Structure and dynamics of a pentameric KCTD5/Cullin3/Gβγ E3 ubiquitin ligase complex

Nguyen, D. M.; Rath, D. H.; Devost, D.; Petrain, D.; Rizk, R.; Ji, A. X.; Narayanan, N.; Yong, D.; Zhai, A.; Kuntz, D. A.; Mian, M. U. Q.; Pomroy, N. C.; Keszei, A. F. A.; Benlekbir, S.; Mazhab-Jafari, M. T.; Rubinstein, J. L.; Hebert, T. E.; Prive, G. G.

doi:10.1101/2023.09.20.558662

bioRxiv · 10.1101/2023.09.20.558662

Structure and dynamics of a pentameric KCTD5/Cullin3/Gβγ E3 ubiquitin ligase complex

Nguyen, D. M.·Rath, D. H.·Devost, D.·Petrain, D.·Rizk, R.·Ji, A. X.·Narayanan, N.·Yong, D.·Zhai, A.·Kuntz, D. A.·Mian, M. U. Q.·Pomroy, N. C.·Keszei, A. F. A.·Benlekbir, S.·Mazhab-Jafari, M. T.·Rubinstein, J. L.·Hebert, T. E.·Prive, G. G.

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Abstract

Heterotrimeric G proteins can be regulated by post-translational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain (CTD), engages CUL3 to form the central scaffold of a cullin- RING E3 ligase complex (CRL3KCTD5) that ubiquitylates G{beta}{gamma} and reduces G{beta}{gamma} protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3NTD/G{beta}1{gamma}2 assembly reveals a highly dynamic complex with rotations of over 60{degrees} between the KCTD5BTB/CUL3NTD and KCTD5CTD/G{beta}{gamma} moieties of the structure. CRL3KCTD5 engages the E3 ligase ARIH1 to ubiquitylate G{beta}{gamma} in an E3-E3 super-assembly, and extension of the structure to include full- length CUL3 with RBX1 and an ARIH1[~]ubiquitin conjugate reveals that some conformational states position the ARIH1[~]ubiquitin thioester bond to within 10 [A] of lysine-23 of G{beta} and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3NTD/G{beta}{gamma} complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex. Significance StatementIn humans, [~]600 enzyme complexes can carry out protein ubiquitylation, and the most abundant class of these are the cullin3-RING-ligase complexes (CRL3s). CRL3s are multiprotein complexes built around a BTB/cullin3 core, and the incorporation of different BTB proteins into this scaffold results in distinct architectures that ubiquitylate a wide range of substrates. In most cases, it is not known how the complexes are tuned to their substrates. We show that the BTB protein KCTD5 is the central organizer in a CRL3KCTD5 complex, and that the architecture and internal dynamics of KCTD5 are essential for positioning a G{beta}{gamma} substrate protein near an activated ubiquitin for the transfer reaction. This explains how KCTD5 targets G{beta}{gamma} for proteasomal degradation and regulates cellular activities.

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Nguyen, D. M., Rath, D. H., Devost, D., Petrain, D., Rizk, R., Ji, A. X., Narayanan, N., Yong, D., Zhai, A., Kuntz, D. A., Mian, M. U. Q., Pomroy, N. C., Keszei, A. F. A., Benlekbir, S., Mazhab-Jafari, M. T., Rubinstein, J. L., Hebert, T. E., Prive, G. G.. 2023-09-20. Structure and dynamics of a pentameric KCTD5/Cullin3/Gβγ E3 ubiquitin ligase complex. https://doi.org/10.1101/2023.09.20.558662

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