InterPro : IPR003579

Name  Small GTPase superfamily, Rab type Short Name  Small_GTPase_Rab_type
Type  Family Description  Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity [].Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base [].The small GTPase superfamily can be divided into at least 8 different families, including:Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus.Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export.Rab small GTPases. GTP-binding proteins involved in vesicular traffic.Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation.Ras small GTPases. GTP-binding proteins involved in signalling pathways.Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking.Roc small GTPases domain. Small GTPase domain always found associated with the COR domain.Rab-like GTPases are key regulators of most if not all vesicular trafficking events between the various subcellular compartments within the eukaryotic cell. Rab-related proteins have been implicated in regulating the formation of vesicles at the donor membrane, as well as the movement, tethering and docking of vesicles, and their fusion with the acceptor membrane []. The regulatory capacity of Rab-like proteins is dependent on their ability to cycle between GTP-bound active and GDP-bound inactive states. Activation of a Rab is coupled to its association with intracellular membranes, allowing it to recruit downstream effector proteins to the cytoplasmic surface of a subcellular compartment [].The crystal structures of a number of Rab GTPases have been determined: , Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase []. , Sec4 []., Rab5a [].
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Proteins

InterPro protein domain ID --> Contigs

 

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1 Parent Features

Id Name Short Name Type
IPR001806 Small GTPase superfamily Small_GTPase Family

10 Publications

First Author Title Year Journal Volume Pages
Bourne HR The GTPase superfamily: conserved structure and molecular mechanism. 1991 Nature 349 117-27
Valencia A The ras protein family: evolutionary tree and role of conserved amino acids. 1991 Biochemistry 30 4637-48
Paduch M Structure of small G proteins and their regulators. 2001 Acta Biochim Pol 48 829-50
Pai EF Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. 1990 EMBO J 9 2351-9
Bourne HR The GTPase superfamily: a conserved switch for diverse cell functions. 1990 Nature 348 125-32
Stroupe C Crystal structures of a Rab protein in its inactive and active conformations. 2000 J Mol Biol 304 585-98
Rak A Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase. 2003 Science 302 646-50
Terzyan S Refinement of the structure of human Rab5a GTPase domain at 1.05 A resolution. 2004 Acta Crystallogr D Biol Crystallogr 60 54-60
Ali BR Multiple regions contribute to membrane targeting of Rab GTPases. 2004 J Cell Sci 117 6401-12
Jahn R Principles of exocytosis and membrane fusion. 2004 Ann N Y Acad Sci 1014 170-8



To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)