Structural basis of ubiquitin ligase Nedd4-2 autoinhibition and regulation by calcium and 14-3-3 proteins

. 2025 May 26 ; 16 (1) : 4875. [epub] 20250526

Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid40419858

Grantová podpora
23-04686S Grantová Agentura České Republiky (Grant Agency of the Czech Republic)
67985823 Akademie Věd České Republiky (Academy of Sciences of the Czech Republic)
LM2023042 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
LM2023050 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
90254 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
52310440 International Visegrad Fund (IVF)

Odkazy

PubMed 40419858
PubMed Central PMC12106849
DOI 10.1038/s41467-025-60207-4
PII: 10.1038/s41467-025-60207-4
Knihovny.cz E-zdroje

Nedd4-2 E3 ligase regulates Na+ homeostasis by ubiquitinating various channels and membrane transporters, including the epithelial sodium channel ENaC. In turn, Nedd4-2 dysregulation leads to various conditions, including electrolytic imbalance, respiratory distress, hypertension, and kidney diseases. However, Nedd4-2 regulation remains mostly unclear. The present study aims at elucidating Nedd4-2 regulation by structurally characterizing Nedd4-2 and its complexes using several biophysical techniques. Our cryo-EM reconstruction shows that the C2 domain blocks the E2-binding surface of the HECT domain. This blockage, ubiquitin-binding exosite masking by the WW1 domain, catalytic C922 blockage and HECT domain stabilization provide the structural basis for Nedd4-2 autoinhibition. Furthermore, Ca2+-dependent C2 membrane binding disrupts C2/HECT interactions, but not Ca2+ alone, whereas 14-3-3 protein binds to a flexible region of Nedd4-2 containing the WW2 and WW3 domains, thereby inhibiting its catalytic activity and membrane binding. Overall, our data provide key mechanistic insights into Nedd4-2 regulation toward fostering the development of strategies targeting Nedd4-2 function.

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Popovic, D., Vucic, D. & Dikic, I. Ubiquitination in disease pathogenesis and treatment. PubMed DOI

Foot, N., Henshall, T. & Kumar, S. Ubiquitination and the regulation of membrane proteins. PubMed DOI

Rotin, D. & Kumar, S. Physiological functions of the HECT family of ubiquitin ligases. PubMed DOI

Li, W. et al. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle’s dynamics and signaling. PubMed DOI PMC

Zheng, N. & Shabek, N. Ubiquitin ligases: structure, function, and regulation. PubMed DOI

Harvey, K. F. & Kumar, S. Nedd4-like proteins: an emerging family of ubiquitin-protein ligases implicated in diverse cellular functions. PubMed DOI

Staub, O. et al. WW domains of Nedd4 bind to the proline-rich PY motifs in the epithelial Na PubMed DOI PMC

Goel, P., Manning, J. A. & Kumar, S. NEDD4-2 (NEDD4L): the ubiquitin ligase for multiple membrane proteins. PubMed DOI PMC

Bernassola, F., Chillemi, G. & Melino, G. HECT-Type E3 Ubiquitin ligases in cancer. PubMed DOI

Rizzo, F. & Staub, O. NEDD4-2 and salt-sensitive hypertension. PubMed DOI

Vanli-Yavuz, E. N. et al. Investigation of the possible association of NEDD4-2 (NEDD4L) gene with idiopathic photosensitive epilepsy. PubMed DOI

Mund, T., Lewis, M. J., Maslen, S. & Pelham, H. R. Peptide and small molecule inhibitors of HECT-type ubiquitin ligases. PubMed DOI PMC

Sudol, M. Structure and function of the WW domain. PubMed DOI

Plant, P. J., Yeger, H., Staub, O., Howard, P. & Rotin, D. The C2 domain of the ubiquitin protein ligase Nedd4 mediates Ca PubMed DOI

Kim, H. C. & Huibregtse, J. M. Polyubiquitination by HECT E3s and the determinants of chain type specificity. PubMed DOI PMC

Wang, J. et al. Calcium activates Nedd4 E3 ubiquitin ligases by releasing the C2 domain-mediated auto-inhibition. PubMed DOI PMC

Escobedo, A. et al. Structural basis of the activation and degradation mechanisms of the E3 ubiquitin ligase Nedd4L. PubMed DOI

Wiesner, S. et al. Autoinhibition of the HECT-type ubiquitin ligase Smurf2 through its C2 domain. PubMed DOI

Mari, S. et al. Structural and functional framework for the autoinhibition of Nedd4-family ubiquitin ligases. PubMed DOI

Chen, Z. et al. A tunable brake for HECT ubiquitin ligases. PubMed DOI PMC

Zhu, K. et al. Allosteric auto-inhibition and activation of the Nedd4 family E3 ligase Itch. PubMed DOI PMC

Wang, Z. et al. A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases. PubMed DOI PMC

Maspero, E. et al. Structure of the HECT:ubiquitin complex and its role in ubiquitin chain elongation. PubMed DOI PMC

Maspero, E. et al. Structure of a ubiquitin-loaded HECT ligase reveals the molecular basis for catalytic priming. PubMed DOI

Bhalla, V. et al. Serum- and glucocorticoid-regulated kinase 1 regulates ubiquitin ligase neural precursor cell-expressed, developmentally down-regulated protein 4-2 by inducing interaction with 14-3-3. PubMed DOI

