Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation

Bernhard C. Lechtenberg, Akhil Rajput, Ruslan Sanishvili, Małgorzata K. Dobaczewska, Carl F. Ware, Peter D. Mace and Stefan J. Riedl ()
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Bernhard C. Lechtenberg: NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute
Akhil Rajput: Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute
Ruslan Sanishvili: Advanced Photon Source, Argonne National Laboratory
Małgorzata K. Dobaczewska: NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute
Carl F. Ware: Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute
Peter D. Mace: University of Otago
Stefan J. Riedl: NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute

Nature, 2016, vol. 529, issue 7587, 546-550

Abstract: Abstract Ubiquitination is a central process affecting all facets of cellular signalling and function1. A critical step in ubiquitination is the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate or a growing ubiquitin chain, which is mediated by E3 ubiquitin ligases. RING-type E3 ligases typically facilitate the transfer of ubiquitin from the E2 directly to the substrate2,3. The RING-between-RING (RBR) family of RING-type E3 ligases, however, breaks this paradigm by forming a covalent intermediate with ubiquitin similarly to HECT-type E3 ligases4,5,6. The RBR family includes Parkin4 and HOIP, the central catalytic factor of the LUBAC (linear ubiquitin chain assembly complex)7. While structural insights into the RBR E3 ligases Parkin and HHARI in their overall auto-inhibited forms are available8,9,10,11,12,13, no structures exist of intact fully active RBR E3 ligases or any of their complexes. Thus, the RBR mechanism of action has remained largely unknown. Here we present the first structure, to our knowledge, of the fully active human HOIP RBR in its transfer complex with an E2~ubiquitin conjugate, which elucidates the intricate nature of RBR E3 ligases. The active HOIP RBR adopts a conformation markedly different from that of auto-inhibited RBRs. HOIP RBR binds the E2~ubiquitin conjugate in an elongated fashion, with the E2 and E3 catalytic centres ideally aligned for ubiquitin transfer, which structurally both requires and enables a HECT-like mechanism. In addition, three distinct helix–IBR-fold motifs inherent to RBRs form ubiquitin-binding regions that engage the activated ubiquitin of the E2~ubiquitin conjugate and, surprisingly, an additional regulatory ubiquitin molecule. The features uncovered reveal critical states of the HOIP RBR E3 ligase cycle, and comparison with Parkin and HHARI suggests a general mechanism for RBR E3 ligases.

Date: 2016
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DOI: 10.1038/nature16511

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