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1.
Mol Med ; 29(1): 34, 2023 03 14.
Article in English | MEDLINE | ID: mdl-36918822

ABSTRACT

The homologous to the E6-AP carboxyl terminus (HECT)-type E3 ubiquitin ligases are the selective executers in the protein ubiquitination, playing a vital role in modulation of the protein function and stability. Evidence shows the regulatory role of HECT-type E3 ligases in various steps of the autophagic process. Autophagy is an intracellular digestive and recycling process that controls the cellular hemostasis. Defective autophagy is involved in tumorigenesis and has been detected in various types of cancer cells. A growing body of findings indicates that HECT-type E3 ligases, in particular members of the neural precursor cell expressed developmentally downregulated protein 4 (NEDD4) including NEDD4-1, NEDD4-L, SMURFs, WWPs, and ITCH, play critical roles in dysregulation or dysfunction of autophagy in cancer cells. The present review focuses on NEDD4 E3 ligases involved in defective autophagy in cancer cells and discusses their autophagic function in different cancer cells as well as substrates and the signaling pathways in which they participate, conferring a basis for the cancer treatment through the modulating of these E3 ligases.


Subject(s)
Neoplasms , Ubiquitin-Protein Ligases , Ubiquitin-Protein Ligases/genetics , Nedd4 Ubiquitin Protein Ligases/genetics , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/metabolism , Ubiquitination , Proteins/metabolism , Autophagy , Neoplasms/therapy
2.
Pathol Oncol Res ; 29: 1610931, 2023.
Article in English | MEDLINE | ID: mdl-36825281

ABSTRACT

Gastric cancer (GC) is one of the most pernicious gastrointestinal tumors with extraordinarily high incidence and mortality. Ubiquitination modification of cellular signaling proteins has been shown to play important roles in GC tumorigenesis, progression, and prognosis. The E3 ubiquitin ligase is the crucial enzyme in the ubiquitination reaction and determines the specificity of ubiquitination substrates, and thus, the cellular effects. The HECT E3 ligases are the second largest E3 ubiquitin ligase family characterized by containing a HECT domain that has E3 ubiquitin ligase activity. The HECT E3 ubiquitin ligases have been found to engage in GC progression. However, whether HECT E3 ligases function as tumor promoters or tumor suppressors in GC remains controversial. In this review, we will focus on recent discoveries about the role of the HECT E3 ubiquitin ligases, especially members of the NEDD4 and other HECT E3 ligase subfamilies, in GC.


Subject(s)
Stomach Neoplasms , Ubiquitin-Protein Ligases , Humans , Ubiquitin-Protein Ligases/genetics , Ubiquitination , Carcinogenesis , Ubiquitins , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/genetics , Nedd4 Ubiquitin Protein Ligases/metabolism
3.
PLoS One ; 16(10): e0258315, 2021.
Article in English | MEDLINE | ID: mdl-34637467

ABSTRACT

The Nedd4 family contains several structurally related but functionally distinct HECT-type ubiquitin ligases. The members of the Nedd4 family are known to recognize substrates through their multiple WW domains, which recognize PY motifs (PPxY, LPxY) or phospho-threonine or phospho-serine residues. To better understand protein interactor recognition mechanisms across the Nedd4 family, we report the development and implementation of a python-based tool, PxYFinder, to identify PY motifs in the primary sequences of previously identified interactors of Nedd4 and related ligases. Using PxYFinder, we find that, on average, half of Nedd4 family interactions are likely PY-motif mediated. Further, we find that PPxY motifs are more prevalent than LPxY motifs and are more likely to occur in proline-rich regions and that PPxY regions are more disordered on average relative to LPxY-containing regions. Informed by consensus sequences for PY motifs across the Nedd4 interactome, we rationally designed a focused peptide library and employed a computational screen, revealing sequence- and biomolecular interaction-dependent determinants of WW-domain/PY-motif interactions. Cumulatively, our efforts provide a new bioinformatic tool and expand our understanding of sequence and structural factors that contribute to PY-motif mediated interactor recognition across the Nedd4 family.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/metabolism , Protein Interaction Mapping , Amino Acid Sequence , Conserved Sequence , Gene Ontology , Molecular Docking Simulation , Molecular Sequence Annotation , Peptide Library , Protein Binding , Solvents/chemistry , Ubiquitination
4.
Mol Cell ; 81(21): 4413-4424.e5, 2021 11 04.
Article in English | MEDLINE | ID: mdl-34480849

