Relevant bibliographies by topics / E3 LIGASE ACTIVITY

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Academic literature on the topic 'E3 LIGASE ACTIVITY'

Author: Grafiati
Published: 11 September 2023

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Journal articles on the topic "E3 LIGASE ACTIVITY"

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Pao, Kuan-Chuan, Nicola T. Wood, Axel Knebel, Karim Rafie, Mathew Stanley, Peter D. Mabbitt, Ramasubramanian Sundaramoorthy, Kay Hofmann, Daan M. F. van Aalten, and Satpal Virdee. "Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity." Nature 556, no. 7701 (April 2018): 381–85. http://dx.doi.org/10.1038/s41586-018-0026-1.

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Marblestone, Jeffrey G., K. G. Suresh Kumar, Michael J. Eddins, Craig A. Leach, David E. Sterner, Michael R. Mattern, and Benjamin Nicholson. "Novel Approach for Characterizing Ubiquitin E3 Ligase Function." Journal of Biomolecular Screening 15, no. 10 (September 23, 2010): 1220–28. http://dx.doi.org/10.1177/1087057110380456.

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The ubiquitin-proteasome system is central to the regulation of numerous cellular events, and dysregulation may lead to disease pathogenesis. E3 ubiquitin ligases typically function in concert with E1 and E2 enzymes to recruit specific substrates, thereby coordinating their ubiquitylation and subsequent proteasomal degradation or cellular activity. E3 ligases have been implicated in a wide range of pathologies, and monitoring their activity in a rapid and cost-effective manner would be advantageous in drug discovery. The relative lack of high-throughput screening (HTS)–compliant E3 ligase assays has significantly hindered the discovery of E3 inhibitors. Herein, the authors describe a novel HTS-compliant E3 ligase assay platform that takes advantage of a ubiquitin binding domain’s inherent affinity for polyubiquitin chains, permitting the analysis of ubiquitin chain formation in an E3 ligase-dependent manner. This assay has been used successfully with members of both the RING and HECT families, demonstrating the platform’s broad utility for analyzing a wide range of E3 ligases. The utility of the assay platform is demonstrated by the identification of inhibitors of the E3 ligase CARP2. As the number of E3 ligases associated with various disease states increases, the ability to quantitate the activity of these enzymes in an expeditious manner becomes imperative in drug discovery.
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Li, Qianyan, Arshdeep Kaur, Kyoko Okada, Richard J. McKenney, and JoAnne Engebrecht. "Differential requirement for BRCA1-BARD1 E3 ubiquitin ligase activity in DNA damage repair and meiosis in the Caenorhabditis elegans germ line." PLOS Genetics 19, no. 1 (January 30, 2023): e1010457. http://dx.doi.org/10.1371/journal.pgen.1010457.

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The tumor suppressor BRCA1-BARD1 complex regulates many cellular processes; of critical importance to its tumor suppressor function is its role in genome integrity. Although RING E3 ubiquitin ligase activity is the only known enzymatic activity of the complex, the in vivo requirement for BRCA1-BARD1 E3 ubiquitin ligase activity has been controversial. Here we probe the role of BRCA1-BARD1 E3 ubiquitin ligase activity in vivo using C. elegans. Genetic, cell biological, and biochemical analyses of mutants defective for E3 ligase activity suggest there is both E3 ligase-dependent and independent functions of the complex in the context of DNA damage repair and meiosis. We show that E3 ligase activity is important for nuclear accumulation of the complex and specifically to concentrate at meiotic recombination sites but not at DNA damage sites in proliferating germ cells. While BRCA1 alone is capable of monoubiquitylation, BARD1 is required with BRCA1 to promote polyubiquitylation. We find that the requirement for E3 ligase activity and BARD1 in DNA damage signaling and repair can be partially alleviated by driving the nuclear accumulation and self-association of BRCA1. Our data suggest that in addition to E3 ligase activity, BRCA1 may serve a structural role for DNA damage signaling and repair while BARD1 plays an accessory role to enhance BRCA1 function.
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Kim, Jong Hum, Seok Keun Cho, Tae Rin Oh, Moon Young Ryu, Seong Wook Yang, and Woo Taek Kim. "MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in Arabidopsis thaliana." Proceedings of the National Academy of Sciences 114, no. 46 (October 30, 2017): E10009—E10017. http://dx.doi.org/10.1073/pnas.1713574114.

