6WTG

SdeA DUB Domain in complex with Ubiquitin

Summary for 6WTG

• Entry DOI: 10.2210/pdb6wtg/pdb
• Descriptor: Ubiquitinating/deubiquitinating enzyme SdeA, Ubiquitin (3 entities in total)
• Functional Keywords: bacterial effector, complex, hydrolase
• Biological source: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513); More
• Total number of polymer chains: 2
• Total formula weight: 29521.38

Authors

Kenny, S.,Sheedlo, M.,Das, C. (deposition date: 2020-05-02, release date: 2021-03-03, Last modification date: 2023-10-18)

Primary citation

Sheedlo, M.J.,Kenny, S.,Podkorytov, I.S.,Brown, K.,Ma, J.,Iyer, S.,Hewitt, C.S.,Arbough, T.,Mikhailovskii, O.,Flaherty, D.P.,Wilson, M.A.,Skrynnikov, N.R.,Das, C.
Insights into Ubiquitin Product Release in Hydrolysis Catalyzed by the Bacterial Deubiquitinase SdeA.
Biochemistry, 60:584-596, 2021

PubMed Abstract: We report the co-crystal structure of the (catalytic Cys)-to-Ala mutant of the deubiquitinase domain of the effector SdeA (SdeA) with its ubiquitin (Ub) product. Most of the intermolecular interactions are preserved in this product-bound structure compared to that of the previously characterized complex of SdeA with the suicide inhibitor ubiquitin vinylmethyl ester (Ub-VME), whose structure models the acyl-enzyme thioester intermediate. Nuclear magnetic resonance (NMR) titration studies show a chemical shift perturbation pattern that suggests that the same interactions also exist in solution. Isothermal titration calorimetry and NMR titration data reveal that the affinity of wild-type (WT) SdeA for Ub is significantly lower than that of the Cys-to-Ala mutant. This is potentially due to repulsive interaction between the thiolate ion of the catalytic Cys residue in WT SdeA and the carboxylate group of the C-terminal Gly76 residue in Ub. In the context of SdeA catalysis, this electrostatic repulsion arises after the hydrolysis of the scissile isopeptide bond in the acyl-enzyme intermediate and the consequent formation of the C-terminal carboxylic group in the Ub fragment. We hypothesize that this electrostatic repulsion may expedite the release of the Ub product by SdeA. We note that similar repulsive interactions may also occur in other deubiquitinases and hydrolases of ubiquitin-like protein modifiers and may constitute a fairly general mechanism of product release within this family. This is a potentially important feature for a family of enzymes that form extensive protein-protein interactions during enzyme-substrate engagement.

PubMed: 33583181
DOI: 10.1021/acs.biochem.0c00760

Experimental method

X-RAY DIFFRACTION (2.63 Å)