TABLE 1.
Summary of deubiquitination efficiency (nm−1 × min−1) for proteasome and associated DUBs
Enzymatic efficiency of polyUb chain disassembly by deubiquitination enzymes in this study was calculated using Equation 1 (see “Experimental Procedures”). Disassembly efficiency of Ub2 substrate was determined by quantifying the Ub2 gel band intensity. Values for Ub4, Ub6+, and UbcH5b-Ubn were determined by following the decrease in signal intensity of residual substrate relative to the entire signal generated by Ub in all of its forms.
| Ub2 |
Ub4 |
Ub6+ |
Ubch5b-Ubn (heterogeneous) | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Lys11 | Lys48 | Lys63 | Lys48 | Lys63 | Lys11 | Lys48 | Lys63 | ||
| Rpn8 + 11 | 0.12 ± 0.03 | 0.07 ± 0.01 | 0.05 ± 0.02 | 0.046 ± 0.00 | 0.07 ± 0.01 | 0.8 ± 0.2 | 0 | 0.61 ± 0.11 | 0.54 ± 0.06 |
| Lid-core | 0.22 ± 0.01 | 0.12 ± 0.05 | 0.13 ± 0.03 | 0.06 ± 0.01 | 0.13 ± 0.02 | 2.9 ± 0.4 | 0 | 2.04 ± 0.34 | 0.76 ± 0.06 |
| Ubp6 | 0.20 ± 0.02 | 0.28 ± 0.04 | 0.14 ± 0.04 | 0.15 ± 0.01 | 0.42 ± 0.14 | 3.5 ± 0.3 | 1.17 ± 0.12 | 2.49 ± 0.08 | 0.66 ± 0.15 |
| ΔUbp6 26S | 38.29 ± 1.09 | 25.15 ± 4.4 | 19.55 ± 2.31 | 5.81 ± 0.42 | 124.08 ± 0.2 | 100.1 ± 13.1 | 6 ± 1 | 94.2 ± 2.6 | 81 ± 15 |
| 26S | 36.88 ± 3.26 | 21.82 ± 1.36 | 16.58 ± 4.74 | 4.63 ± 0.21 | 141.8 ± 5.9 | 136.1 ± 12.5 | 7.73 ± 1.59 | 80.1 ± 6.5 | 86.7 ± 14.3 |