8HM1

crystal structure of human ubiquitin-like protein from Bacteroides fragilis

Summary for 8HM1

• Entry DOI: 10.2210/pdb8hm1/pdb
• Descriptor: Putative ubiquitin, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: ubiquitin-like protein, cell cycle
• Biological source: Bacteroides fragilis
• Total number of polymer chains: 2
• Total formula weight: 18314.87

Authors

Tong, M.,Chen, Z.,Gao, X. (deposition date: 2022-12-02, release date: 2023-11-29, Last modification date: 2024-10-30)

Primary citation

Jiang, K.,Li, W.,Tong, M.,Xu, J.,Chen, Z.,Yang, Y.,Zang, Y.,Jiao, X.,Liu, C.,Lim, B.,Jiang, X.,Wang, J.,Wu, D.,Wang, M.,Liu, S.J.,Shao, F.,Gao, X.
Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome.
Nat Microbiol, 9:70-84, 2024

PubMed Abstract: Interbacterial antagonism and associated defensive strategies are both essential during bacterial competition. The human gut symbiont Bacteroides fragilis secretes a ubiquitin homologue (BfUbb) that is toxic to a subset of B. fragilis strains in vitro. In the present study, we demonstrate that BfUbb lyses certain B. fragilis strains by non-covalently binding and inactivating an essential peptidyl-prolyl isomerase (PPIase). BfUbb-sensitivity profiling of B. fragilis strains revealed a key tyrosine residue (Tyr119) in the PPIase and strains that encode a glutamic acid residue at Tyr119 are resistant to BfUbb. Crystal structural analysis and functional studies of BfUbb and the BfUbb-PPIase complex uncover a unique disulfide bond at the carboxy terminus of BfUbb to mediate the interaction with Tyr119 of the PPIase. In vitro coculture assays and mouse studies show that BfUbb confers a competitive advantage for encoding strains and this is further supported by human gut metagenome analyses. Our findings reveal a previously undescribed mechanism of bacterial intraspecies competition.

PubMed: 38082149
DOI: 10.1038/s41564-023-01541-5

Experimental method

X-RAY DIFFRACTION (1.29 Å)