Table 1.
Predicted SARS-CoV replicase cleavage products and their mode of expression
| Protein ordera in polyproteins pp1a/pp1ab | Position in polyproteins pp1a/pp1ab (amino acid residues)b | Protein size (amino acid residues) | Associated putative functional domain(s)c | Predicted mode of expression and release from polyproteinsd |
|---|---|---|---|---|
| nsp1-pp1a/pp1ab | 1Met-Gly180 | 180 | ? | TI+PL2pro |
| nsp2-pp1a/pp1ab | 181Ala-Gly818 | 638 | ? | PL2pro |
| nsp3e-pp1a//pp1ab | 819Ala-Gly2740 | 1922 | Ac, X, PL2pro, Y (TM1), ADRP | PL2pro |
| nsp4-pp1a/pp1ab | 2741Lys-Gln3240 | 500 | TM2 | PL2+3CLpro |
| nsp5-pp1a/pp1ab | 3241Ser-Gln3546 | 306 | 3CLpro | 3CLpro |
| nsp6-pp1a/pp1ab | 3547Gly-Gln3836 | 290 | TM3 | 3CLpro |
| nsp7-pp1a/pp1ab | 3837Ser-Gln3919 | 83 | ? | 3CLpro |
| nsp8-pp1a/pp1ab | 3920Ala-Gln4117 | 198 | ? | 3CLpro |
| nsp9-pp1a/pp1ab | 4118Asn-Gln4230 | 113 | ? | 3CLpro |
| nsp10-pp1a/pp1ab | 4231Ala-Gln4369 | 139 | GFL | 3CLpro |
| nsp11-pp1a | 4370Ser-Val4382 | 13 | ? | 3CLpro+TT |
| nsp12-pp1ab | 4370Ser-Gln5301 | 932 | RdRp | RFS+3CLpro |
| nsp13-pp1ab | 5302Ala-Gln5902 | 601 | ZD, NTPase, HEL1 | RFS+3CLpro |
| nsp14-pp1ab | 5903Ala-Gln6429 | 527 | Exonuclease (ExoN homolog) | RFS+3CLpro |
| nsp15-pp1ab | 6430Ser-Gln6775 | 346 | NTD, endoRNase (XendoU homolog) | RFS+3CLpro |
| nsp16-pp1ab | 6776Ala-Asn7073 | 298 | 2′-O-MT | RFS+3CLpro+TT |
Predictions are based on the SARS-CoV sequences published by Michael Smith Genome Sciences Centre (Vancouver, Canada; Entrez Genomes accession number NC_004718 (AY274119)4) and the Centers for Disease Control and Prevention (Atlanta, USA; GenBank accession number AY2787415) and an alignment of SARS-CoV with previously characterized coronavirus sequences as summarized in Refs. 11., 18., 32..
For convenience, replicase cleavage products were provisionally numbered non-structural protein (nsp) 1–16 according to their position in the polyproteins.
Amino acids of replicase proteins pp1a and pp1ab were numbered assuming that, as in other coronaviruses, a −1 ribosomal frameshift occurs; use of the slippery sequence UUUAAAC10 is predicted to yield a peptide bond between Asn4378 and Arg4379 in pp1ab.
Abbreviations: PL2pro, papain-like proteinase 2; ADRP, adenosine diphosphate-ribose 1″-phosphatase; TM, transmembrane domain; 3CLpro, 3C-like cysteine proteinase; GFL, growth factor-like domain; RdRp, RNA-dependent RNA polymerase; ZD, putative Zinc-binding domain; HEL1, superfamily 1 helicase; NTD, nidovirus conserved domain; ExoN, 3′-to-5′ exonuclease; 2′-O-MT, S-adenosylmethionine-dependent ribose 2′-O-methyltransferase. Domains Ac, X, and Y are described in Refs 32., 47..
Indicated are the SARS-CoV proteinases predicted to be involved in cleavage of the N- and/or C-termini of the cleavage products; TI, translation initiation; TT, translation termination; RFS, ORF1a/ORF1b ribosomal frameshift.