9B5C image
Entry Detail
PDB ID:
9B5C
EMDB ID:
Keywords:
Title:
Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - consensus map and model
Biological Source:
PDB Version:
Deposition Date:
2024-03-22
Release Date:
2024-06-05
Method Details:
Experimental Method:
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Ubiquitin-activating enzyme E1 1
Chain IDs:A
Chain Length:1001
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe 972h-
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL40B
Chain IDs:B
Chain Length:76
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe 972h-
Polymer Type:polypeptide(L)
Description:Ubiquitin-conjugating enzyme E2 4
Mutations:C21S,C107S
Chain IDs:C
Chain Length:153
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe 972h-
Polymer Type:polypeptide(L)
Description:Ubiquitin
Chain IDs:D
Chain Length:79
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe 972h-
Primary Citation
Structural basis for transthiolation intermediates in the ubiquitin pathway.
Nature 633 216 223 (2024)
PMID: 39143218 DOI: 10.1038/s41586-024-07828-9

Abstact

Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins1-3. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters4-6. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3HECT complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next.

Legend

Protein

Chemical

Disease

Primary Citation of related structures