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TitleStructural basis for L-isoaspartyl-containing protein recognition by the PCMTD1 cullin-RING E3 ubiquitin ligase.
Journal, issue, pagesbioRxiv, Year 2025
Publish dateMay 21, 2025
AuthorsEric Z Pang / Boyu Zhao / Cameron Flowers / Elizabeth Oroudjeva / Jasmine B Winter / Vijaya Pandey / Michael R Sawaya / James Wohlschlegel / Joseph A Loo / Jose A Rodriguez / Steven G Clarke /
PubMed AbstractA major type of spontaneous protein damage that accumulates with age is the formation of kinked polypeptide chains with L-isoaspartyl residues. Mitigating this damage is necessary for maintaining ...A major type of spontaneous protein damage that accumulates with age is the formation of kinked polypeptide chains with L-isoaspartyl residues. Mitigating this damage is necessary for maintaining proteome stability and prolonging organismal survival. While repair through methylation by PCMT1 has been previously shown to suppress L-isoaspartyl accumulation, we provide an additional mechanism for L-isoaspartyl maintenance through PCMTD1, a cullin-RING ligase (CRL). We combined cryo-EM, native mass spectrometry, and biochemical assays to provide insight on how the assembly and architecture of PCMTD1 in the context of a CRL complex fulfils this alternative mechanism. We show that the PCMTD1 CRL complex specifically binds L-isoaspartyl residues when bound to AdoMet. This work provides evidence for a growing class of E3 ubiquitin ligases that recognize spontaneous covalent modifications as potential substrates for ubiquitylation and subsequent proteasomal degradation.
External linksbioRxiv / PubMed:40475564 / PubMed Central
MethodsEM (single particle)
Resolution3.28 - 9.72 Å
Structure data

70610

9oma

EMDB-70610, PDB-9oma:
Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
Method: EM (single particle) / Resolution: 4.14 Å

70612

9omf

EMDB-70612, PDB-9omf:
Cryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-PCMTD1)
Method: EM (single particle) / Resolution: 9.72 Å

EMDB-70630: Consensus map: Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
Method: EM (single particle) / Resolution: 4.14 Å

EMDB-70631: Focused map of CUL5-RBX2: Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-70632: Focused map of PCMTD1-ELOBC: Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
Method: EM (single particle) / Resolution: 4.18 Å

EMDB-70633: Focused map of PCMTD1: Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
Method: EM (single particle) / Resolution: 3.28 Å

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
KeywordsPROTEIN BINDING / CUL5-RING ubiquitin ligase complex

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