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Structural analysis of the LDL receptor-interacting FERM domain in the E3 ubiquitin ligase IDOL reveals an obscured substrate binding site

DOI: 10.1074/jbc.RA120.014349 DOI Help

Authors: Luca Martinelli (Netherlands Cancer Institute) , Athanasios Adamopoulos (Netherlands Cancer Institute) , Patrik Johansson (AstraZeneca) , Paul T. Wan (AstraZeneca) , Jenny Gunnarsson (AstraZeneca) , Hongwei Guo (AstraZeneca) , Helen Boyd (AstraZeneca) , Noam Zelcer (Amsterdam UMC) , Titia K. Sixma (The Netherlands Cancer Institute & Oncode Institute)
Co-authored by industrial partner: Yes

Type: Journal Paper
Journal: Journal Of Biological Chemistry

State: Published (Approved)
Published: July 2020
Diamond Proposal Number(s): 5133

Abstract: Hepatic abundance of the Low-Density lipoprotein receptor (LDLR) is a critical determinant of circulating plasma LDL-cholesterol levels and hence development of coronary artery disease. The sterol-responsive E3 ubiquitin ligase Inducible Degrader of the LDLR (IDOL) specifically promotes ubiquitination and subsequent lysosomal degradation of the LDLR and thus controls cellular LDL uptake. IDOL contains an extended N-terminal FERM (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) domain, responsible for substrate recognition and plasma-membrane association, and a second C-terminal RING domain, responsible for the E3 ligase activity and homo-dimerization. As IDOL is a putative lipid-lowering drug-target we investigated the molecular details of its substrate recognition. We produced and isolated full-length IDOL protein, which displayed high auto-ubiquitination activity. However, in vitro ubiquitination of its substrate, the intracellular tail of the LDLR, was low. To investigate the structural basis for this we determined crystal structures of the extended FERM domain of IDOL and multiple conformations of its F3ab subdomain. These reveal the archetypal F1-F2-F3 tri-lobed FERM domain structure but show that the F3c subdomain orientation obscures the target binding site. To substantiate this finding, we analyzed the full length FERM domain and a series of truncated FERM constructs by small angle X-ray scattering (SAXS). The scattering data support a compact and globular core FERM domain with a more flexible and extended C-terminal region. This flexibility may explain the low activity in vitro and suggests that IDOL may require activation for recognition of the LDLR.

Journal Keywords: FERM domain; LDL receptor; IDOL; protein structure; low-density lipoprotein (LDL); E3 ubiquitin ligase; enzyme purification; small-angle X-ray scattering (SAXS)

Subject Areas: Biology and Bio-materials, Chemistry


Instruments: B21-High Throughput SAXS