Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation

Crystals

Konstantin M. Boyko¹  Alena Y. Nikolaeva²  Dmitry E. Petrenko²  Anna V. Vlaskina²  Elena V. Britikova³  Vladimir V. Britikov³  Tatiana V. Rakitina⁴  Vladimir I. Timofeev⁴  Anna G. Mikhailova⁴ 

[1] Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia;Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus;Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia;

关键词: crystal structure;    prolyl oligopeptidase;    oligopeptidase B;    intermediate state;    hinge region;    X-ray diffraction analysis;   

DOI  :  10.3390/cryst12050712

来源: DOAJ

【 摘 要 】

Oligopeptidase B (OPB) is the least studied group from the prolyl oligopeptidase family. OPBs are found in bacteria and parasitic protozoa and represent pathogenesis factors of the corresponding infections. OPBs consist of two domains connected by a hinge region and have the characteristics of conformational dynamics, which include two types of movements: the bridging/separation of α/β-hydrolase catalytic and β-propeller-regulatory domains and the movement of a loop carrying catalytic histidine, which regulates an assembly/disassembly of the catalytic triad. In this work, an elucidation of the interdomain dynamics of OPB from Serratia proteamaculans (SpOPB) with and without modification of the hinge region was performed using a combination of X-ray diffraction analysis and small-angle X-ray scattering, which was complemented with an essential dynamics sampling (EDS) simulation. The first crystal structure of catalytically deficient SpOPB (SpOPBS532A) with an intact hinge sequence is reported. Similarly to SpOPB with modified hinges, SpOPBS532A was crystallized in the presence of spermine and adopted an intermediate conformation in the crystal lattice. Despite the similarity of the crystal structures, a difference in the catalytic triad residue arrangement was detected, which explained the inhibitory effect of the hinge modification. The SpOPBS532A structure reconstituted to the wild-type form was used as a starting point to the classical MD followed by EDS simulation, which allowed us to simulate the domain separation and the transition of the enzyme from the intermediate to open conformation. The obtained open state model was in good agreement with the experimental SAXS data.

【 授权许可】

Unknown