ABSTRACT

Based on in vitro studies, it has been demonstrated that the DSIF complex, composed of SPT4 and SPT5, regulates the elongation stage of transcription catalyzed by RNA polymerase II (RNA Pol II). The precise cellular function of SPT5 is not clear, because conventional gene depletion strategies for SPT5 result in loss of cellular viability. Using an acute inducible protein depletion strategy to circumvent this issue, we report that SPT5 loss triggers the ubiquitination and proteasomal degradation of the core RNA Pol II subunit RPB1, a process that we show to be evolutionarily conserved from yeast to human cells. RPB1 degradation requires the E3 ligase Cullin 3, the unfoldase VCP/p97, and a novel form of CDK9 kinase complex. Our study demonstrates that SPT5 stabilizes RNA Pol II specifically at promoter-proximal regions, permitting RNA Pol II release from promoters into gene bodies and providing mechanistic insight into the cellular function of SPT5 in safeguarding accurate gene expression.


Subject(s)
Cullin Proteins/metabolism , Nuclear Proteins/metabolism , RNA Polymerase II/chemistry , RNA Polymerase II/metabolism , Transcriptional Elongation Factors/metabolism , Animals , Cell Survival , Chromosomal Proteins, Non-Histone/metabolism , Cullin Proteins/chemistry , Fibroblasts/metabolism , Humans , Indoleacetic Acids/chemistry , Mice , Nedd4 Ubiquitin Protein Ligases/chemistry , Promoter Regions, Genetic , Proteasome Endopeptidase Complex/chemistry , Proteome , Proteomics/methods , Ubiquitin-Protein Ligases/chemistry , Valosin Containing Protein/chemistry , Valosin Containing Protein/metabolism
5.
Protein Expr Purif ; 173: 105649, 2020 09.
Article in English | MEDLINE | ID: mdl-32334140

ABSTRACT

Nedd4 is an E3 ubiquitin ligase that has received increased attention due to its role in the maintenance of proteostasis and in cellular stress responses. Investigation of Nedd4 enzymology has revealed a complex enzymatic mechanism that involves intermolecular interactions with upstream E2 conjugating enzymes and with substrates and intramolecular interactions that serve to regulate Nedd4 function. Thus, it is imperative that investigations of Nedd4 enzymology that employ recombinant enzyme be conducted with Nedd4 in its native, untagged form. We report herein an optimized, facile method for purification of recombinant human Nedd4 in its full-length form as a stable and active recombinant enzyme. Specifically, Nedd4 can be purified through a two-step purification which employs glutathione-S-transferase and hexahistidine sequences as orthogonal affinity tags. Proteolytic cleavage of Nedd4 was optimized to enable removal of the affinity tags with TEV protease, providing access to the untagged enzyme in yields of 2-3 mg/L. Additionally, investigation of Nedd4 storage conditions reveal that the enzyme is not stable through freeze-thaw cycles, and storage conditions should be carefully considered for preservation of enzyme stability. Finally, Nedd4 activity was validated through three activity assays which measure ubiquitin chain formation, Nedd4 autoubiquitination, and monoubiquitin consumption, respectively. Comparison of the method described herein with previously reported purification methods reveal that our optimized purification strategy enables access to Nedd4 in fewer chromatographic steps and eliminates reagents and materials that are potentially cost-prohibitive. This method, therefore, is more efficient and provides a more accessible route for purifying recombinant full-length Nedd4.


Subject(s)
Escherichia coli , Nedd4 Ubiquitin Protein Ligases , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , Nedd4 Ubiquitin Protein Ligases/biosynthesis , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/genetics , Nedd4 Ubiquitin Protein Ligases/isolation & purification , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification
6.
Cell Physiol Biochem ; 54(1): 1-14, 2020 Jan 10.
Article in English | MEDLINE | ID: mdl-31916733

