title: Structural basis for catalysis and ubiquitin recognition by the severe acute respiratory syndrome coronavirus papain-like protease.
abstract: Papain-like protease (PLpro) is one of two cysteine proteases involved in the proteolytic processing of the polyproteins of Severe acute respiratory syndrome coronavirus (SARS-CoV). PLpro also shows significant in vitro deubiquitinating and de-ISGylating activities, although the detailed mechanism is still unclear. Here, the crystal structure of SARS-CoV PLpro C112S mutant in complex with ubiquitin (Ub) is reported at 1.4 Å resolution. The Ub core makes mostly hydrophilic interactions with PLpro, while the Leu-Arg-Gly-Gly C-terminus of Ub is located in the catalytic cleft of PLpro, mimicking the P4-P1 residues and providing the first atomic insights into its catalysis. One of the O atoms of the C-terminal Gly residue of Ub is located in the oxyanion hole consisting of the main-chain amides of residues 112 and 113. Mutations of residues in the PLpro-Ub interface lead to reduced catalytic activity, confirming their importance for Ub binding and/or catalysis. The structure also revealed an N-cyclohexyl-2-aminethanesulfonic acid molecule near the catalytic triad, and kinetic studies suggest that this binding site is also used by other PLpro inhibitors. Overall, the structure provides a foundation for understanding the molecular basis of coronaviral PLpro catalysis.
authors: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.
authors: Chi-Yuan
authors: CY
authors: Chou
authors: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.
authors: Hsing-Yi
authors: HY
authors: Lai
authors: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.
authors: Hung-Yi
authors: HY
authors: Chen
authors: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.
authors: Shu-Chun
authors: SC
authors: Cheng
authors: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.
authors: Kai-Wen
authors: KW
authors: Cheng
authors: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Tapei 112, Taiwan.
authors: Ya-Wen
authors: YW
authors: Chou
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D010206:Papain / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D059748:Proteolysis; D045473:Severe acute respiratory syndrome-related coronavirus / Q000737:chemistry* / Q000201:enzymology; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D013654:Taurine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D025801:Ubiquitin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D025801:Ubiquitin; D014764:Viral Proteins; C050927:2-(N-cyclohexylamino)ethanesulfonic acid; D013654:Taurine; D010206:Papain
keywords: SARS-CoV; papain-like protease