Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis

Abstract

Ubiquitin-conjugating enzymes (E2) form thioester bonds with ubiquitin (Ub), which are subsequently transferred to target proteins for cellular progress. Ube2K/E2-25K (a class II E2 enzyme) contains a C-terminal ubiquitin-associated (UBA) domain that has been suggested to control ubiquitin recognition, dimerization, or poly-ubiquitin chain formation. Ube2K is a special E2 because it synthesizes K48-linked poly-ubiquitin chains without E3 ubiquitin ligase. We found that a novel interaction between the acceptor di-Ub (Ub₂) and the auxiliary Ube2K promotes the discharging reaction and production of tri-Ub (Ub₃), probably by guiding and positioning the K48 (in the distal Ub) of the acceptor Ub₂ in the active site. We also determined the crystal structure of Ube2K-Ub₂ at 2.47 Å resolution. Based on our structural and biochemical data, we proposed a structural model of Ub₃ synthesis by Ube2K without E3.

Keywords: Crystal structure; K48-linked poly-Ub chain; Single-turnover assay; Ube2K/E2-25K; Ubiquitin.