PDBsum entry: 2g77

Hydrolase activator/protein transport

PDB id: 2g77

Contents

Protein chains

331 a.a. *

173 a.a. *

Ligands

GDP-AF3

Metals

_MG

Waters ×416

* Residue conservation analysis

PDB id:

2g77

Name:

Hydrolase activator/protein transport

Title:

Crystal structure of gyp1 tbc domain in complex with rab33 gtpase bound to gdp and alf3

Structure:

Gtpase-activating protein gyp1. Chain: a. Fragment: gyp1 tbc domain. Synonym: gap for ypt1. Engineered: yes. Mutation: yes. Ras-related protein rab-33b. Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: gyp1. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090.

Biol. unit:

Dimer (from PQS)

Resolution:

2.26Å R-factor: 0.207 R-free: 0.244

Authors:

X.Pan,S.Eathiraj,M.Munson,D.G.Lambright

Key ref:

X.Pan et al. (2006). TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism. Nature, 442, 303-306. PubMed id: 16855591 DOI: 10.1038/nature04847

Date:

27-Feb-06 Release date: 25-Jul-06

Protein chain

Q08484  (GYP1_YEAST) -  GTPase-activating protein GYP1

Seq: 637 a.a.

Struc: 331 a.a.*

Protein chain

O35963  (RB33B_MOUSE) -  Ras-related protein Rab-33B

Seq: 229 a.a.

Struc: 173 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: protein transport (3 terms)
• Biochemical function: Rab GTPase activator activity (2 terms)

DOI no: 10.1038/nature04847

Nature 442:303-306 (2006)

PubMed id: 16855591

TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism.

X.Pan, S.Eathiraj, M.Munson, D.G.Lambright.

ABSTRACT

Rab GTPases regulate membrane trafficking by cycling between inactive (GDP-bound) and active (GTP-bound) conformations. The duration of the active state is limited by GTPase-activating proteins (GAPs), which accelerate the slow intrinsic rate of GTP hydrolysis. Proteins containing TBC (Tre-2, Bub2 and Cdc16) domains are broadly conserved in eukaryotic organisms and function as GAPs for Rab GTPases as well as GTPases that control cytokinesis. An exposed arginine residue is a critical determinant of GAP activity in vitro and in vivo. It has been expected that the catalytic mechanism of TBC domains would parallel that of Ras and Rho family GAPs. Here we report crystallographic, mutational and functional analyses of complexes between Rab GTPases and the TBC domain of Gyp1p. In the crystal structure of a TBC-domain-Rab-GTPase-aluminium fluoride complex, which approximates the transition-state intermediate for GTP hydrolysis, the TBC domain supplies two catalytic residues in trans, an arginine finger analogous to Ras/Rho family GAPs and a glutamine finger that substitutes for the glutamine in the DxxGQ motif of the GTPase. The glutamine from the Rab GTPase does not stabilize the transition state as expected but instead interacts with the TBC domain. Strong conservation of both catalytic fingers indicates that most TBC-domain GAPs may accelerate GTP hydrolysis by a similar dual-finger mechanism.

Selected figure(s)

Figure 2.
Figure 2: Structure of the Gyp1p TBC domain in complex with Rab33–GDP–AlF[3]. Shown is a ribbon representation of the complex with the N-terminal and C-terminal subdomains of Gyp1p and functional regions of Rab33 coloured as indicated by the labelling. No electron density was observed for the loop region between G12 and G13.

Figure 3.
Figure 3: Network of polar interactions in the AlF[3]-binding site and comparison with other GAP–GTPase complexes. a, Interactions in the AlF[3]-binding site in the Gyp1p–Rab33–GDP–AlF[3] complex. b, Interactions in the AlF[4]^- binding site in the RGS4–G [i1]–GDP–AlF[4]^- complex (Protein Data Bank (PDB) ID code 1AGR). c, Interactions in the AlF[3]-binding site in the RasGAP–Ras–GDP–AlF[3] complex (PDB ID code 1WQ1).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 442, 303-306) copyright 2006.

Figures were selected by the author.