9.B.104 The Rhomboid Protease Family

Structures of the prokaryotic homologue of rhomboid proteases reveal a core of six transmembrane helices, with the active-site residues residing in a hydrophilic cavity. The native environment of rhomboid protease is a lipid bilayer. Crystals of GlpG, an Escherichia coli rhomboid protease in a lipid environment were obtained at 1.7Å resolution (Vinothkumar, 2011). The structure revealed well-ordered and partly ordered lipid molecules forming an annulus around the protein. Lipid molecules adapt to the surface features of the protein and arrange such that they match the hydrophobic thickness of GlpG.

The primary function of rhomboids is to cleave integral membrane proteins to release signalling molecules. These signals, when disrupted, can contribute to various diseases. The Ser-His catalytic dyad is buried within the membrane. The substrate entry gate is composed of helix 5 and loop 5 (Lazareno-Saez et al., 2011). Lazareno-Saez et al. (2011) compared the open and closed conformations of GlpG. Possibly loop 4 acts as an anchor for the substrate gate.

The ER-associated degradation (ERAD) pathway serves as an important cellular safeguard by directing incorrectly folded and unassembled proteins from the ER of eukaryotes to the proteasome. Fleig et al. (2012) showed that the evolutionarily conserved rhomboid family protein RHBDL4 is a ubiquitin-dependent ER-resident intramembrane protease that is upregulated upon ER stress. RHBDL4 cleaves single-spanning and polytopic membrane proteins with unstable transmembrane helices, leading to their degradation by the canonical ERAD machinery. RHBDL4 specifically binds the AAA -ATPase p97, suggesting that proteolytic processing and dislocation into the cytosol are functionally linked. The phylogenetic relationship between rhomboids and the ERAD factor derlin suggests that substrates for intramembrane proteolysis and protein dislocation are recruited by a shared mechanism.

The BAG6 complex is an upstream loading factor for tail-anchored membrane proteins entering the TRC40-dependent pathway for posttranslational delivery to the endoplasmic reticulum.  BAG6 also enhances proteasomal degradation of mislocalized proteins by selectively promoting their ubiquitination. BAG6-dependent ubiquitination of mislocalized proteins is reversible, and the glutamine-rich tetratricopeptide repeat-containing protein α, (SGTA) antagonizes this process. Promoting the deubiquitination of mislocalized proteins that are already covalently modified reverses the actions of BAG6, inhibiting its capacity to promote substrate-specific degradation (Leznicki and High 2012).