Structural view and substrate specificity of papain-like protease from Avian Infectious Bronchitis Virus [Protein Structure and Folding]

January 21st, 2015 by Kong, L., Shaw, N., Yan, L., Lou, Z., Rao, Z.

Papain-like protease (PLpro) of Coronaviruses (CoVs) carries out proteolytic maturation of non-structural proteins that play a role in replication of the virus and performs de-ubiquitination of host cell factors to scuttle anti-viral responses. Avian Infectious Bronchitis Virus (IBV), the causative agent of bronchitis in chicken that results in huge economic loses every year in poultry industry globally, encodes a PLpro. The substrate specificities of this PLpro are not clearly understood. Here, we show that IBV PLpro can degrade K-48 and K-63 linked polyubiquitin chains to mono-ubiquitin, but not linear polyubiquitin. To explain the substrate specificities, we have solved the crystal structure of PLpro from IBV at 2.15 Å resolution. The overall structure is reminiscent of the structure of SARS CoV PLpro. However, unlike the SARS CoV PLpro, that lacks the BL1 loop of de-ubiquitinating enzymes, the IBV PLpro has a short BL1-like loop. Access to a conserved catalytic triad consisting of Cys101, His264 and Asp275 is regulated by a flexible BL2 loop. A model of ubiquitin bound IBV CoV PLpro brings out key differences in substrate binding sites of PLpros. In particular, P3 and P4 sub-sites as well as residues interacting with the β-barrel of ubiquitin are different, suggesting different catalytic efficiencies and substrate specificities. We show that IBV PLpro cleaves peptide substrates KKAG-AMC and LRGG-AMC with different catalytic efficiencies. These results demonstrate that substrate specificities of IBV PLpro are different from other PLpros and that IBV PLpro might target different ubiquitinated host factors to aid the propagation of the virus.