Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme

Fei Teng; Yang Wang; Ming Liu; Shuyun Tian; Goran Stjepanovic; Ming-Yuan Su

doi:10.1016/j.str.2023.09.002

Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme

Structure. 2023 Nov 2;31(11):1431-1440.e5. doi: 10.1016/j.str.2023.09.002. Epub 2023 Oct 2.

Authors

Fei Teng¹, Yang Wang², Ming Liu², Shuyun Tian³, Goran Stjepanovic⁴, Ming-Yuan Su⁵

Affiliations

¹ Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China.
² Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China.
³ Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China.
⁴ Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China. Electronic address: goranstjepanovic@cuhk.edu.cn.
⁵ Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: sumy@sustech.edu.cn.

PMID: 37788672
DOI: 10.1016/j.str.2023.09.002

Abstract

CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric BTB-Kelch family proteins combine adapter and substrate receptor into a single polypeptide for the CULLIN3 family. However, the entire structural assembly and molecular details have not been elucidated to date. Here, we present a cryo-EM structure of the CULLIN3^RBX1 in complex with Kelch-like protein 22 (KLHL22) and a mitochondrial glutamate dehydrogenase complex I (GDH1) at 3.06 Å resolution. The structure adopts a W-shaped architecture formed by E3 ligase dimers. Three CULLIN3^KLHL22-RBX1 dimers were found to be dynamically associated with a single GDH1 hexamer. CULLIN3^KLHL22-RBX1 ligase mediated the polyubiquitination of GDH1 in vitro. Together, these results enabled the establishment of a structural model for understanding the complete assembly of BTB-Kelch proteins with CULLIN3 and how together they recognize oligomeric substrates and target them for ubiquitination.

Keywords: CULLIN3-RING ubiquitin ligase; cryo-EM; ubiquitination.

MeSH terms

Carrier Proteins / metabolism
Cryoelectron Microscopy
Cullin Proteins* / metabolism
Protein Binding
Protein Structure, Tertiary
Ubiquitin-Protein Ligases* / metabolism
Ubiquitination

Substances

Ubiquitin-Protein Ligases
Cullin Proteins
Carrier Proteins