Fig. 1. Sequence comparison of coronavirus main proteinases. The alignment was produced using CLUSTAL X, version 1.81 (Thompson et al., 1997), and corrected manually on the basis of the three-dimensional structure of TGEV Mpro. The corresponding sequences of FIPV (strain 79–1146), HCoV (strain 229E), bovine coronavirus (BCoV, isolate LUN), MHV (strain JHM) and IBV (strain Beaudette) were derived from the replicative polyproteins of the respective viruses whose sequences are deposited at the DDBJ/EMBL/GenBank database (accession Nos: FIPV, AF326575; HCoV, X69721; BCoV, AF391542; MHV, M55148; IBV, M95169; TGEV, AJ271965). The β-strands and α-helices as revealed in the TGEV Mpro crystal structure (this study) are shown above the sequence alignment (see also Figures 4 and 5). Black background colour indicates the catalytic cysteine and histidine residues. Grey background colour indicates the key residue of the S1 subsite (TGEV Mpro His162) and its equivalents in other coronavirus main proteinases. Also shown in grey are the phenylalanine and tyrosine residues (TGEV Mpro Phe139 and Tyr160) that are proposed to stabilize the neutral state of His162 (see text for details).