9FPA

DUBS Parachlamydia sp. PcJOS orthorhombic crystal form

Summary for 9FPA

• Entry DOI: 10.2210/pdb9fpa/pdb
• Related: 9FN4
• Descriptor: Ubiquitin, Peptidase C39-like domain-containing protein, CITRIC ACID, ... (4 entities in total)
• Functional Keywords: debiquitinylating enzyme, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 73860.03

Authors

Baumann, U.,Hermanns, T.,Uthoff, M. (deposition date: 2024-06-13, release date: 2025-04-23)

Primary citation

Hermanns, T.,Kolek, S.,Uthoff, M.,de Heiden, R.A.,Mulder, M.P.C.,Baumann, U.,Hofmann, K.
A family of bacterial Josephin-like deubiquitinases with an irreversible cleavage mode.
Mol.Cell, 85:1202-1215.e5, 2025

PubMed Abstract: Many intracellular bacteria secrete deubiquitinase (DUB) effectors into eukaryotic host cells to keep the bacterial surface or the enclosing vesicle membrane free of ubiquitin marks. This study describes a family of DUBs from several bacterial genera, including Simkania, Parachlamydia, Burkholderia, and Pigmentiphaga, which is structurally related to eukaryotic Josephin-type DUBs but contains members that catalyze a unique destructive substrate deubiquitination. These ubiquitin C-terminal clippases (UCCs) cleave ubiquitin before the C-terminal diGly motif, thereby truncating the modifier and leaving a remnant on the substrate. By comparing the crystal structures of substrate-bound clippases and a closely related conventional DUB, we identified the factors causing this shift and found them to be conserved in other clippases, including one highly specific for M1-linked ubiquitin chains. This enzyme class has great potential to serve as tools for studying the ubiquitin system, particularly aspects involving branched chains.

PubMed: 40037356
DOI: 10.1016/j.molcel.2025.02.002

Experimental method

X-RAY DIFFRACTION (2.18 Å)