Crystal Structure of Inhibitor-Bound Bacterial Oligopeptidase B in the Closed State: Similarity and Difference between Protozoan and Bacterial Enzymes

The crystal structure of bacterial oligopeptidase B from (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...

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Bibliographic Details
Published in:International journal of molecular sciences 2023-01, Vol.24 (3), p.2286
Main 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
Format: Article
Language:English
Subjects:
Amino acids
Bacteria
Bioinformatics
Catalysis
Crystal structure
Crystallization
Inhibitors
Ketones
Phylogenetics
Protozoan enzymes
Residues
Serine Endopeptidases - metabolism
Stabilization
Taxonomy
Trypanosoma brucei brucei - metabolism
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Summary:The crystal structure of bacterial oligopeptidase B from (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 (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.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms24032286