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. 2003 Jan;77(2):1415–1426. doi: 10.1128/JVI.77.2.1415-1426.2003

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Copyright © 2003, American Society for Microbiology

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FIG. 3. — Multiple sequence alignment of GAV, coronavirus, and potyvirus 3CL^pro domains. The Clustal X-based alignment of corona- and potyvirus 3CL^pros produced previously (17) was modified slightly to accommodate the results of the tertiary-structure analysis of a porcine coronavirus 3CL^pro (2) and used to align the GAV 3CL^pro sequence. For GAV and coronaviruses, this alignment was further expanded by including upstream and downstream sequences with Clustal X. Shown are the regions enriched in hydrophobic amino acid residues and flanking the 3CL^pro from both the N terminus (C-terminal part of hydrophobic domain [HD3]) and the C terminus (entire HD4). These hydrophobic domains are conserved in all nidoviruses (14). For GAV and coronaviruses, the pp1a/1ab amino acid positions are given on the right; for potyviruses, the numbers refer to the amino acid positions in the 3CL^pro. The column conservation in the two groups of coronavirus/GAV versus potyvirus sequences was highlighted separately with different colors for the following groups of amino acids: green for G, A, L, I, V, M, F, Y, and W; blue for H, K, and R; red for N, Q, E, and D; yellow for P; and violet for S and T. Columns with conserved or identical residues in all sequences are indicated by colons and solid squares, respectively, in the line separating the coronavirus/GAV and potyvirus groups. Empty squares highlight columns with identical residues in the GAV and potyvirus sequences. #, conserved catalytic Cys and His residues; @, P1-binding His residue conserved in all sequences and Thr residue conserved among GAV and potyviruses; solid circle, catalytic Asp residue of potyviruses. ><, positions of cleavage sites separating 3CL^pro from flanking domains in corona- and potyviruses. Abbreviations of virus names and DDBJ/EMBL/GenBank accession numbers for the sequences are as follows: HCoV, human coronavirus (strain 229E) (X69721); TGEV, transmissible gastroenteritis virus (strain Purdue 115) (Z34093); PEDV, porcine epidemic diarrhea virus (strain CV777) (NC_003436); MHVA, murine hepatitis virus (strain A59) (NC_001846); BCoVl, bovine coronavirus (isolate LUN) (AF391542); IBV, avian infectious bronchitis virus (strain Beaudette) (M95169); TVMV, tobacco vein mottling virus (P09814); TUMVQ, turnip mosaic virus (strain Quebec) (Q02597); TEV, tobacco etch virus (P04517); PVY, potato virus Y (strain N) (P18247); PSBMV, pea seed-borne mosaic virus (strain DPD1) (P29152); PPVRA, plum pox virus (strain Rankovic) (P17767); PRSVH, papaya ringspot virus (strain P/mutant HA) (Q01901); PEMVC, pepper mottle virus (California isolate) (Q01500); BSMRV, Brome streak mosaic rymovirus (strain 11-Cal) (Q65730).

FIG. 3. — Multiple sequence alignment of GAV, coronavirus, and potyvirus 3CL^pro domains. The Clustal X-based alignment of corona- and potyvirus 3CL^pros produced previously (17) was modified slightly to accommodate the results of the tertiary-structure analysis of a porcine coronavirus 3CL^pro (2) and used to align the GAV 3CL^pro sequence. For GAV and coronaviruses, this alignment was further expanded by including upstream and downstream sequences with Clustal X. Shown are the regions enriched in hydrophobic amino acid residues and flanking the 3CL^pro from both the N terminus (C-terminal part of hydrophobic domain [HD3]) and the C terminus (entire HD4). These hydrophobic domains are conserved in all nidoviruses (14). For GAV and coronaviruses, the pp1a/1ab amino acid positions are given on the right; for potyviruses, the numbers refer to the amino acid positions in the 3CL^pro. The column conservation in the two groups of coronavirus/GAV versus potyvirus sequences was highlighted separately with different colors for the following groups of amino acids: green for G, A, L, I, V, M, F, Y, and W; blue for H, K, and R; red for N, Q, E, and D; yellow for P; and violet for S and T. Columns with conserved or identical residues in all sequences are indicated by colons and solid squares, respectively, in the line separating the coronavirus/GAV and potyvirus groups. Empty squares highlight columns with identical residues in the GAV and potyvirus sequences. #, conserved catalytic Cys and His residues; @, P1-binding His residue conserved in all sequences and Thr residue conserved among GAV and potyviruses; solid circle, catalytic Asp residue of potyviruses. ><, positions of cleavage sites separating 3CL^pro from flanking domains in corona- and potyviruses. Abbreviations of virus names and DDBJ/EMBL/GenBank accession numbers for the sequences are as follows: HCoV, human coronavirus (strain 229E) (X69721); TGEV, transmissible gastroenteritis virus (strain Purdue 115) (Z34093); PEDV, porcine epidemic diarrhea virus (strain CV777) (NC_003436); MHVA, murine hepatitis virus (strain A59) (NC_001846); BCoVl, bovine coronavirus (isolate LUN) (AF391542); IBV, avian infectious bronchitis virus (strain Beaudette) (M95169); TVMV, tobacco vein mottling virus (P09814); TUMVQ, turnip mosaic virus (strain Quebec) (Q02597); TEV, tobacco etch virus (P04517); PVY, potato virus Y (strain N) (P18247); PSBMV, pea seed-borne mosaic virus (strain DPD1) (P29152); PPVRA, plum pox virus (strain Rankovic) (P17767); PRSVH, papaya ringspot virus (strain P/mutant HA) (Q01901); PEMVC, pepper mottle virus (California isolate) (Q01500); BSMRV, Brome streak mosaic rymovirus (strain 11-Cal) (Q65730).