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Ubiquitin E3 ligases are crucial for eliminating misfolded proteins before they form cytotoxic aggregates that threaten cell fitness and survival. However, it remains unclear how emerging misfolded proteins in the cytoplasm can be selectively recognized and eliminated by E3 ligases in plants. We found that Misfolded Protein Sensing RING E3 ligase 1 (MPSR1) is an indispensable E3 ligase required for plant survival after protein-damaging stress. Under no stress, MPSR1 is prone to rapid degradation by the 26S proteasome, concealing its protein quality control (PQC) E3 ligase activity. Upon proteotoxic stress, MPSR1 directly senses incipient misfolded proteins and tethers ubiquitins for subsequent degradation. Furthermore, MPSR1 sustains the structural integrity of the proteasome complex at the initial stage of proteotoxic stress. Here, we suggest that the MPSR1 pathway is a constitutive mechanism for proteostasis under protein-damaging stress, as a front-line surveillance system in the cytoplasm.
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Bustos, Francisco, Sunil Mathur, Carmen Espejo-Serrano, Rachel Toth, C. James Hastie, Satpal Virdee, and Greg M. Findlay. "Activity-based probe profiling of RNF12 E3 ubiquitin ligase function in Tonne-Kalscheuer syndrome." Life Science Alliance 5, no. 11 (June 28, 2022): e202101248. http://dx.doi.org/10.26508/lsa.202101248.

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Ubiquitylation enzymes are involved in all aspects of eukaryotic biology and are frequently disrupted in disease. One example is the E3 ubiquitin ligase RNF12/RLIM, which is mutated in the developmental disorder Tønne-Kalscheuer syndrome (TOKAS). RNF12 TOKAS variants largely disrupt catalytic E3 ubiquitin ligase activity, which presents a pressing need to develop approaches to assess the impact of variants on RNF12 activity in patients. Here, we use photocrosslinking activity-based probes (photoABPs) to monitor RNF12 RING E3 ubiquitin ligase activity in normal and pathogenic contexts. We demonstrate that photoABPs undergo UV-induced labelling of RNF12 that is consistent with its RING E3 ligase activity. Furthermore, photoABPs robustly report the impact of RNF12 TOKAS variants on E3 activity, including variants within the RING domain and distal non-RING regulatory elements. Finally, we show that this technology can be rapidly deployed in human pluripotent stem cells. In summary, photoABPs are versatile tools that can directly identify disruptions to RING E3 ubiquitin ligase activity in human disease, thereby providing new insight into pathogenic mechanisms.
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Chinnam, Meenalakshmi, Chao Xu, Rati Lama, Xiaojing Zhang, Carlos D. Cedeno, Yanqing Wang, Aimee B. Stablewski, David W. Goodrich, and Xinjiang Wang. "MDM2 E3 ligase activity is essential for p53 regulation and cell cycle integrity." PLOS Genetics 18, no. 5 (May 19, 2022): e1010171. http://dx.doi.org/10.1371/journal.pgen.1010171.

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MDM2 and MDM4 are key regulators of p53 and function as oncogenes when aberrantly expressed. MDM2 and MDM4 partner to suppress p53 transcriptional transactivation and polyubiquitinate p53 for degradation. The importance of MDM2 E3-ligase-mediated p53 regulation remains controversial. To resolve this, we generated mice with an Mdm2 L466A mutation that specifically compromises E2 interaction, abolishing MDM2 E3 ligase activity while preserving its ability to bind MDM4 and suppress p53 transactivation. Mdm2L466A/L466A mice exhibit p53-dependent embryonic lethality, demonstrating MDM2 E3 ligase activity is essential for p53 regulation in vivo. Unexpectedly, cells expressing Mdm2L466A manifest cell cycle G2-M transition defects and increased aneuploidy even in the absence of p53, suggesting MDM2 E3 ligase plays a p53-independent role in cell cycle regulation and genome integrity. Furthermore, cells bearing the E3-dead MDM2 mutant show aberrant cell cycle regulation in response to DNA damage. This study uncovers an uncharacterized role for MDM2’s E3 ligase activity in cell cycle beyond its essential role in regulating p53’s stability in vivo.
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Gong, Yao, and Yue Chen. "UbE3-APA: a bioinformatic strategy to elucidate ubiquitin E3 ligase activities in quantitative proteomics study." Bioinformatics 38, no. 8 (February 9, 2022): 2211–18. http://dx.doi.org/10.1093/bioinformatics/btac069.

