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TitleMechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases.
Journal, issue, pagesNat Struct Mol Biol, Vol. 31, Issue 2, Page 378-389, Year 2024
Publish dateFeb 7, 2024
AuthorsJoanna Liwocha / Jerry Li / Nicholas Purser / Chutima Rattanasopa / Samuel Maiwald / David T Krist / Daniel C Scott / Barbara Steigenberger / J Rajan Prabu / Brenda A Schulman / Gary Kleiger /
PubMed AbstractE3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked ...E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s.
External linksNat Struct Mol Biol / PubMed:38326650 / PubMed Central
MethodsEM (single particle)
Resolution3.55 - 8.12 Å
Structure data

EMDB-17798: CUL2-RBX1-ELOB/C-FEM1C-SIL1 conformation 1
Method: EM (single particle) / Resolution: 7.72 Å

EMDB-17799: CUL2-RBX1-ELOB/C-FEM1C-SIL1 conformation 2
Method: EM (single particle) / Resolution: 7.54 Å

EMDB-17800: NEDD8-CUL2-RBX1-ELOB/C-FEM1C-SIL1 conformation 1
Method: EM (single particle) / Resolution: 7.19 Å

EMDB-17801: NEDD8-CUL2-RBX1-ELOB/C-FEM1C-SIL1 conformation 2
Method: EM (single particle) / Resolution: 6.88 Å

EMDB-17802: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL1-RBX1-SKP1-FBXW7 with trapped UBE2R2-donor UB-acceptor UB-cyclin E peptide
Method: EM (single particle) / Resolution: 8.12 Å

EMDB-17803: Consensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide
Method: EM (single particle) / Resolution: 3.76 Å

17822

8pql

EMDB-17822, PDB-8pql:
K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide
Method: EM (single particle) / Resolution: 3.76 Å

EMDB-18767: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB~acceptor UB-BRD4
Method: EM (single particle) / Resolution: 7.5 Å

EMDB-19856: Focused map 1- K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
Method: EM (single particle) / Resolution: 3.55 Å

EMDB-19857: Focused map 2 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
Method: EM (single particle) / Resolution: 3.76 Å

EMDB-19858: Focused map 3 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
Method: EM (single particle) / Resolution: 3.89 Å

EMDB-19859: Focused map 4 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
Method: EM (single particle) / Resolution: 3.89 Å

EMDB-19860: Focused map 5 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
Method: EM (single particle) / Resolution: 3.94 Å

Chemicals

ChemComp-SY8:
5-azanylpentan-2-one

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
  • 9606 (fungus)
KeywordsLIGASE / CUL2 / FEM1C / ELOBC / SIL1 / Ubiquitin / Ubiquitin Ligase / Ubiquitin chain formation / Poliubiquitylation

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