The 3C-like protease (3CL(pro)) of severe acute respiratory syndrome (SARS) has been proposed as an attractive target for drug design. His(41) and Cys(145) were essential for the active site as the principal catalytic residues. In this study, we mutated the two sites, expressed four resulting mutants in Escherichia coli and characterized. All mutants showed undetectable activity in trans-cleavage assay. In addition. we introduced a 31-mer peptide containing an auto-cleavage site to the N-terminal of the proteases and found the peptide could be cleaved efficiently by 3CLsc itself, but, among the four mutants, only the mutant cys(145) --> Ser showed residual activity as detected by the auto-cleavage assay. The data supported the proposition unequivocally that SARS-CoV 3CL(pro) was a member of serine proteases involving His(41) and Cys(145) residues at the active site. The auto-cleavage assay also provided a sensitive and reliable compensation to the traditional trans-cleavage assay. (C) 2004 Elsevier Inc. All rights reserved.