The mechanism of neural precursor cell expressed developmentally down-regulated 4-2 (Nedd4-2)/NEDD4L-catalyzed polyubiquitin chain assembly

The mechanism of Nedd4-2 has been quantitatively explored for the first time using biochemically defined kinetic assays examining rates of I-125-polyubiquitin chain assembly as a functional readout. We demonstrate that Nedd4-2 exhibits broad specificity for E2 paralogs of the Ubc4/5 clade to assemble Lys(63)-linked polyubiquitin chains. Full-length Nedd4-2 catalyzes free I-125-polyubiquitin chain assembly by hyperbolic Michaelis-Menten kinetics with respect to Ubc5B approximate to ubiquitin thioester concentration (K-m = 44 +/- 6 nm; k(cat) = 0.020 +/- 0.007 s(-1)) and substrate inhibition above 0.5 m (K-i = 2.5 +/- 1.3 m) that tends to zero velocity, requiring ordered binding at two functionally distinct E2 approximate to ubiquitin-binding sites. The Ubc5BC85A product analog non-competitively inhibits Nedd4-2 (K-i = 2.0 +/- 0.5 m), consistent with the presence of the second E2-binding site. In contrast, the isosteric Ubc5BC85S-ubiquitin oxyester substrate analog exhibits competitive inhibition at the high-affinity Site 1 (K-i = 720 +/- 340 nm) and non-essential activation at the lower-affinity Site 2 (K-act = 750 +/- 260 nm). Additional studies utilizing Ubc5BF62A, defective in binding the canonical E2 site, demonstrate that the cryptic Site 1 is associated with thioester formation, whereas binding at the canonical site (Site 2) is associated with polyubiquitin chain elongation. Finally, previously described Ca2+-dependent C2 domain-mediated autoinhibition of Nedd4-2 is not observed under our reported experimental conditions. These studies collectively demonstrate that Nedd4-2 catalyzes polyubiquitin chain assembly by an ordered two-step mechanism requiring two dynamically linked E2 approximate to ubiquitin-binding sites analogous to that recently reported for E6AP, the founding member of the Hect ligase family.