Table 1. HCV helicase residues with unusual ionization states at physiological pH.
| 1HEI subA Hel-1a ‘closed’ pKa | 8OHM Hel-1b ‘open’ pKa | 1A1V Hel-1a:DNA ‘closed’ pKa | Comments | |
|---|---|---|---|---|
| His203 | 0.8 | 5.3 | 5.5 | SFII helicase motif I:HAPT |
| Lys210 | 4.9 | 8.1 | 1.7 | SFII helicase motif I:GSGK |
| K210A (37–39,50) | ||||
| K210Q (37) | ||||
| K210N (36) | ||||
| K210E (40,41) | ||||
| Lys272 | 8.6 | 8.4 | 10.3 | TxGx motif (33) |
| Asp290 | 7.7 | 3.4 | 10.3 | SFII helicase motif II: DECH |
| D290A (38,39) | ||||
| D290N (36) | ||||
| His293 | 2.2 | 3.7 | 2.5 | SFII helicase motif II:DECH |
| H293A (36,37) | ||||
| H293K (36) | ||||
| H293Q (36) | ||||
| His333 | 4.8 | 3.6 | 3.7 | Conserved in all HCV isolates (27) |
| His369 | 4.0 | 4.6 | 2.3 | SFII helicase motif IV: HSKKKCD |
| H369A, H369K (this study) | ||||
| Lys373 | 9.9 | 8.0 | 8.8 | SFII helicase motif IV: HSKKKCD |
| Conserved in all HCV isolates (27) | ||||
| Asp375 | 5.0 | 6.4 | 4.2 | SFII helicase motif IV: HSKKKCD |
| Lys380 | 10.7 | 10.1 | 8.4 | Conserved in all HCV isolates (27) |
| Glu480 | 4.0 | 3.9 | 8.0 | Conserved in all HCV isolates (27) |
| Glu493 | 6.8 | 7.1 | 7.6 | pH dependent- DNA binding |
| E493Q, E493K (this study) | ||||
| Asp496 | 5.7 | 4.4 | 5.9 | Conserved in all HCV isolates (27) |
| His613 | 3.5 | 3.5 | 3.4 | |
| Asp626 | 10.3 | n.d. | n.d. |
The pKas for the enzyme without ligands in the closed conformation were calculated by using the coordinates for subunit A in PDB file 1HEI. The values for HCV helicase in the open conformation were obtained by analyzing file 8OHM, and values for the DNA bound enzyme were obtained using coordinates in PDB file 1A1V. Known roles and/or site-directed mutants of each residue are noted in the last column. Major changes are underlined. The MCCE program did not determine a pKa for residues labeled n.d.