rab-binding domain profile *
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Rab  are small GTPases implicated in vesicle trafficking. Like the other small
GTPases, Rab proteins act as molecular switches, with an active GTP-bound form
that  interacts  with its target or effector protein and an inactive GDP-bound
form. A subgroup of Rab effectors contain in their N-terminal part a conserved
region  of  around 70 amino acid residues, the Rab-binding domain (RabBD) . In
some Rab effector domains an atypical FYVE-type zinc finger is inserted in the
central part [1].

The  crystal  structure  of the Rab effector domain of Rabphilin-3A in complex
with Rab3A has been solved [2] (see <PDB:1ZBD>). The structure consists of two
long  helices  separated  by  an atypical FYVE-type zinc finger which adopts a
conformation  similar  to  classical  ones (see <PDOC50178>). The central zinc
finger  does  not  directly interact with Rab3A. The amino acids important for
this  interaction  are located around a short C-terminal motif (SGAWFF) and an
acidic cluster in the N-terminal area.

Proteins known to contain a Rab-binding domain are listed below:

 - Mammalian  Synaptotagmin-like  1  (SYTL1)  (exophilin  7).  Its Rab-binding
   domain does not contain an inclusive FYVE-type like zinc finger.
 - Mammalian  Synaptotagmin-like  2  (SYTL2)  (exophilin  4).  Its Rab-binding
   domain does not contain an inclusive FYVE-type like zinc finger.
 - Mammalian Synaptotagmin-like 3 (SYTL3) (exophilin 6).
 - Mammalian Synaptotagmin-like 4 (SYTL4) (exophilin 2 or granuphilin).
 - Mammalian Synaptotagmin-like 5 (SYTL5).
 - Animal Rabphilin-3A (exophilin 1).
 - Mammalian Noc2 protein, a rabphilin 3A-like protein without C2 domains.
 - Mammalian  Slp  homolog  lacking  C2  domains-a  (Slac2-a or exophilin 3 or
   melanophilin).
 - Mammalian  Slp  homolog  lacking C2 domains-b (Slac2-b or exophilin 5). Its
   Rab-binding domain does not contain an inclusive FYVE-type like zinc
   finger.
 - Mammalian  Slp  homolog lacking C2 domains-c (Slac2-c or MyRIP or Exophilin
   8).
 - Mammalian Rim1.
 - Animal Rim2, a family of neuronal Rab effectors.

The profile we developed covers the entire Rab-binding domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: July 2003 / First entry.

[ 1] Fukuda M.
     "Distinct Rab binding specificity of Rim1, Rim2, rabphilin, and Noc2.
     Identification of a critical determinant of Rab3A/Rab27A recognition
     by Rim2."
     J. Biol. Chem. 278:15373-15380(2003).
     PubMed=12578829; DOI=10.1074/jbc.M212341200
[ 2] Ostermeier C., Brunger A.T.
     "Structural basis of Rab effector specificity: crystal structure of
     the small G protein Rab3A complexed with the effector domain of
     rabphilin-3A."
     Cell 96:363-374(1999).
     PubMed=10025402

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