ABSTRACT

BACKGROUND/AIMS: Deubiquitinating enzymes (DUBs) are crucially involved in controlling signal transductions, and reverse ubiquitination by removing the ubiquitin from protein substrates. The Hippo signaling has an important role in tissue growth, cell proliferation, differentiation, and apoptosis. Since disruption of the Hippo signaling is associated with a number of diseases, it is imperative to investigate the molecular mechanism of the Hippo signaling. METHODS: DUB screening was performed using the kidney of the mouse unilateral ureteric obstruction (UUO) model to identify the cellular mechanism of the DUB-regulated Hippo signaling. In addition, kidney cells were used to confirm cell proliferation and protein levels in the Hippo signaling pathway. Densitometric analysis was conducted to compare the expression level of proteins using Image J. RESULTS: We found that YOD1, also known as OTU1, is downregulated in the mouse UUO model. We also demonstrated that YOD1 binds to and deubiquitinates neural precursor cell expressed developmentally down-regulated protein 4 (NEDD4). Furthermore, we observed that YOD1 suppresses NEDD4-induced cell proliferation. CONCLUSION: YOD1 regulates the Hippo signaling pathway through NEDD4, and the K63-linked polyubiquitin chain of NEDD4 plays an important role. Also, our results indicate that YOD1 plays an important role in kidney diseases.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/metabolism , Signal Transduction , Thiolester Hydrolases/metabolism , Animals , Cell Line , Cell Proliferation , Disease Models, Animal , Hippo Signaling Pathway , Humans , Mice , Mutagenesis , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/genetics , Protein Binding , Protein Serine-Threonine Kinases/metabolism , Renal Insufficiency, Chronic/metabolism , Renal Insufficiency, Chronic/pathology , Thiolester Hydrolases/chemistry , Ubiquitin/genetics , Ubiquitin/metabolism , Ubiquitination
7.
Cell Death Dis ; 10(12): 904, 2019 12 02.
Article in English | MEDLINE | ID: mdl-31787758

ABSTRACT

Tumorigenesis, tumor growth, and prognosis are highly related to gene alterations and post-translational modifications (PTMs). Ubiquitination is a critical PTM that governs practically all aspects of cellular function. An increasing number of studies show that E3 ubiquitin ligases (E3s) are important enzymes in the process of ubiquitination that primarily determine substrate specificity and thus need to be tightly controlled. Among E3s, neural precursor cell expressed developmentally downregulated 4-1 (NEDD4-1) has been shown to play a critical role in modulating the proliferation, migration, and invasion of cancer cells and the sensitivity of cancer cells to anticancer therapies via regulating multiple substrates. This review discusses some significant discoveries on NEDD4-1 substrates and the signaling pathways in which NEDD4-1 participates. In addition, we introduce the latest potential therapeutic strategies that inhibit or activate NEDD4-1 activity using small molecules. NEDD4-1 likely acts as a novel drug target or diagnostic marker in the battle against cancer.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/metabolism , Animals , Autophagy , Humans , Models, Biological , Nedd4 Ubiquitin Protein Ligases/chemistry , Oncogenes , Substrate Specificity , Ubiquitination
8.
J Biol Chem ; 294(52): 19934-19949, 2019 12 27.
Article in English | MEDLINE | ID: mdl-31732561

ABSTRACT

The HECT E3 ligase family comprises three subfamilies: NEDD4 E3 ubiquitin protein ligase (NEDD4), HECT and RLD domain-containing E3 ubiquitin protein ligase (HERC), and "other." Most previous studies have focused on the NEDD4 subfamily. Apoptosis-resistant E3 ligase 1 (AREL1) belongs to "other" subfamily HECT that inhibits apoptosis by ubiquitinating and degrading proapoptotic proteins. Here, we report the crystal structure of the extended HECT domain of AREL1 (amino acids (aa) 436-823) at 2.4 Å resolution and its ubiquitination of the proapoptotic protein second mitochondria-derived activator of caspase (SMAC). We found that the extended HECT domain adopts an inverted, T-shaped, bilobed conformation and harbors an additional loop (aa 567-573) absent in all other HECT members. We also show that the N-terminal extended region (aa 436-482) preceding the HECT domain is indispensable for its stability and activity and that without this region, the HECT domain becomes inactive. AREL1 ubiquitinated SMAC, primarily on Lys62 and Lys191 We solved the crystal structure of the tetrameric form of SMAC to 2.8 Å resolution, revealing the Lys62 and Lys191 locations. The AREL1 HECT domain assembled Lys33-, Lys48-, and Lys63-linked polyubiquitin chains. Moreover, E701A substitution in the AREL1 HECT domain substantially increased its autopolyubiquitination and SMAC ubiquitination activity, whereas deletion of the last three amino acids at the C terminus completely abrogated AREL1 autoubiquitination and reduced SMAC ubiquitination. Finally, an AREL1-specific ubiquitin variant inhibited SMAC ubiquitination in vitro Our findings may assist in the development of AREL1 inhibitors that block its anti-apoptotic activity in cancer.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/chemistry , Ubiquitin-Protein Ligases/chemistry , Apoptosis Regulatory Proteins/chemistry , Apoptosis Regulatory Proteins/metabolism , Crystallography, X-Ray , Humans , Mitochondrial Proteins/chemistry , Mitochondrial Proteins/metabolism , Molecular Dynamics Simulation , Mutagenesis, Site-Directed , Nedd4 Ubiquitin Protein Ligases/genetics , Nedd4 Ubiquitin Protein Ligases/metabolism , Protein Domains , Protein Structure, Quaternary , Protein Structure, Tertiary , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination
9.
Sci Rep ; 9(1): 15076, 2019 10 21.
Article in English | MEDLINE | ID: mdl-31636332

