4LCD

Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3

Summary for 4LCD

• Entry DOI: 10.2210/pdb4lcd/pdb
• Descriptor: E3 ubiquitin-protein ligase RSP5, Protein SNA3, Ubiquitin (3 entities in total)
• Functional Keywords: ligase, e3, rsp5, nedd4, ubiquitin, hect, sna3, thioester, maleimide, crosslink, ligase-protein binding complex, ligase/protein binding
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Cellular location: Cytoplasm: P39940; Membrane; Multi-pass membrane protein: P14359; Ubiquitin: Cytoplasm (By similarity): P0CG48
• Total number of polymer chains: 6
• Total formula weight: 125228.63

Authors

Kamadurai, H.B.,Miller, D.,Schulman, B.A. (deposition date: 2013-06-21, release date: 2013-08-14, Last modification date: 2024-02-28)

Primary citation

Kamadurai, H.B.,Qiu, Y.,Deng, A.,Harrison, J.S.,Macdonald, C.,Actis, M.,Rodrigues, P.,Miller, D.J.,Souphron, J.,Lewis, S.M.,Kurinov, I.,Fujii, N.,Hammel, M.,Piper, R.,Kuhlman, B.,Schulman, B.A.
Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3.
Elife, 2:e00828-e00828, 2013

PubMed Abstract: Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate. Here we report that the second step of ligation is mediated by a distinct catalytic architecture established by both the HECT E3 and its covalently linked ubiquitin. The structure of a chemically trapped proxy for an E3∼ubiquitin-substrate intermediate reveals three-way interactions between ubiquitin and the bilobal HECT domain orienting the E3∼ubiquitin thioester bond for ligation, and restricting the location of the substrate-binding domain to prioritize target lysines for ubiquitination. The data allow visualization of an E2-to-E3-to-substrate ubiquitin transfer cascade, and show how HECT-specific ubiquitin interactions driving multiple reactions are repurposed by a major E3 conformational change to promote ligation. DOI:http://dx.doi.org/10.7554/eLife.00828.001.

PubMed: 23936628
DOI: 10.7554/eLife.00828

Experimental method

X-RAY DIFFRACTION (3.1 Å)