Our deepest condolences go out to his family and friends, and to all those who had the privilege of working with him. Rest in peace, Amos. Your work will live on long after you are gone.
PROSITE documentation PDOC50916Rab-binding domain profile
View entry in original PROSITE document format
View entry in raw text format (no links)
PURL: https://purl.expasy.org/prosite/documentation/PDOC50916
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.
Last update:July 2003 / First entry.
-------------------------------------------------------------------------------
PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Fukuda M. |
| Title | Distinct Rab binding specificity of Rim1, Rim2, rabphilin, and Noc2. Identification of a critical determinant of Rab3A/Rab27A recognition by Rim2. | |
| Source | J. Biol. Chem. 278:15373-15380(2003). | |
| PubMed ID | 12578829 | |
| DOI | 10.1074/jbc.M212341200 |
| 2 | Authors | Ostermeier C. Brunger A.T. |
| Title | Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A. | |
| Source | Cell 96:363-374(1999). | |
| PubMed ID | 10025402 |
PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.