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Abstract Motivation Ubiquitination is widely involved in protein homeostasis and cell signaling. Ubiquitin E3 ligases are critical regulators of ubiquitination that recognize and recruit specific ubiquitination targets for the final rate-limiting step of ubiquitin transfer reactions. Understanding the ubiquitin E3 ligase activities will provide knowledge in the upstream regulator of the ubiquitination pathway and reveal potential mechanisms in biological processes and disease progression. Recent advances in mass spectrometry-based proteomics have enabled deep profiling of ubiquitylome in a quantitative manner. Yet, functional analysis of ubiquitylome dynamics and pathway activity remains challenging. Results Here, we developed a UbE3-APA, a computational algorithm and stand-alone python-based software for Ub E3 ligase Activity Profiling Analysis. Combining an integrated annotation database with statistical analysis, UbE3-APA identifies significantly activated or suppressed E3 ligases based on quantitative ubiquitylome proteomics datasets. Benchmarking the software with published quantitative ubiquitylome analysis confirms the genetic manipulation of SPOP enzyme activity through overexpression and mutation. Application of the algorithm in the re-analysis of a large cohort of ubiquitination proteomics study revealed the activation of PARKIN and the co-activation of other E3 ligases in mitochondria depolarization-induced mitophagy process. We further demonstrated the application of the algorithm in the DIA (data-independent acquisition)-based quantitative ubiquitylome analysis. Availability and implementation Source code and binaries are freely available for download at URL: https://github.com/Chenlab-UMN/Ub-E3-ligase-Activity-Profiling-Analysis, implemented in python and supported on Linux and MS Windows. Supplementary information Supplementary data are available at Bioinformatics online.
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Horn-Ghetko, Daniel, David T. Krist, J. Rajan Prabu, Kheewoong Baek, Monique P. C. Mulder, Maren Klügel, Daniel C. Scott, Huib Ovaa, Gary Kleiger, and Brenda A. Schulman. "Ubiquitin ligation to F-box protein targets by SCF–RBR E3–E3 super-assembly." Nature 590, no. 7847 (February 3, 2021): 671–76. http://dx.doi.org/10.1038/s41586-021-03197-9.

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AbstractE3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates1,2. However, rather than functioning individually, many neddylated cullin–RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family—which together account for nearly half of all ubiquitin ligases in humans—form E3–E3 super-assemblies3–7. Here, by studying CRLs in the SKP1–CUL1–F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3–E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3–E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3–E3 super-assembly may therefore underlie widespread ubiquitylation.
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Kelsall, Ian R., Jiazhen Zhang, Axel Knebel, J. Simon C. Arthur, and Philip Cohen. "The E3 ligase HOIL-1 catalyses ester bond formation between ubiquitin and components of the Myddosome in mammalian cells." Proceedings of the National Academy of Sciences 116, no. 27 (June 17, 2019): 13293–98. http://dx.doi.org/10.1073/pnas.1905873116.

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The linear ubiquitin assembly complex (LUBAC) comprises 3 components: HOIP, HOIL-1, and Sharpin, of which HOIP and HOIL-1 are both members of the RBR subfamily of E3 ubiquitin ligases. HOIP catalyses the formation of Met1-linked ubiquitin oligomers (also called linear ubiquitin), but the function of the E3 ligase activity of HOIL-1 is unknown. Here, we report that HOIL-1 is an atypical E3 ligase that forms oxyester bonds between the C terminus of ubiquitin and serine and threonine residues in its substrates. Exploiting the sensitivity of HOIL-1–generated oxyester bonds to cleavage by hydroxylamine, and macrophages from knock-in mice expressing the E3 ligase-inactive HOIL-1[C458S] mutant, we identify IRAK1, IRAK2, and MyD88 as physiological substrates of the HOIL-1 E3 ligase during Toll-like receptor signaling. HOIL-1 is a monoubiquitylating E3 ubiquitin ligase that initiates the de novo synthesis of polyubiquitin chains that are attached to these proteins in macrophages. HOIL-1 also catalyses its own monoubiquitylation in cells and most probably the monoubiquitylation of Sharpin, in which ubiquitin is also attached by an oxyester bond. Our study establishes that oxyester-linked ubiquitylation is used as an intracellular signaling mechanism.
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Li, Haoyan, Yanjia Fang, Chunyi Niu, Hengyi Cao, Ting Mi, Hong Zhu, Junying Yuan, and Jidong Zhu. "Inhibition of cIAP1 as a strategy for targeting c-MYC–driven oncogenic activity." Proceedings of the National Academy of Sciences 115, no. 40 (September 4, 2018): E9317—E9324. http://dx.doi.org/10.1073/pnas.1807711115.

