Structural Basis of the Binding of Merlin FERM Domain to the E3 Ubiquitin Ligase Substrate Adaptor DCAF1

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 (4.1 protein, ezrin, radixin, and moesin) domain, responsible for substrate recognition and plasma membrane association, and a second C-terminal RING domain, responsible for the E3 ligase activity and homodimerization. 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 autoubiquitination 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 trilobed 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.

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Identification of a PGXPP degron motif in dishevelled and structural basis for its binding to the E3 ligase KLHL12

Open Biology ◽

10.1098/rsob.200041 ◽

2020 ◽

Vol 10 (6) ◽

pp. 200041 ◽

Cited By ~ 1

Author(s):

Zhuoyao Chen ◽

Gregory A. Wasney ◽

Sarah Picaud ◽

Panagis Filippakopoulos ◽

Masoud Vedadi ◽

...

Keyword(s):

Ubiquitin Ligase ◽

Molecular Mechanisms ◽

Hydrophobic Interactions ◽

E3 Ubiquitin Ligase ◽

Structural Basis ◽

E3 Ligases ◽

Kelch Domain ◽

Ring E3 Ligases ◽

Ring E3 ◽

New Protein

Wnt signalling is dependent on dishevelled proteins (DVL1-3), which assemble an intracellular Wnt signalosome at the plasma membrane. The levels of DVL1-3 are regulated by multiple Cullin-RING E3 ligases that mediate their ubiquitination and degradation. The BTB-Kelch protein KLHL12 was the first E3 ubiquitin ligase to be identified for DVL1-3, but the molecular mechanisms determining its substrate interactions have remained unknown. Here, we mapped the interaction of DVL1-3 to a ‘PGXPP' motif that is conserved in other known partners and substrates of KLHL12, including PLEKHA4, PEF1, SEC31 and DRD4. To determine the binding mechanism, we solved a 2.4 Å crystal structure of the Kelch domain of KLHL12 in complex with a DVL1 peptide that bound with low micromolar affinity. The DVL1 substrate adopted a U-shaped turn conformation that enabled hydrophobic interactions with all six blades of the Kelch domain β-propeller. In cells, the mutation or deletion of this motif reduced the binding and ubiquitination of DVL1 and increased its stability confirming this sequence as a degron motif for KLHL12 recruitment. These results define the molecular mechanisms determining DVL regulation by KLHL12 and establish the KLHL12 Kelch domain as a new protein interaction module for a novel proline-rich motif.

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Structural Basis of the Activation and Degradation Mechanisms of the E3 Ubiquitin Ligase Nedd4L

Structure ◽

10.1016/j.str.2014.08.016 ◽

2014 ◽

Vol 22 (10) ◽

pp. 1446-1457 ◽

Cited By ~ 32

Author(s):

Albert Escobedo ◽

Tiago Gomes ◽

Eric Aragón ◽

Pau Martín-Malpartida ◽

Lidia Ruiz ◽

...

Keyword(s):

Ubiquitin Ligase ◽

E3 Ubiquitin Ligase ◽

Structural Basis ◽

Degradation Mechanisms

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Structural basis for feedforward control in the PINK1/parkin pathway

10.1101/2021.08.16.456440 ◽

2021 ◽

Author(s):

Véronique Sauvé ◽

George Sung ◽

Emma MacDougall ◽

Guennadi Kozlov ◽

Anshu Saran ◽

...

Keyword(s):

Ubiquitin Ligase ◽

Feedforward Control ◽

E3 Ubiquitin Ligase ◽

Evolutionary Development ◽

Structural Basis ◽

Intermediate Step ◽

Vinyl Sulfone ◽

Mitochondrial Quality Control ◽

High Affinity Site ◽

Nmr Titrations

PINK1 and parkin constitute a mitochondrial quality control system mutated in Parkinson's disease. PINK1, a kinase, phosphorylates ubiquitin to recruit parkin, an E3 ubiquitin ligase, to mitochondria. PINK1 controls both parkin localization and activity through phosphorylation of both ubiquitin and the ubiquitin-like (Ubl) domain of parkin. Here, we observe that phospho-ubiquitin can bind to two distinct sites on parkin, a high affinity site on RING1 that controls parkin localization, and a low affinity site on RING0 that releases parkin autoinhibition. Surprisingly, NMR titrations and ubiquitin vinyl sulfone assays show that the RING0 site has higher affinity for phospho-ubiquitin than the phosphorylated Ubl. Parkin could be activated by micromolar concentrations of tetra-phospho-ubiquitin chains that mimic a mitochondrion bearing multiple phosphorylated ubiquitins. A chimeric form of parkin with the Ubl domain replaced by ubiquitin was readily activated by PINK1 phosphorylation. In all cases, mutation of the binding site on RING0 abolished parkin activation. The feedforward mechanism of parkin activation confers robustness and rapidity to the PINK1-parkin pathway and likely represents an intermediate step in its evolutionary development.

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Structure of the HLTF HIRAN domain and its functional implications in regression of a stalled replication fork

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798320008074 ◽

2020 ◽

Vol 76 (8) ◽

pp. 729-735

Author(s):

Asami Hishiki ◽

Mamoru Sato ◽

Hiroshi Hashimoto

Keyword(s):

Dna Binding ◽

Ubiquitin Ligase ◽

Replication Fork ◽

Structural Information ◽

E3 Ubiquitin Ligase ◽

Dna Helicase ◽

Structural Basis ◽

The Past ◽

Functional Implications ◽

Fork Regression

HLTF (helicase-like transcription factor) is a yeast RAD5 homolog that is found in mammals. HLTF has E3 ubiquitin ligase and DNA helicase activities, and is a pivotal protein in template-switched DNA synthesis that allows DNA replication to continue even in the presence of DNA damage by utilizing a newly synthesized undamaged strand as a template. In addition, HLTF has a DNA-binding domain termed HIRAN (HIP116 and RAD5 N-terminal). HIRAN has been hypothesized to play a role in DNA binding; however, the structural basis of its role in DNA binding has remained unclear. In the past five years, several crystal structures of HIRAN have been reported. These structures revealed new insights into the molecular mechanism underlying DNA binding by HIRAN. Here, the structural information on HIRAN is summarized and the function of HIRAN in recognizing the 3′-terminus of the daughter strand at a stalled replication fork and the implications for its involvement in fork regression are discussed.

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