Table 4.
Protein RNA cross-links identified in free and bound Prp43
| Domain | Residue | Peptide | RNA | Prp43/Ntr1 | Prp43 | Relative enrichment b/f (%) |
|---|---|---|---|---|---|---|
| RecA-1 | M154 | 151VAAMSVAQR159 | UG | + | + | 33.3 |
| RecA-1 | Y174 | 168LGEEVGYSIR177 | UG | + | + | 24.0 |
| RecA-1 | n.i | 190YM(OX)TDGM(OX)LLREAM(OX)EDHDLSR208 | U | + | + | n.d. |
| RecA-2 | K418 | 408VESLLVSPISKASAQQR424 | U-HPO3 | + | − | 6.3 |
| RecA-2 | Y440 | 439LYTEEAFQK447 | UG | + | + | 3.7 |
| Ratchet | Y595 | 591SDEAYEYGIHK601 | UG | + | + | 132.2 |
| Ratchet | Y630 | 630YNLELNTTDYESPK643 | GU | + | + | 7.3 |
| Ratchet | n.i | 605DHYLNYRSLSAADNIR620 | GU | + | + | n.d |
| Ratchet | Y610 | 605DHYLNYR611 | U | + | + | 339.6 |
| Ratchet | S614 | 612SLSAADNIR620 | UG | + | − | 169.7 |
n.i.: not identified; n.d.: non-determined; (-)cross-link was not sequenced, identification based on MS1; b: bound; f: free. The domain and the cross-linked residue (when identified) are indicated, as well as the RNA oligonucleotide.