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Protooncogenec-MYC, a master transcription factor, is a major driver of human tumorigenesis. Development of pharmacological agents for inhibiting c-MYC as an anticancer therapy has been a longstanding but elusive goal in the cancer field. E3 ubiquitin ligase cIAP1 has been shown to mediate the activation of c-MYC by destabilizing MAD1, a key antagonist of c-MYC. Here we developed a high-throughput assay for cIAP1 ubiquitination and identified D19, a small-molecule inhibitor of E3 ligase activity of cIAP1. We show that D19 binds to the RING domain of cIAP1 and inhibits the E3 ligase activity of cIAP1 by interfering with the dynamics of its interaction with E2. Blocking cIAP1 with D19 antagonizes c-MYC by stabilizing MAD1 protein in cells. Furthermore, we show that D19 and an improved analog (D19-14) promote c-MYC degradation and inhibit the oncogenic function of c-MYC in cells and xenograft animal models. In contrast, we show that activating E3 ubiquitin ligase activity of cIAP1 by Smac mimetics destabilizes MAD1, the antagonist of MYC, and increases the protein levels of c-MYC. Our study provides an interesting example using chemical biological approaches for determining distinct biological consequences from inhibiting vs. activating an E3 ubiquitin ligase and suggests a potential broad therapeutic strategy for targeting c-MYC in cancer treatment by pharmacologically modulating cIAP1 E3 ligase activity.
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Dissertations / Theses on the topic "E3 LIGASE ACTIVITY"

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Dickens, Michael. "Small molecule inhibitors of Mdm2 E3 ubiquitin ligase activity." Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/11960/.

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Half of cancers retain wild type p53 but have alterations in the pathways involved in p53 regulation. Murine double minute 2 (Mdm2) regulates p53 by acting as an E3 ubiquitin ligase, which tags p53 for degradation through the proteasome. A small molecule inhibitor, a 5-deazaflavin analogue, has previously been identified by high throughput screening to inhibit Mdm2 E3 ubiquitin ligase activity, thereby reactivating apoptotic function of p53 selectively in cancer cells. Ninety 5-deazaflavin analogues have been synthesised by an optimized existing method and a novel method of synthesis, using the required 6-anilinouracil and 2-p-toluenesulfonyloxybenzaldehyde.The biological ability of the 5-deazaflavin analogues to act as inhibitors of Mdm2 E3 ubiquitin ligase activity to reactivate p53 has been ascertained. A new quantitative biological assay was developed, by scientists based at the Beatson Institute, for 5-deazaflavin compounds, showing excellent inhibition of Mdm2 E3 ubiquitin ligase activity on the previous qualitative biological assay, to yield IC50 data. The biological results have established a clear and logical structure-activity relationship comprising of an electron-withdrawing hydrophobic substituent at the nine position and the N10 phenyl being a prerequisite for activity as a Mdm2 inhibitor. Also meta substitution of the N10 phenyl improves activity against Mdm2 E3 ubiquitin ligase activity. Hit optimization has occurred with 10-(3-chlorophenyl)-9-trifluoromethyl-5-deazaflavin being thirty times more active than the previous identified hit compound, 10-(4-chlorophenyl)-7-nitro-5-deazaflavin. Using the X-ray crystal structure of the Mdm2/MdmX heterodimer, an improved understanding of how Mdm2 acts as an E3 ubiquitin ligase is described and used to form a hypothesis of how 5-deazaflavin analogues function as inhibitors of Mdm2. The work suggests the principle that small molecular weight compounds can inhibit E3 ubiquitin ligases as a possible anti-cancer therapy, and provide the foundation and framework for additional studies and investigation in a new and developing field of medicinal chemistry.
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ZANCHETTA, MELANIA EVA. "BRAF35 as target of MID1/TRIM18 E3 ligase activity." Doctoral thesis, Università degli Studi di Trieste, 2016. http://hdl.handle.net/11368/2908069.