ABSTRACT

The recognition of PPxY viral Late domains by the third WW domain of the HECT-E3 ubiquitin ligase NEDD4 (hNEDD4-WW3) is essential for the completion of the budding process of numerous enveloped viruses, including Ebola, Marburg, HTLV1 or Rabies. hNEDD4-WW3 has been validated as a promising target for the development of novel host-oriented broad spectrum antivirals. Nonetheless, finding inhibitors with good properties as therapeutic agents remains a challenge since the key determinants of binding affinity and specificity are still poorly understood. We present here a detailed structural and thermodynamic study of the interactions of hNEDD4-WW3 with viral Late domains combining isothermal titration calorimetry, NMR structural determination and molecular dynamics simulations. Structural and energetic differences in Late domain recognition reveal a highly plastic hNEDD4-WW3 binding site that can accommodate PPxY-containing ligands with varying orientations. These orientations are mostly determined by specific conformations adopted by residues I859 and T866. Our results suggest a conformational selection mechanism, extensive to other WW domains, and highlight the functional relevance of hNEDD4-WW3 domain conformational flexibility at the binding interface, which emerges as a key element to consider in the search for potent and selective inhibitors of therapeutic interest.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/metabolism , Viral Proteins/chemistry , Amino Acid Motifs , Binding Sites , Databases, Protein , Humans , Ligands , Magnetic Resonance Spectroscopy , Molecular Dynamics Simulation , Peptides/chemistry , Peptides/metabolism , Protein Binding , Protein Domains , Thermodynamics
10.
J Biol Chem ; 294(46): 17421-17436, 2019 11 15.
Article in English | MEDLINE | ID: mdl-31578285

ABSTRACT

NEDD4-1 E3 ubiquitin protein ligase (NEDD4-1) and WW domain-containing E3 ubiquitin ligase (WWP2) are HECT family ubiquitin E3 ligases. They catalyze Lys ubiquitination of themselves and other proteins and are important in cell growth and differentiation. Regulation of NEDD4-1 and WWP2 catalytic activities is important for controlling cellular protein homeostasis, and their dysregulation may lead to cancer and other diseases. Previous work has implicated noncatalytic regions, including the C2 domain and/or WW domain linkers in NEDD4-1 and WWP2, in contributing to autoinhibition of the catalytic HECT domains by intramolecular interactions. Here, we explored the molecular mechanisms of these NEDD4-1 and WWP2 regulatory regions and their interplay with allosteric binding proteins such as Nedd4 family-interacting protein (NDFIP1), engineered ubiquitin variants, and linker phosphomimics. We found that in addition to influencing catalytic activities, the WW domain linker regions in NEDD4-1 and WWP2 can impact product distribution, including the degree of polyubiquitination and Lys-48 versus Lys-63 linkages. We show that allosteric activation by NDFIP1 or engineered ubiquitin variants is largely mediated by relief of WW domain linker autoinhibition. WWP2-mediated ubiquitination of WW domain-binding protein 2 (WBP2), phosphatase and tensin homolog (PTEN), and p62 proteins by WWP2 suggests that substrate ubiquitination can also be influenced by WW linker autoinhibition, although to differing extents. Overall, our results provide a deeper understanding of the intricate and multifaceted set of regulatory mechanisms in the control of NEDD4-1-related ubiquitin ligases.