Ichimura, T. et al. 14-3-3 proteins modulate the expression of epithelial Na PubMed DOI

Chandran, S. et al. Neural precursor cell-expressed developmentally down-regulated protein 4-2 (Nedd4-2) regulation by 14-3-3 protein binding at canonical serum and glucocorticoid kinase 1 (SGK1) phosphorylation sites. PubMed DOI PMC

Pohl, P., Joshi, R., Petrvalska, O., Obsil, T. & Obsilova, V. 14-3-3-protein regulates Nedd4-2 by modulating interactions between HECT and WW domains. PubMed DOI PMC

Joshi, R. et al. Nedd4-2 binding to 14-3-3 modulates the accessibility of its catalytic site and WW domains. PubMed DOI PMC

Ishikawa, K. et al. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. PubMed DOI

Fotia, A. B. et al. The role of individual Nedd4-2 (KIAA0439) WW domains in binding and regulating epithelial sodium channels. PubMed DOI

Kamadurai, H. B. et al. Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. PubMed DOI PMC

French, M. E., Kretzmann, B. R. & Hicke, L. Regulation of the RSP5 ubiquitin ligase by an intrinsic ubiquitin-binding site. PubMed DOI PMC

Zhang, W. et al. System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes. PubMed DOI PMC

Nalefski, E. A. & Falke, J. J. The C2 domain calcium-binding motif: structural and functional diversity. PubMed DOI PMC

Petoukhov, M. V. et al. New developments in the ATSAS program package for small-angle scattering data analysis. PubMed DOI PMC

Kyte, J. & Doolittle, R. F. A simple method for displaying the hydropathic character of a protein. PubMed DOI

Obsilova, V. & Obsil, T. Structural insights into the functional roles of 14-3-3 proteins. PubMed DOI PMC

Huang, L. et al. Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade. PubMed DOI

Verdecia, M. A. et al. Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase. PubMed DOI

Eletr, Z. M. & Kuhlman, B. Sequence determinants of E2-E6AP binding affinity and specificity. PubMed DOI PMC

Ogunjimi, A. A. et al. Regulation of Smurf2 ubiquitin ligase activity by anchoring the E2 to the HECT domain. PubMed DOI

Persaud, A. et al. Tyrosine phosphorylation of NEDD4 activates its ubiquitin ligase activity. PubMed DOI

Todaro, D. R., Augustus-Wallace, A. C., Klein, J. M. & Haas, A. L. The mechanism of neural precursor cell expressed developmentally down-regulated 4-2 (Nedd4-2)/NEDD4L-catalyzed polyubiquitin chain assembly. PubMed DOI PMC

Todaro, D. R., Augustus-Wallace, A. C., Klein, J. M. & Haas, A. L. Oligomerization of the HECT ubiquitin ligase NEDD4-2/NEDD4L is essential for polyubiquitin chain assembly. PubMed DOI PMC

Obsil, T., Ghirlando, R., Klein, D. C., Ganguly, S. & Dyda, F. Crystal structure of the 14-3-3zeta:serotonin N-acetyltransferase complex. a role for scaffolding in enzyme regulation. PubMed DOI

Obsilova, V. et al. 14-3-3zeta C-terminal stretch changes its conformation upon ligand binding and phosphorylation at Thr232. PubMed DOI

Meyer, S., Savaresi, S., Forster, I. C. & Dutzler, R. Nucleotide recognition by the cytoplasmic domain of the human chloride transporter ClC-5. PubMed DOI

Wellhauser, L. et al. Nucleotides bind to the C-terminus of ClC-5. PubMed DOI PMC

Das, S., Dixon, J. E. & Cho, W. Membrane-binding and activation mechanism of PTEN. PubMed DOI PMC

Ansell, G. B.

Julkowska, M. M., Rankenberg, J. M. & Testerink, C. Liposome-binding assays to assess specificity and affinity of phospholipid-protein interactions. PubMed DOI

Niesen, F. H., Berglund, H. & Vedadi, M. The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. PubMed DOI

Laue, T. M., Shah, B. D., Ridgeway, T. M. & Pelletier, S. L. in

Brautigam, C. A. Calculations and publication-quality illustrations for analytical ultracentrifugation data. PubMed DOI

Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. PubMed DOI PMC

Dam, J., Velikovsky, C. A., Mariuzza, R. A., Urbanke, C. & Schuck, P. Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s). PubMed DOI PMC

Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. PubMed DOI

Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. PubMed DOI PMC

Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. PubMed DOI PMC

Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. PubMed DOI

Jamali, K. et al. Automated model building and protein identification in cryo-EM maps. PubMed PMC

Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. PubMed DOI PMC

Trcka, F. et al. Human stress-inducible Hsp70 has a high propensity to form ATP-dependent antiparallel dimers that are differentially regulated by cochaperone binding. PubMed DOI PMC

Kavan, D. & Man, P. MSTools-web based application for visualization and presentation of HXMS data. DOI

Masson, G. R. et al. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. PubMed DOI PMC

Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. PubMed DOI PMC

Panjkovich, A. & Svergun, D. I. CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data. PubMed DOI PMC

Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J. & Svergun, D. I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. DOI

Svergun, D. I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. DOI

Yang, X. et al. Structural basis for protein-protein interactions in the 14-3-3 protein family. PubMed DOI PMC

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. PubMed DOI PMC

Grant, T. D. Ab initio electron density determination directly from solution scattering data. PubMed DOI

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