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Rhomboid proteases are a family of proteins that
cleave the transmembrane domain of membrane proteins. An example of a
rhomboid protein is GlpG, found in the membrane of Escherichia coli.
GlpG and all other rhomboid proteases have six hydrophobic segments that
span the membrane and give the enzyme a serpentine characteristic.
For more information see
Biochemistry Online: Chapter 7B - Mechanisms of Enzyme Catalysis
II. General Structure
Backbone and sidechains with highlighted transmembrane subunits
Rhomboid with transmembrane helices represented as barrels or "Rockets"
Protein backbone with highlighted subunits and
prominent residues (colored pink) in the active site
specific mutagenesis has shown that four residues are crucial to
catalytic activity. His 150, Asn 154, Ser 201, His 254 all reside
in the central v shaped active site.
Protein backbone with prominent residues in the active
site in the presence of water
- The catalytic
mechanism is believed to be a dyad of Serine 201 and Histidine 254.
Histidine activates Serine for nucleophilic attack on the ligand.
- Water molecules
are present in the active site. The presence of water over the
protein surface in such a wide distribution is supports the theory
that water enters the active site by more than one single path or
L1 subunit (colored gray) and prominent residues (colored yellow) in the
active site in the presence of water
structure supports the hypothesis that the L1 subunit serves as a
gate during ligand binding. L1 consists mainly of α-helix and four
consecutive 310 helices. During binding, the
upper portion of the lateral gate
(L1) interacts with Trp-136 and Arg-137
(colored blue), thereby altering the location of L1 in such a manner
that the ligand can dock in its place.
Protein (spacefill) interacting with DNA
Protein backbone and Hbonds in the
presence of water