Crystal structure of Rab geranylgeranyltransferase at 2.0 Å resolution

Background: Rab geranylgeranyltransferase (RabGGT) catalyzes the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. Unlike protein farnesyltransferase (FT) and type I geranylgeranyltransferase, which both prenylate monomeric small G proteins or short peptides, RabGGT can prenylate Rab only when Rab is in a complex with Rab escort protein (REP). Results: The crystal structure of rat RabGGT at 2.0 Angstrom resolution reveals an assembly of four distinct structural modules. The beta subunit forms an alpha-alpha barrel that contains most of the residues in the active site. The a subunit consists of a helical domain, an immunoglobulin (lg)-like domain, and a leucine-rich repeat (LRR) domain. The N-terminal region of the alpha subunit binds to the active site in the beta subunit; residue His2 alpha directly coordinates a zinc ion. The prenyl-binding pocket of RabGGT is deeper than that in FT. Conclusions: LRR and lg domains are often involved in protein-protein interactions; in RabGGT they might participate in the recognition and binding of REP. The binding of the N-terminal peptide of the alpha subunit to the active site suggests an autoinhibition mechanism that might contribute to the inability of RabGGT to recognize short peptides or Rab alone as its substrate. Replacement of residues Trp102 beta and Tyr154 beta in FT by Ser48 beta and Leu99 beta, respectively, in RabGGT largely determine the different lipid-binding specificities of the two enzymes.