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TRIM proteins are a family of ubiquitin E3 ligase enzymes characterized by the presence of a conserved N-terminus, the tripartite motif, which consists of a RING finger domain, two B-box motifs and an alpha-helical Coiled-coil region (RBCC). We focused our attention on TRIM18/MID1, the gene responsible for the X-linked form of Opitz G/BBB syndrome, a congenital disease characterized by defects in midline development and mental retardation. More recently, MID1 has also been found as overexpressed in some aggressive prostate cancers. The role of MID1 within the cell and the target(s) of its E3 ubiquitin activity during cellular processes are still not completely unravelled. In order to better investigate MID1 function and to find new cellular partners for this protein a two hybrid assay was performed in our laboratory. By means of this screening, BRCA2-Associated Factor 35 (BRAF35 or HMG20b) was identified as a novel MID1 interacting protein. BRAF35 is a non-canonical High-Mobility-Group (HMG) protein that has a role in both neuronal differentiation and in cell cycle progression. Moreover BRAF35 sumoylation has been shown to be fundamental for its antineurogenic activity and is inhibited by the interaction with its homologue iBraf. The aim of the project was to characterise the functional role of MID1/BRAF35 interaction and to understand if MID1, as an E3 ubiquitin ligase, regulates BRAF35 during cytokinesis. The first evidence obtained from the preliminary screening was confirmed through MBP pull-down assay and co-immunoprecipitation, identifying the coiled-coil region of both proteins as responsible for the binding. We further investigated on a possible regulation of BRAF35 by the ubiquitin proteasome system and we recognized BRAF35 as a poly-ubiquitinated protein and we found that its abundance is regulated in a proteasome-dependent manner. In addition, overexpression of MID1 or its domain-deleted mutants altered BRAF35 stability and post-translational modification suggesting a MID1-dependent BRAF35 ubiquitination that implicates also K63-polyUb dependent signalling involvement. Additionally, we found that MID1 and BRAF35 colocalize not only during interphase but also at the intercellular bridge during cytokinesis. Consistent with this observation, we observed a cell cycle-related regulation of BRAF35 protein level. Moreover, MID1 depletion rescued the cytokinetic defect caused by BRAF35 silencing, leading to a decrease of binucleation, but promoted a blebbing phenotype in dividing cells. This indicates that a fine regulation of the two proteins for the completion of cytokinesis is required and suggests an additional and new role for MID1 in cytokinesis regulation.
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Fu, Wei. "Regulation of FOXO stability and activity by MDM2 E3 ligase." [Tampa, Fla] : University of South Florida, 2007. http://purl.fcla.edu/usf/dc/et/SFE0002222.

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Pao, Kuan-Chuan. "Design and synthesis of an E3 ligase activity-based probe and its application for the discovery of a new class of E3 ligase." Thesis, University of Dundee, 2018. https://discovery.dundee.ac.uk/en/studentTheses/6239e172-60b3-47c3-81e1-f4b0a577f1a4.

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The ubiquitylation cascade regulates multiple cellular functions and is involved in numerous diseases. The distinct transfer cascade, involving E1-E2-E3 enzymes, serves as a promising target for drug development. However, E3 ligases (E3s) represent an important class of enzymes yet there are currently no effective tools for profiling their activity. Herein, a new class of E3 activity-based probe (ABP) is presented which is built by re-engineering ubiquitin (Ub)-charged E2 conjugating enzymes. The utility of these probes has been demonstrated by the rapid dissection of the activation determinants of the RING-Between-RING E3 (RBR) E3, Parkin. Furthermore, biotin-E3 ABPs allow us to systematically discover and dissect the E3 activities of a broad spectrum of E3s that are associated with different diseases. By interfacing the ABPs with mass spectrometry, we establish an activity based protein profiling (ABPP) system and apply it to uncover a new class of E3. We show that MYCBP2 is an E3 ligase with a novel mechanism of action that ubiquitylates threonine residues. MYCBP2 contains a RING domain, that recruits the ubiquitin-loaded E2, and a novel Zn-binding fold that contains two catalytic cysteine residues which relay the Ub to substrate via two thioester intermediates (RING-Cys-Relay, RCR). This discovery demonstrates the power and potential of our E3 activity based protein profiling (ABPP) system.
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Koliopoulos, Marios Grigorios. "Structural and functional basis for TRIM25 E3 ligase catalytic activity and NS1-mediated suppression." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/10038260/.

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Ubiquitination is a post-translational modification of proteins with broad regulatory roles across cellular biology. This process involves the addition of ubiquitin molecules on target proteins, altering their cellular role and properties. Ubiquitination is performed by an enzymatic cascade consisting of three enzymes: ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2) and ubiquitin ligases (E3). The tripartite motif (TRIM) family of proteins constitutes one of the largest subfamilies of RING E3 ligases and the majority of them are contributing to the regulation of innate immune responses. They are characterized by a conserved tripartite motif in their N-terminal region which comprises a RING domain, one or two B-box domains and a coiled-coil region. Self-association is believed to be crucial for catalytic activity of TRIM proteins, however, the precise molecular mechanism underlying this observation remains elusive. The work presented in this thesis provides insights into the E3 ligase function of TRIM25 and shows how its oligomeric state is linked to its catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and a ubiquitin-loaded E2 identifies the structural and mechanistic features that promote activation of E2~Ub allowing us to propose a model for the regulation of activity in the full-length protein. In the second part of this thesis, the molecular details of Influenza A NS1-mediated TRIM25 inhibition are presented. The crystal structures of NS1 bound to TRIM25 along with biochemical analysis allowed us to identify the interacting domains and propose a model for the inhibition of substrate ubiquitination during viral infection. The results of this project extend our understanding of the mechanism, structure and regulation of TRIM E3 ligases and their substrates, leading to increased chances of targeting specific steps of the ubiquitination pathway during disease.
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Valentini, E. "UNDERSTANDING THE CATALYTIC MECHANISMS OF UBIQUITIN-E3 LIGASES." Doctoral thesis, Università degli Studi di Milano, 2016. http://hdl.handle.net/2434/354478.

