Crystal structures reveal an induced-fit binding of a substrate-like aza-peptide epoxide to SARS coronavirus main peptidase

The SARS coronavirus main peptidase (SARS-CoV M-pro) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of M-pro at a resolution of 1.82 angstrom, in space group P2(1) at pH 6.0. In contrast to the previously reported structure of M-pro in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of M-pro reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of Mpro having an additional Ala at the N terminus of each protomer (M-+A(-1)(pro)), both at a resolution of 2.00 angstrom, in space group P4(3)2(1)2: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M-+A(-1)(pro) are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of M-pro exist in dynamic equilibrium. The structural data further suggest that the binding of APE to Mpro follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle. (c) 2006 Elsevier Ltd. All rights reserved.