Molecule of the Month: Rhomboid Protease GlpG
Some proteases cut proteins embedded in cell membranes
Proteases in Membranes?
Active Site Machinery
Exploring the Structure
Rhomboid Protease GlpG (PDB entries 2ic8, 2nrf and 2xow)
Intramembrane proteases perform a tricky job. They need to sit comfortably inside a hydrophobic membrane, but they also need to use water and water-binding amino acids to perform their reaction. They do this by having a flexible loop that covers the active site, allowing their targets and water to enter. Three structures reveal some of this flexibility, although many controversies still remain, since study of membrane proteins requires use of artificial methods to stabilize the proteins outside of membranes. PDB entry 2ic8 (left) shows a tightly-closed form and 2nrf (center) shows a wide-open form. PDB entry 2xow (right) shows the protein closed around an inhibitor. Click on the images here to compare the structures in an interactive Jmol.
Topics for Further Discussion
- PDB entry 3b4r includes two copies of the protein, one in a closed form and one in an open form. You can use the "Structure Comparison" tool to compare these two forms.
- Membrane proteins typically have a band of hydrophobic amino acids on the outside, which interacts with the surrounding membrane. To take a look at this, go to the PDB page for any of the rhomboid proteases (or any other membrane-spanning protein) and then choose a CPK style and hydrophobicity color in your favorite 3D viewing program.
Related PDB-101 Resources
- Browse Protein Synthesis
- Browse Enzymes
- Y. Ha (2009) Structure and mechanism of intramembrane protease. Seminars in Cell and Developmental Biology 20, 240-250.
- M. Freeman (2008) Rhomboid proteases and their biological functions. Annual Review of Genetics 42, 191-210.
- S. Urban and Y. Shi (2008) Core principles of intramembrane proteolysis: comparison of rhomboid and site-2 family proteases. Current Opinion in Structural Biology 18, 432-441.
August 2011, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2011_8