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E3 ubiquitin ligases are key regulatory enzymes of the ubiquitination pathway as they are responsible for substrate specificity. This thesis aimed at deciphering the molecular mechanisms through which two different E3 ligases, Nedd4 and Rabex-5, exert their activity. Nedd4 is the prototype for HECT-E3 ligase while Rabex-5, containing an A20 zinc finger domain (ZnF_A20) instead of a canonical RING, could be defined as an atypical RING-E3 ligase. In the case of Nedd4, we provided the first crystal structure of the catalytic intermediate of HECTNedd4~Ub in complex with Ub non-covalently bound to the UBD present in the N-lobe of HECTNedd4. Our structure represents the next step of the transfer of UbD from the catalytic cysteine of E2 to the one of E3 in which the UbD C-terminal tail is in an extended conformation primed for catalysis. Our data strongly supports the sequential addition model proposed for HECT proteins. Within this study we also clarified some aspects of Rabex-5 as E3 ligase. By yeast-two-hybrid, GST-pull-down assays and ITC analysis, we identified specific E2 partners, Ube2D and Ube2E families, that bind Rabex-5 only when in their active Ub-loaded state. Performing in vitro auto-ubiquitination assay and disulfide stability assay we confirmed that ZnF_A20 is the minimal domain responsible for the catalytic activity. To obtain the structure of the Rabex-51-74:E2-Ub complex, we tested, unfortunately without success, crystallization trials and SAXS analysis with various samples. We also analyzed Rabex-5 catalytic activity towards on H-Ras, which is the unique substrate of Rabex-5 so far identified, and we disproved that H-Ras is a Rabex-5 substrate. To identify candidate substrates we profiled 20.000 human proteins using a microarray-based ubiquitination screening. A list of 67 proteins represent the most statistically stringent and conservative estimate for Rabex-5 substrates that we are going to validate in the nearest future, starting from the ones involved in the endocytic pathway.
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Furlan, Giulia [Verfasser]. "Phosphorylation of the E3 ubiquitin ligase PUB22 controls its ubiquitination activity to dampen the immune response / Giulia Furlan." Halle, 2017. http://d-nb.info/1141177102/34.

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Foster, Benjamin. "An in vitro biochemical investigation into the conformation, binding and E3-ubiquitin ligase activity of mammalian UHRF1 with reconstituted chromatin." Thesis, Imperial College London, 2017. http://hdl.handle.net/10044/1/55875.

