We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Crystal Structure of Inhibitor-Bound Bacterial Oligopeptidase B in the Closed State: Similarity and Difference between Protozoan and Bacterial Enzymes.
- Authors
Petrenko, Dmitry E.; Karlinsky, David M.; Gordeeva, Veronika D.; Arapidi, Georgij P.; Britikova, Elena V.; Britikov, Vladimir V.; Nikolaeva, Alena Y.; Boyko, Konstantin M.; Timofeev, Vladimir I.; Kuranova, Inna P.; Mikhailova, Anna G.; Bocharov, Eduard V.; Rakitina, Tatiana V.
- Abstract
The crystal structure of bacterial oligopeptidase B from Serratia proteamaculans (SpOpB) in complex with a chloromethyl ketone inhibitor was determined at 2.2 Å resolution. SpOpB was crystallized in a closed (catalytically active) conformation. A single inhibitor molecule bound simultaneously to the catalytic residues S532 and H652 mimicked a tetrahedral intermediate of the catalytic reaction. A comparative analysis of the obtained structure and the structure of OpB from Trypanosoma brucei (TbOpB) in a closed conformation showed that in both enzymes, the stabilization of the D-loop (carrying the catalytic D) in a position favorable for the formation of a tetrahedral complex occurs due to interaction with the neighboring loop from the β-propeller. However, the modes of interdomain interactions were significantly different for bacterial and protozoan OpBs. Instead of a salt bridge (as in TbOpB), in SpOpB, a pair of polar residues following the catalytic D617 and a pair of neighboring arginine residues from the β-propeller domain formed complementary oppositely charged surfaces. Bioinformatics analysis and structural modeling show that all bacterial OpBs can be divided into two large groups according to these two modes of D-loop stabilization in closed conformations.
- Subjects
BACTERIAL enzymes; CRYSTAL structure; KETONES; SINGLE molecules; TRYPANOSOMA brucei; PEPTIDASE
- Publication
International Journal of Molecular Sciences, 2023, Vol 24, Issue 3, p2286
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms24032286