9EA5

Structure of Citrobacter BubCD D104A mutant

Summary for 9EA5

• Entry DOI: 10.2210/pdb9ea5/pdb
• Related: 9EA4
• Descriptor: Citrobacter BubCD, SODIUM ION, ACETIC ACID, ... (4 entities in total)
• Functional Keywords: ubiquitin, e1, dub, ligase
• Biological source: Citrobacter sp. RHBSTW-00271
• Total number of polymer chains: 2
• Total formula weight: 102059.48

Authors

Ye, Q.,Corbett, K.D. (deposition date: 2024-11-10, release date: 2025-09-24, Last modification date: 2025-11-26)

Primary citation

Ye, Q.,Gong, M.,Cai, J.,Chambers, L.R.,Zhou, H.,Suhandynata, R.T.,Corbett, K.D.
Mechanistic basis for protein conjugation in a diverged bacterial ubiquitination pathway.
Nat.Struct.Mol.Biol., 2025

PubMed Abstract: Ubiquitination is a fundamental eukaryotic protein post-translational modification pathway, in which ubiquitin or a ubiquitin-like protein (Ubl) is typically conjugated to a lysine of a target protein. Ubiquitination is initiated by adenylation of the Ubl C terminus, followed by sequential formation of Ubl-cysteine thioester intermediates with E1, E2 and (optionally) E3 proteins before formation of the final Ubl-lysine isopeptide linkage. Recent work has revealed two ubiquitination-related bacterial pathways in the context of antiphage immunity. Bioinformatics analyses have hinted at the existence of additional uncharacterized bacterial pathways that include ubiquitination-like machinery. Here, we describe the architecture and biochemical mechanisms of an alternative Bub (bacterial ubiquitination-like) pathway, revealing structural parallels and mechanistic differences when compared to other ubiquitination pathways. We show that Bub operons encode functional E1, E2 and Ubl proteins that are related to their eukaryotic counterparts but likely function through oxyester rather than thioester intermediates. We also identify an enzyme family in Bub operons with a conserved catalytic site and a role in Ubl-target conjugation. The genomic context of Bub operons suggests that they also function in antiphage immunity and we present evidence that one Bub pathway may regulate translation in response to stress. Overall, our results reveal an uncharacterized family of bacterial ubiquitination-related pathways with a distinctive biochemical mechanism.

PubMed: 41184514
DOI: 10.1038/s41594-025-01696-1

Experimental method

X-RAY DIFFRACTION (2 Å)