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In the eukaryotic genome, DNA and histone modifications regulate chromatin function and mediate basic processes such as gene transcription, DNA repair and DNA replication. Maintaining chromatin modifications after DNA replication is essential for chromatin homeostasis, especially for regions of the genome that need to be kept silenced such as repetitive elements. The maintenance DNA methyltransferase, DNMT1, is responsible for ensuring that cytosine methylation at CpG dinucleotides, and thus proper transcriptional programmes, are propagated to the daughter cells. DNMT1 is specifically recruited to newly replicated, hemi-methylated DNA and the E3-ubiquitin ligase UHRF1 (Ubiquitin-like containing PHD- and RING-finger domains protein 1) plays a critical role for this. The mechanisms of the recruitment of DNMT1 to chromatin via UHRF1 are currently an area of active investigation. Several studies using modified nucleosomes, histone peptides and DNA oligonucleotides have identified UHRF1 to bind to hemi-methylated CpG dinucleotides and to histone H3 di- or tri-methylated at Lys-9. Since UHRF1 was also found to interact with DNMT1, it was postulated that UHRF1 acts as an adapter that directly recruits DNMT1 to newly replicated DNA. Additionally, it has recently been reported that the E3-ubiquitin ligase activity of its C-terminal RING-finger is required for the recruitment of DNMT1 to replication forks. Ubiquitylation of either K18 or K23 on histone H3 that is recognised by a ubiquitin-interacting motif within DNMT1 appears to be critical for DNMT1 targeting but the recruitment mechanism has so far not been completely elucidated. This study has investigated the binding and E3-ubiquitin ligase activity of UHRF1 in the context of physiologically relevant chromatin substrates. Using a fully reconstituted system, the chromatin binding and enzymatic activity of UHRF1 and how this is linked to its intra-molecular arrangement have been elucidated. In the context of modified nucleosome substrates, we observe an increase in binding of recombinant UHRF1 in the presence of hemi-methylated DNA whilst with histone H3K9me2/3, only a small increase in binding is detected. We also provide evidence that binding to nucleosome core particles is enhanced by a basic region between the SRA-domain and the RING-finger. This so called polybasic region or PBR has previously been implicated in the regulation of UHRF1 binding to H3K9me2/3 marks. Our findings therefore suggest that binding of UHRF1 to physiological chromatin substrates is more complex than previously thought. In-solution crosslinking/mass spectrometry experiments using the full-length protein confirm that UHRF1 exhibits complex intra-molecular contacts that can potentially regulate its interaction with chromatin or other factors. In addition to reported contacts between the PBR with the Tandem-Tudor domain and between the PHD-finger and the SRA-domain, the UBL-domain also makes extensive contacts to other regions within UHRF1. These appear to be weak and dynamic. Crucially, removal of the UBL-domain does not affect nucleosome binding but does result in a strong reduction in UHRF1 E3-ubiquitin ligase activity. Further experiments suggest that the UBL-domain is involved in establishing the enzyme/substrate complex between the E2-conjugating enzyme and the chromatin substrate and in stimulating the transfer of ubiquitin from the E2~Ub complex to histone H3. In summary, by combining a crosslinking/mass spectrometry approach to interrogate the intra-molecular arrangement of UHRF1 with fully reconstituted enzyme and chromatin-binding assays using physiologically relevant substrates, we have identified a function for the UBL-domain of UHRF1. Our results suggest that the UBL is highly flexible in solution and that it forms transient contacts with other parts of UHRF1 and the E2-conjugating enzyme that are required for the formation of the E2/E3/substrate complex in allosterically activating ubiquitin transfer from the E2~Ub to the histone target substrate. These findings assign, for the first time, a function for the UBL-domain and pave the way for further investigation of the involvement of this domain in the physiological role of UHRF1.
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Gao, Chengzhuo. "Mechanisms Underlying the Regulation and Functions of HDAC7." Case Western Reserve University School of Graduate Studies / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=case1213890889.

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Courivaud, Thomas. "Caractérisation d'un nouveau mécanisme d'action de la E3 ubiquitine ligase WWP1 et régulation de son activité dans la cancérogenèse." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066300/document.

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La voie de signalisation TGF-β joue un rôle biphasique durant la cancérogenèse. Mon laboratoire a identifié une nouvelle protéine inhibitrice de la voie TGF-β, WWP1. WWP1 est une E3 ubiquitine ligase qui induit la polyubiquitination et la dégradation du récepteur de type I au TGF-β. De plus, le gène WWP1 est amplifié dans une large proportion de cancers mammaires et prostatiques, suggérant que WWP1 pourrait jouer un rôle clé dans les processus de cancérogenèse liés au TGF-β. Mon projet de thèse était donc de caractériser la régulation de l’activité catalytique de WWP1 ainsi que son mécanisme d’action dans la cellule. Mes résultats montrent qu’à l’état basal, WWP1 est monoubiquitinée, son activité de polyubiquitination étant réduite par l’effet inhibiteur qu’exercent les domaines C2 et/ou WW sur son domaine HECT. En présence de substrats, la protéine WWP1 « s’ouvre » et peut alors induire la polyubiquitination et la dégradation de ses substrats. De plus, nous avons observé qu’un mutant de WWP1, détecté dans un cancer de la prostate, est incapable de s’autoréguler selon ce modèle. Il présente une plus forte activité ligase envers lui-même et ses substrats, ce qui entraîne une atténuation de la réponse cytostatique du TGF-β pouvant conférer une activité oncogénique à WWP1. De plus, nous avons identifié STARD13 comme un nouveau partenaire de WWP1. STARD13 est une protéine à activité RhoGAP, considérée comme un suppresseur de tumeur. Nous avons montré que STARD13 permet l’association de WWP1 avec la GTPase RhoA, entraînant ainsi la polyubiquitination et la dégradation de RhoA. De façon intéressante, le complexe WWP1/STARD13 est impliqué dans le remodelage de l’architecture du cytosquelette en dégradant préférentiellement la forme activée de RhoA. Ces résultats ont permis d’identifier un nouveau rôle de WWP1 qui pourrait jouer un rôle essentiel durant la migration des cellules cancéreuses lors du processus métastatique. La caractérisation de nouveaux mécanismes de régulation et d’action de WWP1 devrait permettre à terme d’identifier si WWP1 est un marqueur diagnostique dans le cancer et/ou une nouvelle cible thérapeutique pour le développement de médicaments anticancéreux
The TGF-β pathway plays a biphasic role during cancerogenesis. My laboratory identified a new protein, WWP1, as a negative regulator of TGF-β signaling. WWP1 is an E3 ubiquitin ligase that triggers polyubiquitination and degradation of TGF-β type I receptor. A genomic amplification of WWP1 is found in a large portion of mammary and prostatic tumors, suggesting a key role for WWP1 during carcinogenesis related to TGF-β. My thesis project was to determine the regulation of the catalytic activity of WWP1 and a new molecular mechanism of action of WWP1 whose deregulation can be implicated in cancerogenesis. My results indicate that at steady states, WWP1 is monoubiquitinated, its polyubiquitination activity being silenced due to the inhibitory effects of C2 or/and WW domains on its Hect domain. In presence of substrates, WWP1 is « opened » and induces polyubiquitination and degradation of its substrates. Moreover, a WWP1 mutation found in prostate cancer disrupts this regulatory mechanism. It possesses an increased ligase activity towards itself and its substrates, which leads to the attenuation of TGF-β cytostatic signaling, a consequence that could conceivably confer tumorigenic properties to WWP1. We also identified STARD13 as a novel WWP1 interacting partner. STARD13 has a RhoGAP activity, and is considered as a tumor suppressor. We have shown that STARD13 mediates the association of WWP1 with the GTPase RhoA, ultimately leading to RhoA polyubiquitination and degradation. Interestingly, the WWP1/STARD13 complex is involved in the actin cytoskeleton rearrangement by preferentially targeting the active form of RhoA for degradation. These results reveal a previously unrecognized role for WWP1, which could play a key role in the migration of cancer cells during metastasis. Characterization of new regulation and action mechanisms for WWP1 should allow identifying whether WWP1 is a diagnosis biomarker in cancer and/or a new therapeutic target for the development of anticancer drugs
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Books on the topic "E3 LIGASE ACTIVITY"