Subject(s)
Carrier Proteins/genetics , Membrane Proteins/genetics , Nedd4 Ubiquitin Protein Ligases/genetics , Ubiquitin-Protein Ligases/genetics , Carrier Proteins/chemistry , Endosomal Sorting Complexes Required for Transport , Humans , Lysine/chemistry , Membrane Proteins/chemistry , Nedd4 Ubiquitin Protein Ligases/chemistry , PTEN Phosphohydrolase/chemistry , PTEN Phosphohydrolase/genetics , Protein Binding/genetics , Protein Structure, Tertiary , RNA-Binding Proteins/chemistry , Ubiquitin/chemistry , Ubiquitin/genetics , Ubiquitin-Protein Ligases/chemistry , Ubiquitination/genetics
11.
Cell Death Dis ; 10(8): 545, 2019 07 18.
Article in English | MEDLINE | ID: mdl-31320629

ABSTRACT

Neuronal precursor cell expressed developmentally downregulated 4-2 (NEDD4-2) is an E3 ubiquitin ligase to regulate ion transport by controlling cellular trafficking/endocytosis and lysosomal degradation of ion channels and transporters. Thus, NEDD4-2 is relevant to neuronal excitability and epileptic encephalopathies in human patients. However, the regulatory molecules for NEDD4-2 dephosphorylation have been still elusive. Here, we demonstrate that pyridoxal-5'-phosphate phosphatase/chronophin (PLPP/CIN) specifically dephosphorylated NEDD4-2 serine (S) 448 site. PLPP/CIN deletion inhibited NEDD4-2 ubiquitination, and diminished the responsiveness of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) by facilitating NEDD4-2-mediated ubiquitination of GluA1 subunit under physiological condition. PLPP/CIN overexpression reversed these effects. These PLPP/CIN-mediated processes were required for the increased seizure severity and its progression in response to kainic acid (KA). Therefore, we suggest the novel function of PLPP/CIN as a NEDD4-2 phosphatase, which may be a potential therapeutic target for NEDD4-2-associated diseases as well as various neurological and psychiatric disorders, including epilepsy.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/metabolism , Neurons/metabolism , Phosphoric Monoester Hydrolases/metabolism , Receptors, AMPA/metabolism , Seizures/metabolism , Ubiquitination/genetics , Animals , Humans , KCNQ Potassium Channels/genetics , KCNQ Potassium Channels/metabolism , Kainic Acid/toxicity , Mice , Mice, Inbred C57BL , Mice, Transgenic , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/genetics , Neurons/drug effects , Phosphates/metabolism , Phosphoric Monoester Hydrolases/genetics , Receptors, AMPA/chemistry , Receptors, AMPA/genetics , Seizures/genetics , Ubiquitination/drug effects , Up-Regulation
12.
J Cell Biochem ; 120(8): 12859-12869, 2019 08.
Article in English | MEDLINE | ID: mdl-30854719

ABSTRACT

The development of covalent drugs, specifically in cancer therapeutics, has recently sparked interest among the pharmaceutical research community. While representing a significant fraction of the drugs in the market, very few have been deliberately designed to interact covalently with their biological target. One of the enzymes that have been both covalently and noncovalently targeted is the Neural Precursor Cell Expressed Developmentally Downregulated gene 4-1 (Nedd4-1). This enzyme has been found to have multiple physiological implications, including its involvement in cancer invasion. A critical gap still remains in the molecular understanding of the structural mechanism upon the covalent and noncovalent binding to Nedd4-1. In this study, we explore the most optimal binding mechanism in the inhibition of the catalytic site of the Nedd4-1. Our results exhibited a greater stability in the covalent complex compared with the noncovalent complex. This was supported by the secondary structure elements that were more dominant in the covalently inhibited complex. This complex disclosed an optimal free binding energy landscape, induced by the catalytic site energy contributions that showed to be more favorable. The insights demonstrating the above binding mechanism of Nedd4-1 establishes covalent inhibition as the preferred method of inhibition of the enzyme. This investigation aids in the understanding of the structural mechanism of Nedd4-1 inhibition and would assist in the design of more potent covalent inhibitors at the catalytic site of Nedd4-1.


