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TitleStructural diversity and oligomerization of bacterial ubiquitin-like proteins.
Journal, issue, pagesStructure, Year 2025
Publish dateApr 8, 2025
AuthorsMinheng Gong / Qiaozhen Ye / Yajie Gu / Lydia R Chambers / Andrey A Bobkov / Neal K Arakawa / Mariusz Matyszewski / Kevin D Corbett /
PubMed AbstractBacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have ...Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three β-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three β-grasp domains and form homodimers and helical filaments mediated by conserved Ca ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins and suggest that Ca-mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.
External linksStructure / PubMed:40250427
MethodsEM (helical sym.) / EM (single particle)
Resolution2.43 - 3.08 Å
Structure data

46576

9d59

EMDB-46576, PDB-9d59:
Structure of Citrobacter multi-ubiquitin protein filament
Method: EM (helical sym.) / Resolution: 2.43 Å

46577

9d5a

EMDB-46577, PDB-9d5a:
Structure of Citrobacter multi-ubiquitin protein, local refinement of one full-length protomer
Method: EM (single particle) / Resolution: 2.73 Å

46578

9d5b

EMDB-46578, PDB-9d5b:
Structure of Methylobacterium brachiatum multi-ubiquitin protein filament
Method: EM (helical sym.) / Resolution: 3.08 Å

Chemicals

ChemComp-CA:
Unknown entry

Source
  • citrobacter sp. rhbstw-00271 (bacteria)
  • methylobacterium brachiatum (bacteria)
KeywordsPROTEIN BINDING / filament / beta-grasp / ubiquitin

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