The papain-like protease determines a virulence trait that varies among members of the SARS-coronavirus species
(a) Schematic representation of a PLP amino acid sequence alignment (315 amino acids) with European- and Chinese reservoir-associated SARS-related CoV strains which highlights the sequence diversity in the PLP domain. The alignment shows strains (represented as grey lines) with unique mutations (black vertical bars). The ubiquitin-binding surfaces are highlighted in orange (Ub1) and magenta (Ub2), respectively. The proposed localization of Ub1 and Ub2 is depicted in the cartoon below the alignment. SA- and SR-PLP, which were investigated in the presented study, are highlighted in red. Homology modelling for SR-PLP was done to compare the interaction surfaces between SA- and SR-PLP, respectively, and the two ubiquitin molecules of a K48-linked di-ubiquitin. Molecular graphics and analyzes were performed with the UCSF Chimera package  with the crystal structure of SARS-CoV PLP in complex with a K48-linked di-ubiquitin (PDB entry 5e6j) as template and the amino acid sequence of SR-PLP as a target. Putative amino acid contact points between SA- and SR-PLP and Ub1 (b) and Ub2 (c) highlight the conformational variability of both PLPs in ubiquitin-binding. The tertiary structure of SA-PLP is shown in dark blue, while the SR-PLP tertiary structure is shown in light blue.