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Structure paper

TitleDoa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 410, Year 2024
Publish dateJan 9, 2024
AuthorsJ Josephine Botsch / Roswitha Junker / Michèle Sorgenfrei / Patricia P Ogger / Luca Stier / Susanne von Gronau / Peter J Murray / Markus A Seeger / Brenda A Schulman / Bastian Bräuning /
PubMed AbstractTransmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in ...Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity.
External linksNat Commun / PubMed:38195637 / PubMed Central
MethodsEM (single particle)
Resolution3.58 - 6.73 Å
Structure data

17597

8pd0

EMDB-17597, PDB-8pd0:
cryo-EM structure of Doa10 in MSP1E3D1
Method: EM (single particle) / Resolution: 3.58 Å

17608

8pda

EMDB-17608, PDB-8pda:
cryo-EM structure of Doa10 with RING domain in MSP1E3D1
Method: EM (single particle) / Resolution: 3.58 Å

EMDB-17609: Low resolution map of Doa10 in MSP1E3D1
Method: EM (single particle) / Resolution: 6.73 Å

EMDB-17610: Doa10 in MSP2N2
Method: EM (single particle) / Resolution: 5.77 Å

Chemicals

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

ChemComp-PX6:
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsLIGASE / ERAD / Doa10 / March6 / TEB4 / retrotranslocation / ubiquitination / Ubc6 / sybody / SQLE / squalenemonooxygenase

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