Structure of Rhomboid Protease in Complex with β-Lactam Inhibitors Defines the S2′ Cavity

• Published in: Structure (London) 2013-06, Vol.21 (6), p.1051-1058
• Main Authors: Vinothkumar, Kutti R., Pierrat, Olivier A., Large, Jonathan M., Freeman, Matthew
• Format: Article
• Language: English
• Subjects: beta-Lactams - antagonists & inhibitors; beta-Lactams - chemistry; Catalysis; Models, Molecular; Peptide Hydrolases - chemistry; Peptide Hydrolases - metabolism; Protein Conformation; Short
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2013.03.013

Rhomboids are evolutionarily conserved serine proteases that cleave transmembrane proteins within the membrane. The increasing number of known rhomboid functions in prokaryotes and eukaryotes makes them attractive drug targets. Here, we describe structures of the Escherichia coli rhomboid GlpG in complex with β-lactam inhibitors. The inhibitors form a single bond to the catalytic serine and the carbonyl oxygen of the inhibitor faces away from the oxyanion hole. The hydrophobic N-substituent of β-lactam inhibitors points into a cavity within the enzyme, providing a structural explanation for the specificity of β-lactams on rhomboid proteases. This same cavity probably represents the S2′ substrate binding site of GlpG. We suggest that the structural changes in β-lactam inhibitor binding reflect the state of the enzyme at an initial stage of substrate binding to the active site. The structural insights from these enzyme-inhibitor complexes provide a starting point for structure-based design for rhomboid inhibitors. [Display omitted] •Structures of E. coli GlpG, in complex with three different β-lactam inhibitors•The acyl enzyme structures define the S2′ substrate binding site in GlpG•Biochemical analysis reveals a preference for large hydrophobic groups at S2′ cavityThe GlpG-β-lactam structures reveal the changes essential for formation of S2′ cavity The structures of the E. coli rhomboid GlpG, an intramembrane serine protease in complex with β-lactam inhibitors, reported by Vinothkumar et al., reveal the nature and formation of the S2′ cavity. The differences in this cavity may form the basis of substrate/inhibitor specificity and structure-based drug design.