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Insights into the catalytic mechanism of archaeal peptidoglycan endoisopeptidases from methanogenic phages.
Int J Biol Macromol
January 2025
Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address:
Archaeal peptidoglycan, a crucial component of the cell walls of Methanobacteria and Methanopyri, enhances the tightness of methanogenic cells and their resistance to known lytic enzymes and antibiotics. Although archaeal peptidoglycan endoisopeptidases (Pei) can reportedly degrade archaeal peptidoglycan, their biochemistry is still largely unknown. In this study, we investigated the activity and catalytic properties of the endoisopeptidases PeiW and PeiP using synthesized isopeptides identical to natural substrates.
View Article and Find Full Text PDFActivation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations.
J Chem Inf Model
January 2025
Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
Cezanne-2 (Cez2) is a deubiquitinylating (DUB) enzyme involved in the regulation of ubiquitin-driven cellular signaling and selectively targets Lys11-linked polyubiquitin chains. As a representative member of the ovarian tumor (OTU) subfamily DUBs, it performs cysteine proteolytic isopeptide bond cleavage; however, its exact catalytic mechanism is not yet resolved. In this work, we used different computational approaches to get molecular insights into the Cezanne-2 catalytic mechanism.
View Article and Find Full Text PDFE2-Ub-R74G strategy reveals E2-specific ubiquitin conjugation profiles in live cells.
Nat Chem Biol
January 2025
State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China.
The E2 ubiquitin (Ub)-conjugating enzyme primarily determines Ub conjugation as Ub-isopeptide (lysine), Ub-oxyester (serine/threonine) or Ub-thioester (cysteine). However, E2-specific Ub conjugation profiles within cells remain elusive. Here we developed the fusion E2-Ub-R74G profiling (FUSEP) strategy to access E2-specific Ub conjugation profiles in cells with amino acid resolution.
View Article and Find Full Text PDFProteomic Analysis of Single Hairs.
Methods Mol Biol
December 2024
University of California - Davis, Department of Environmental Toxicology, Davis, CA, USA.
Hair is a ubiquitous and robust mammalian tissue with biological, clinical, forensic, social, and economic significance. The hair shaft proteome reflects both structural proteins, dominated by cuticular intermediate filament keratins and associated proteins, and proteins involved in the final cellular processes of terminally differentiating corneocytes prior to cornification. These distinct biological processes involve cell maintenance, biosynthesis, senescence, and xenobiotic response.
View Article and Find Full Text PDFHighly Efficient Transpeptidase-Catalyzed Isopeptide Ligation.
J Am Chem Soc
January 2025
Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia.
Transpeptidases are specialized enzymes that have evolved for site-selective modification of peptides and proteins at their backbone termini. Approaches for adapting transpeptidases to catalyze side chain modifications are substantially more restricted, and typically rely on large recognition tags or require specific reaction conditions that are not easily compatible with broader applications. Here we show that the engineered asparaginyl ligase AEP1 catalyzes direct isopeptide ligation by accepting an internal 2,3-diaminopropionic acid (Dap) residue adjacent to Leu, a motif that mimics the canonical N-terminal Gly-Leu substrate.
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