Structural basis for Rab GTPase activation by VPS9 domain exchange factors

Nat Struct Mol Biol. 2007 May;14(5):406-12. doi: 10.1038/nsmb1232. Epub 2007 Apr 22.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

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


  • Guanine Nucleotide Exchange Factors
  • RAB22A protein, human
  • RABEP1 protein, human
  • RABGEF1 protein, human
  • Vesicular Transport Proteins
  • Guanosine Diphosphate
  • rab GTP-Binding Proteins