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TitleThe deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation.
Journal, issue, pagesSci Rep, Vol. 16, Issue 1, Year 2026
Publish dateMar 7, 2026
AuthorsHao Li / Haipeng Guan / Tom A Rapoport /
PubMed AbstractMany eukaryotic proteins are modified with a polyubiquitin chain and then recruited to either the Cdc48 ATPase (p97 or VCP in mammals) or the 26S proteasome by conserved cofactors. They can then ...Many eukaryotic proteins are modified with a polyubiquitin chain and then recruited to either the Cdc48 ATPase (p97 or VCP in mammals) or the 26S proteasome by conserved cofactors. They can then shuttle between the Cdc48 ATPase and the 26S proteasome before being degraded. How substrates avoid being trapped on the Cdc48 ATPase complex is incompletely understood, as they can undergo repeated cycles of translocation through the ATPase pore. Here, we show that the deubiquitinating enzyme (DUB) Otu1 (Yod1 in mammals) can break this futile cycle. Otu1 trims the ubiquitin chain of the substrate before its translocation through the Cdc48 pore is initiated, allowing transfer to the proteasome and subsequent degradation. A cryo-EM structure shows that the mammalian homolog Yod1 binds to p97 simultaneously with other Cdc48/p97 cofactors. As in the yeast system, polypeptide translocation through the ATPase pore is initiated by the unfolding of a ubiquitin molecule, suggesting that the mechanism of substrate processing is conserved in all eukaryotes.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42811-6.
External linksSci Rep / PubMed:41795027 / PubMed Central
MethodsEM (single particle)
Resolution2.97 - 3.05 Å
Structure data

73365

9yrc

EMDB-73365, PDB-9yrc:
p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-73375: Global refinement map of p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-73376: Local refinement map of p97Ufd1-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP, focused on p97 D1 ring and Npl4
Method: EM (single particle) / Resolution: 3.05 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsTRANSLOCASE / p97 / VCP / AAA+ ATPase

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