9D5B

Structure of Methylobacterium brachiatum multi-ubiquitin protein filament

Summary for 9D5B

• Entry DOI: 10.2210/pdb9d5b/pdb
• EMDB information: 46578
• Descriptor: Multi-ubiquitin domain-containing protein, CALCIUM ION (2 entities in total)
• Functional Keywords: ubiquitin, filament, beta-grasp, protein binding
• Biological source: Methylobacterium brachiatum
• Total number of polymer chains: 4
• Total formula weight: 117247.30

Authors

Gong, M.,Gu, Y.,Corbett, K.D. (deposition date: 2024-08-13, release date: 2025-04-02, Last modification date: 2025-06-18)

Primary citation

Gong, M.,Ye, Q.,Gu, Y.,Chambers, L.R.,Bobkov, A.A.,Arakawa, N.K.,Matyszewski, M.,Corbett, K.D.
Structural diversity and oligomerization of bacterial ubiquitin-like proteins.
Structure, 33:1016-1026.e4, 2025

PubMed Abstract: 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.

PubMed: 40250427
DOI: 10.1016/j.str.2025.03.011

Experimental method

ELECTRON MICROSCOPY (3.08 Å)