Structural basis for Rab GTPase activation by VPS9 domain exchange factors

UMMS Affiliation

Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology

Publication Date


Document Type



Binding Sites; Crystallography, X-Ray; Enzyme Activation; Guanine Nucleotide Exchange Factors; Guanosine Diphosphate; Humans; Mutation; Protein Conformation; Vesicular Transport Proteins; rab GTP-Binding Proteins


Life Sciences | Medicine and Health Sciences


RABEX-5 and other exchange factors with VPS9 domains regulate endocytic trafficking through activation of the Rab family GTPases RAB5, RAB21 and RAB22. Here we report the crystal structure of the RABEX-5 catalytic core in complex with nucleotide-free RAB21, a key intermediate in the exchange reaction pathway. The structure reveals how VPS9 domain exchange factors recognize Rab GTPase substrates, accelerate GDP release and stabilize the nucleotide-free conformation. We further identify an autoinhibitory element in a predicted amphipathic helix located near the C terminus of the VPS9 domain. The autoinhibitory element overlaps with the binding site for the multivalent effector RABAPTIN-5 and potently suppresses the exchange activity of RABEX-5. Autoinhibition can be partially reversed by mutation of conserved residues on the nonpolar face of the predicted amphipathic helix or by assembly of the complex with RABAPTIN-5.

DOI of Published Version



Nat Struct Mol Biol. 2007 May;14(5):406-12. Epub 2007 Apr 22. Link to article on publisher's site

Journal/Book/Conference Title

Nature structural and molecular biology

Related Resources

Link to Article in PubMed

PubMed ID