5D1K

Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7

Summary for 5D1K

• Entry DOI: 10.2210/pdb5d1k/pdb
• Related: 5D1L 5D1M
• Descriptor: Ubiquitin-conjugating enzyme E2 D2, E3 ubiquitin-protein ligase RNF25, 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: ubiquitin conjugating enzyme (e2), ubiquitin ligase (e3), ring finger, ubiquitination, ubiquitin, ligase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 32863.93

Authors

Liang, Y.-H.,Li, S.,Weissman, A.M.,Ji, X. (deposition date: 2015-08-04, release date: 2015-10-28, Last modification date: 2023-09-27)

Primary citation

Li, S.,Liang, Y.H.,Mariano, J.,Metzger, M.B.,Stringer, D.K.,Hristova, V.A.,Li, J.,Randazzo, P.A.,Tsai, Y.C.,Ji, X.,Weissman, A.M.
Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B.
J.Biol.Chem., 290:30225-30239, 2015

PubMed Abstract: RING proteins constitute the largest class of E3 ubiquitin ligases. Unlike most RINGs, AO7 (RNF25) binds the E2 ubiquitin-conjugating enzyme, UbcH5B (UBE2D2), with strikingly high affinity. We have defined, by co-crystallization, the distinctive means by which AO7 binds UbcH5B. AO7 contains a structurally unique UbcH5B binding region (U5BR) that is connected by an 11-amino acid linker to its RING domain, forming a clamp surrounding the E2. The U5BR interacts extensively with a region of UbcH5B that is distinct from both the active site and the RING-interacting region, referred to as the backside of the E2. An apparent paradox is that the high-affinity binding of the AO7 clamp to UbcH5B, which is dependent on the U5BR, decreases the rate of ubiquitination. We establish that this is a consequence of blocking the stimulatory, non-covalent, binding of ubiquitin to the backside of UbcH5B. Interestingly, when non-covalent backside ubiquitin binding cannot occur, the AO7 clamp now enhances the rate of ubiquitination. The high-affinity binding of the AO7 clamp to UbcH5B has also allowed for the co-crystallization of previously described and functionally important RING mutants at the RING-E2 interface. We show that mutations having marked effects on function only minimally affect the intermolecular interactions between the AO7 RING and UbcH5B, establishing a high degree of complexity in activation through the RING-E2 interface.

PubMed: 26475854
DOI: 10.1074/jbc.M115.685867

Experimental method

X-RAY DIFFRACTION (1.78 Å)