6IF1

Crystal structure of Ube2K and K48-linked di-ubiquitin complex

Summary for 6IF1

• Entry DOI: 10.2210/pdb6if1/pdb
• Descriptor: Ubiquitin-conjugating enzyme E2 K, Ubiquitin (3 entities in total)
• Functional Keywords: complex, ligase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 61786.64

Authors

Lee, J.-G.,Youn, H.-S.,Lee, Y.,An, J.Y.,Park, K.R.,Kang, J.Y.,Lim, J.J.,Eom, S.H. (deposition date: 2018-09-18, release date: 2018-11-21, Last modification date: 2023-11-22)

Primary citation

Lee, J.G.,Youn, H.S.,Kang, J.Y.,Park, S.Y.,Kidera, A.,Yoo, Y.J.,Eom, S.H.
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.
Biochem. Biophys. Res. Commun., 506:102-107, 2018

PubMed 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 (Ub) and the auxiliary Ube2K promotes the discharging reaction and production of tri-Ub (Ub), probably by guiding and positioning the K48 (in the distal Ub) of the acceptor Ub in the active site. We also determined the crystal structure of Ube2K-Ub at 2.47 Å resolution. Based on our structural and biochemical data, we proposed a structural model of Ub synthesis by Ube2K without E3.

PubMed: 30336976
DOI: 10.1016/j.bbrc.2018.10.067

Experimental method

X-RAY DIFFRACTION (2.466 Å)