Subject(s)
Enzyme Inhibitors/chemistry , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/metabolism , Binding Sites , Catalytic Domain/drug effects , Enzyme Inhibitors/pharmacology , Humans , Models, Molecular , Molecular Dynamics Simulation , Protein Binding , Protein Stability , Protein Structure, Secondary , Structure-Activity Relationship
13.
J Biol Chem ; 293(47): 18192-18206, 2018 11 23.
Article in English | MEDLINE | ID: mdl-30287686

ABSTRACT

The NEDD4-2 (neural precursor cell-expressed developmentally down-regulated 4-2) HECT ligase catalyzes polyubiquitin chain assembly by an ordered two-step mechanism requiring two functionally distinct E2∼ubiquitin-binding sites, analogous to the trimeric E6AP/UBE3A HECT ligase. This conserved catalytic mechanism suggests that NEDD4-2, and presumably all HECT ligases, requires oligomerization to catalyze polyubiquitin chain assembly. To explore this hypothesis, we examined the catalytic mechanism of NEDD4-2 through the use of biochemically defined kinetic assays examining rates of 125I-labeled polyubiquitin chain assembly and biophysical techniques. The results from gel filtration chromatography and dynamic light-scattering analyses demonstrate for the first time that active NEDD4-2 is a trimer. Homology modeling to E6AP revealed that the predicted intersubunit interface has an absolutely conserved Phe-823, substitution of which destabilized the trimer and resulted in a ≥104-fold decrease in kcat for polyubiquitin chain assembly. The small-molecule Phe-823 mimic, N-acetylphenylalanyl-amide, acted as a noncompetitive inhibitor (Ki = 8 ± 1.2 mm) of polyubiquitin chain elongation by destabilizing the active trimer, suggesting a mechanism for therapeutically targeting HECT ligases. Additional kinetic experiments indicated that monomeric NEDD4-2 catalyzes only HECT∼ubiquitin thioester formation and monoubiquitination, whereas polyubiquitin chain assembly requires NEDD4-2 oligomerization. These results provide evidence that the previously identified sites 1 and 2 of NEDD4-2 function in trans to support chain elongation, explicating the requirement for oligomerization. Finally, we identified a conserved catalytic ensemble comprising Glu-646 and Arg-604 that supports HECT-ubiquitin thioester exchange and isopeptide bond formation at the active-site Cys-922 of NEDD4-2.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/metabolism , Polyubiquitin/metabolism , Amino Acid Motifs , Catalysis , Catalytic Domain , Humans , Kinetics , Nedd4 Ubiquitin Protein Ligases/genetics , Polyubiquitin/chemistry , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism
14.
Cell Rep ; 24(12): 3312-3323.e5, 2018 09 18.
Article in English | MEDLINE | ID: mdl-30232011

ABSTRACT

Ubiquitination is essential for protein degradation and signaling and pivotal to many physiological processes. Ubiquitination of a subset of G-protein-coupled receptors (GPCRs) by the E3 ligase NEDD4-2 is required for p38 activation, but how GPCRs activate NEDD4-2 to promote ubiquitin-mediated signaling is not known. Here, we report that the GPCR protease-activated receptor-1 (PAR1) stimulates c-Src-mediated tyrosine phosphorylation and activation of NEDD4-2 to promote p38 signaling and endothelial barrier disruption. Using mass spectrometry, we identified a unique phosphorylated tyrosine (Y)-485 within the 2,3-linker peptide between WW domain 2 and 3 of NEDD4-2 in agonist-stimulated cells. Mutation of NEDD4-2 Y485 impaired E3 ligase activity and failed to rescue PAR1-stimulated p38 activation and endothelial barrier permeability. The purinergic P2Y1 receptor also required c-Src and NEDD4-2 tyrosine phosphorylation for p38 activation. These studies reveal a novel role for c-Src in GPCR-induced NEDD4-2 activation, which is critical for driving ubiquitin-mediated p38 inflammatory signaling.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/chemistry , Receptor, PAR-1/metabolism , Signal Transduction , Capillary Permeability , Human Umbilical Vein Endothelial Cells/metabolism , Humans , Nedd4 Ubiquitin Protein Ligases/genetics , Nedd4 Ubiquitin Protein Ligases/metabolism , Protein Domains , Receptors, Purinergic P2Y1/metabolism , Tyrosine/genetics , Tyrosine/metabolism , p38 Mitogen-Activated Protein Kinases/metabolism , src-Family Kinases/metabolism
15.
Protein J ; 37(6): 500-509, 2018 12.
Article in English | MEDLINE | ID: mdl-30232697

