Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.26 kDa 
• Atom Count: 4590 
• Modelled Residue Count: 504 
• Deposited Residue Count: 608 
• Unique protein chains: 2

2G77

Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3

• PDB DOI: 10.2210/pdb2G77/pdb

• Classification: HYDROLASE ACTIVATOR/PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-02-27 Released: 2006-07-25 
• Deposition Author(s): Pan, X., Eathiraj, S., Munson, M., Lambright, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.244 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

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

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

(2006) Nature 442: 303-306

• PubMed: 16855591 
• DOI: 10.1038/nature04847
• Primary Citation of Related Structures:  
  2G77


• PubMed 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.

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Organizational Affiliation: 

Program in Molecular Medicine & Department of Biochemistry and Molecular Pharmacology, UMASS Medical School, Two Biotech, 373 Plantation Street, Worcester, Massachusetts 01605, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase-activating protein GYP1	A	410	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: GYP1
UniProt
Find proteins for Q08484 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08484  Go to UniProtKB:  Q08484

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-33B	B	198	Mus musculus	Mutation(s): 4  Gene Names: Rab33b
UniProt & NIH Common Fund Data Resources
Find proteins for O35963 (Mus musculus) Explore O35963  Go to UniProtKB:  O35963
IMPC:  MGI:1330805

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
AF3	E [auth B]	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.244 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.2	α = 90
b = 94.526	β = 90
c = 102.561	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-27 
• Released Date: 2006-07-25 
Deposition Author(s): Pan, X., Eathiraj, S., Munson, M., Lambright, D.G.

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations