Intriguingly one E residue may serve
Intriguingly, one E2 residue may serve as a molecular ‘gate’ to allow the C-terminus of ubiquitin to access the closed E2~Ub conformations favorable for ubiquitin transfer. This residue, Asp87 in UbcH5 family members, resides on one side of the opening that leads to the active site Cys (Fig. 4D). In the structures of the RNF4 and BIRC7 RINGs bound to UbcH5~Ub, the Asp side chain is positioned to form hydrogen bonds to the backbone of the ubiquitin C-terminal tail. How RING binding promotes the positioning of this Asp is unclear, but this may occur through the allosteric link between the critical Arg of the RING with Gln92, which neighbors Asp87. Given the lack of observable changes in structure in this region when RING-type E3:E2 and RING-type E3:E2~Ub structures are compared, the effect is likely to be a subtle one, probably involving small but important changes in electrostatics. The steric and chemical nature of this molecular gate is critical for activity, as even a Glu xec severely impacts ubiquitination . The residue corresponding to Asp87 is conserved as Asp, Asn, or Ser in most E2s, with the exceptions of UbcH7 and UbcH8, neither of which has been shown to function with RING-type E3s. Notably, the SUMO-specific E2, Ubc9, which encodes a Ser at the position analogous to Asp87 in UbcH5C, makes a similar contact with the C-terminus of SUMO in the SUMO–RanGAP1–Ubc9–Nup358 structure, consistent with a general mechanistic feature of ubiquitin and ubiquitin-like transfer .
E2-binding domains distinct from the RING domain
Perspective and future directions In the 14years since RING finger function was discovered, our knowledge of RING-type ubiquitin ligases has increased dramatically. Through their targeting of a diverse array of substrates, we are beginning to appreciate the range of roles played by this family of E3s in development, in maintaining homeostasis, and in response to cellular signals. Many challenges remain, however, as exemplified by the fact that substrates for most RING-type E3:E2 pairs are not yet known, A common feature of RING-type domains is a tendency to form active homo- and/or heterodimers. For C-terminal interleaved dimers, the distal RING-type domain provides additional contacts to ubiquitin (E2~Ub) to facilitate the closed E2~Ub conformation and promote catalysis. E3 dimerization/oligomerization, in instances where multiple RING-type domains can bind E2~Ub, could also enhance the probability of successful ubiquitin chain formation by increasing the local concentration of RING-type domains accessible to substrate. In the cases of BRCA1–BARD1 and RING1B–Bmi1, which dimerize through non-RING interactions, positioning of the second inactive (i.e., non-E2-binding) RING finger is not predicted to play a direct role in the binding of E2~Ub. In these cases, the function of dimerization in ubiquitination remains enigmatic. A central remaining question in RING-type E3-mediated ubiquitination is what regulates the processivity of ubiquitination and thus the fate of the substrate. The answer is likely complicated and includes E3 dimerization/oligomerization, the affinity for substrate, the relative affinities for E2 versus E2~Ub, and ubiquitin-binding domains intrinsic to E3s or E3 complexes. All of these potentially positive factors are, of course, countered by DUBs net secondary productivity (NSP) are associated with E3s or substrates. Another factor that, in some cases, facilitates ubiquitination is the non-covalent binding of ubiquitin to the backside of a subclass of E2s. An emerging factor, reviewed herein, is the contribution of non-RING regions of E3s binding to E2s using surfaces distinct from the shared RING- and E1-interacting interface. In some cases, these interactions compete with non-covalent ubiquitin backside binding and limit ubiquitination. In other cases, binding to a similar region of the E2 increases the affinity of the E2:E3 interaction and thereby enhances processivity of ubiquitination. These secondary sites of E2 binding may also provide a means to tether the E2 to the E3 complex, without continuous RING finger binding, and thereby provide a potential means to ‘reload’ E2 with ubiquitin (E2~Ub) without dissociation from the E3 complex. Whether such E2-specific binding is of general importance in vivo in determining combinatorial specificity in RING-type domain:E2 interactions and in the processivity of ubiquitination now become important questions.