ABSTRACT

Covalent inhibition has recently gained a resurgence of interest in several drug discovery areas. The expansion of this approach is based on evidence elucidating the selectivity and potency of covalent inhibitors when bound to particular amino acids of a biological target. The Nedd4-1, an E3 ubiquitin ligase, is characterized by two covalent binding sites, of which catalytic Cyscat and allosteric Cysallo are enclosed. This enzyme has demonstrated inhibition at both the above-mentioned binding sites; however, a detailed molecular understanding of the structural mechanism of inhibition upon Cyscat and Cysallo binding remains vague. This prompted us to provide the first account of investigating the preferential covalent binding mode and the underlying structural and molecular dynamic implications. Based on the molecular dynamic analyses, it was evident that although both catalytic and allosteric covalent binding led to greater stability of the enzyme, a preferential covalent mechanism of inhibition was seen in the allosteric-targeted system. This was supported by a more favorable binding energy in the allosteric site compared to the catalytic site, in addition to the larger number of residue interactions and stabilizing hydrogen bonds occurring in the allosteric covalent bound complex. The fundamental dynamic analysis presented in this report compliments, as well as adds to previous experimental findings, thus leading to a crucial understanding of the structural mechanism by which Nedd4-1 is inhibited. The findings from this study may assist in the design of more target-specific Nedd4-1 covalent inhibitors exploring the surface-exposed cysteine residues.


Subject(s)
Molecular Dynamics Simulation , Nedd4 Ubiquitin Protein Ligases/chemistry , Allosteric Regulation , Catalysis , Humans , Protein Domains , Structure-Activity Relationship
16.
J Phys Chem B ; 122(15): 4219-4230, 2018 04 19.
Article in English | MEDLINE | ID: mdl-29595969

ABSTRACT

Sequence alignment of the four WW domains from human Nedd4-1 (neuronal precursor cell expressed developmentally down-regulated gene 4-1) reveals that the highest sequence diversity exists in loop I. Three residues in this type I ß-turn interact with the PPxY motif of the human epithelial Na+ channel (hENaC) subunits, indicating that peptide affinity is defined by the loop I sequence. The third WW domain (WW3*) has the highest ligand affinity and unlike the other three hNedd4-1 WW domains or other WW domains studied contains the highly statistically preferred proline at the ( i + 1) position found in ß-turns. In this report, molecular dynamics simulations and experimental data were combined to characterize loop I stability and dynamics. Exchange of the proline to the equivalent residue in WW4 (Thr) results in the presence of a predominantly open seven residue Ω loop rather than the type I ß-turn conformation for the wild-type apo-WW3*. In the presence of the ligand, the structure of the mutated loop I is locked into a type I ß-turn. Thus, proline in loop I ensures a stable peptide binding-competent ß-turn conformation, indicating that amino acid sequence modulates local flexibility to tune binding preferences and stability of dynamic interaction motifs.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/chemistry , Proline/chemistry , Binding Sites , Humans , Ligands , Molecular Dynamics Simulation , Protein Conformation
17.
Sci Rep ; 7(1): 4521, 2017 07 03.
Article in English | MEDLINE | ID: mdl-28674435

ABSTRACT

p38α plays an important role in many inflammatory diseases, such as skin inflammation, endotoxic shock and arthritis. Ubiquitination is a vital posttranslational modification of proteins and plays a crucial regulatory role in inflammatory cells. It has been reported that ubiquitination of Tak1 and TAB1 upstream of p38α can regulate p38α activation respectively. However, p38α ubiquitination is not yet clear. In this paper, we showed that E3 ubiquitin ligase Nedd4 is a regulatory component of the p38α pathway and is responsible for polyubiquitination of p38α through K48-linked and K63-linked polyubiquitination. The levels of p38α and its downstream target TNF-α were increased in Nedd4 deficient macrophages response to LPS compared with wild-type cells. AP-1 activity and degradation of p38α were induced by Nedd4 in a dose-dependent manner. Furthermore, we found that phosphorylation of p38α is involved in the interactions between p38α and Nedd4 and subsequently promotes polyubiquitination of p38α, especially K48-linked polyubiquitination by Nedd4. The different conformation of two p38α isoforms (p38αV1 and p38αV2) might be the cause of their different interactions with Nedd4 and their polyubiquitination sites by Nedd4. Thus, NEDD4 is a previously unknown component of the p38α signaling complex necessary for TNF-α activation.


Subject(s)
Mitogen-Activated Protein Kinase 14/metabolism , Nedd4 Ubiquitin Protein Ligases/metabolism , Transcription Factor AP-1/metabolism , Tumor Necrosis Factor-alpha/biosynthesis , Animals , Cell Line, Tumor , Gene Knockdown Techniques , Humans , Lipopolysaccharides/immunology , Macrophages/immunology , Macrophages/metabolism , Mice , Mitogen-Activated Protein Kinase 14/chemistry , Models, Molecular , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/genetics , Phosphorylation , Protein Conformation , Protein Domains , Proteolysis , Ubiquitination
18.
EMBO Rep ; 18(9): 1618-1630, 2017 09.
Article in English | MEDLINE | ID: mdl-28747490

ABSTRACT

The Nedd4 family E3 ligases are key regulators of cell growth and proliferation and are often misregulated in human cancers and other diseases. The ligase activities of Nedd4 E3s are tightly controlled via auto-inhibition. However, the molecular mechanism underlying Nedd4 E3 auto-inhibition and activation is poorly understood. Here, we show that the WW domains proceeding the catalytic HECT domain play an inhibitory role by binding directly to HECT in the Nedd4 E3 family member Itch. Our structural and biochemical analyses of Itch reveal that the WW2 domain and a following linker allosterically lock HECT in an inactive state inhibiting E2-E3 transthiolation. Binding of the Ndfip1 adaptor or JNK1-mediated phosphorylation relieves the auto-inhibition of Itch in a WW2-dependent manner. Aberrant activation of Itch leads to migration defects of cortical neurons during development. Our study provides a new mechanism governing the regulation of Itch.


Subject(s)
Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/metabolism , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/metabolism , Allosteric Regulation , Animals , Crystallography, X-Ray , Endosomal Sorting Complexes Required for Transport/metabolism , Humans , Mice , Nedd4 Ubiquitin Protein Ligases/genetics , Phosphorylation , Protein Binding , Protein Structure, Tertiary , Proteolysis , Ubiquitin-Protein Ligases/antagonists & inhibitors , Ubiquitin-Protein Ligases/genetics , Ubiquitination , WW Domains
19.
Sci Rep ; 6: 27137, 2016 06 03.
Article in English | MEDLINE | ID: mdl-27256588

ABSTRACT

Epithelial sodium channels (ENaCs) play critical roles in the maintenance of fluid and electrolyte homeostasis, and their genetic abnormalities cause one type of hereditary salt-sensitive hypertension, Liddle syndrome. As we reported previously, both human and rodent Nedd4L/Nedd4-2 showed molecular diversity, with and without a C2 domain in their N-terminal. Nedd4L/Nedd4-2 isoforms with a C2 domain are hypothesized to be related closely to ubiquitination of ENaCs. We generated Nedd4-2 C2 domain knockout mice. We demonstrate here that loss of Nedd4-2 C2 isoform causes salt-sensitive hypertension under conditions of a high dietary salt intake in vivo. The knockout mice had reduced urinary sodium excretion, osmotic pressure and increased water intake and urine volume with marked dilatation of cortical tubules while receiving a high salt diet. To the contrary, there was no difference in metabolic data between wild-type and knockout mice receiving a normal control diet. In the absence of Nedd4-2 C2 domain, a high salt intake accelerated ENaC expression. Coimmunoprecipitation studies revealed suppressed ubiquitination for ENaC with a high salt intake. Taken together, our findings demonstrate that during a high oral salt intake the Nedd4-2 C2 protein plays a pivotal role in maintaining adaptive salt handling in the kidney.


Subject(s)
Hypertension/chemically induced , Kidney/metabolism , Nedd4 Ubiquitin Protein Ligases/genetics , Sodium Chloride, Dietary/adverse effects , Adaptation, Physiological , Animals , Epithelial Sodium Channels/metabolism , Humans , Hypertension/genetics , Hypertension/metabolism , Mice , Mice, Knockout , Nedd4 Ubiquitin Protein Ligases/chemistry , Nedd4 Ubiquitin Protein Ligases/metabolism , Protein Isoforms/genetics , Protein Isoforms/metabolism , Ubiquitination
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