7YWP

Closed conformation of Oligopeptidase B from Serratia proteomaculans with covalently bound TCK

Summary for 7YWP

• Entry DOI: 10.2210/pdb7ywp/pdb
• Descriptor: Oligopeptidase B, N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide (3 entities in total)
• Functional Keywords: hydrolase
• Biological source: Serratia proteamaculans
• Total number of polymer chains: 1
• Total formula weight: 78593.49

Authors

Petrenko, D.E.,Boyko, K.M.,Nikolaeva, A.Y.,Vlaskina, A.V.,Mikhailova, A.G.,Timofeev, V.I.,Rakitina, T.V. (deposition date: 2022-02-14, release date: 2023-02-22, Last modification date: 2024-02-07)

Primary citation

Petrenko, D.E.,Karlinsky, D.M.,Gordeeva, V.D.,Arapidi, G.P.,Britikova, E.V.,Britikov, V.V.,Nikolaeva, A.Y.,Boyko, K.M.,Timofeev, V.I.,Kuranova, I.P.,Mikhailova, A.G.,Bocharov, E.V.,Rakitina, T.V.
Crystal Structure of Inhibitor-Bound Bacterial Oligopeptidase B in the Closed State: Similarity and Difference between Protozoan and Bacterial Enzymes.
Int J Mol Sci, 24:-, 2023

PubMed Abstract: 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.

PubMed: 36768612
DOI: 10.3390/ijms24032286

Experimental method

X-RAY DIFFRACTION (2.2 Å)