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Barañano, Kristin W. Angelman Syndrome. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0055.

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Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by maternal deficiency of the epigenetically imprinted gene UBE3A. It is characterized by severe developmental delay, an ataxic gait disorder, an apparent happy demeanor with frequent smiling or laughing, and severe expressive language impairments. Understanding the neurobiology of AS has focused on understanding how UBE3A is regulated by neuronal activity, as well as the targets of its ubiquitin E3 ligase activity. This has led to a model of the role of UBE3A in the regulation of experience-dependent sculpting of synaptic circuits. At this time, treatment is largely supportive, but efforts directed toward reversing the epigenetic silencing machinery may lead to improved synaptic function in AS patients.
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Book chapters on the topic "E3 LIGASE ACTIVITY"

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Ren, Hong Yu, Cam Patterson, Douglas M. Cyr, and Meredith F. N. Rosser. "Reconstitution of CHIP E3 Ubiquitin Ligase Activity." In Methods in Molecular Biology, 93–103. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-295-3_8.

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Ohtake, Fumiaki, and Shigeaki Kato. "The E3 Ubiquitin Ligase Activity of Transcription Factor AHR Permits Nongenomic Regulation of Biological Pathways." In The AH Receptor in Biology and Toxicology, 143–56. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118140574.ch10.

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Tieroyaare Dongdem, Julius, and Cletus Adiyaga Wezena. "Functional Significance of the E3 Ubiquitin Ligases in Disease and Therapeutics." In Hydrolases [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.100534.

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E3 ubiquitin ligases of which there are >600 putative in humans, constitute a family of highly heterogeneous proteins and protein complexes that are the ultimate enzymes responsible for the recruitment of an ubiquitin loaded E2 ubiquitin-conjugating enzyme, recognise the appropriate protein substrate and directly or indirectly transfer the ubiquitin load onto the substrate. The aftermath of an E3 ligase activity is usually the formation of an isopeptide bond between the free carboxylate group of ubiquitin’s C-terminal Gly76 and an ε-amino group of the substrate’s Lys, even though non-canonical ubiquitylation on non-amine groups of target proteins have been observed. E3 ligases are grouped into four distinct families: HECT, RING-finger/U-box, RBR and PHD-finger. E3 ubiquitin ligases play critical roles in subcellular signalling cascades in eukaryotes. Dysfunctional E3 ubiquitin ligases therefore tend to inflict dramatic effects on human health and may result in the development of various diseases including Parkinson’s, Amyotrophic Lateral Sclerosis, Alzheimer’s, cancer, etc. Being regulators of numerous cellular processes, some E3 ubiquitin ligases have become potential targets for therapy. This chapter will present a comprehensive review of up-to-date findings in E3 ligases, their role in the pathology of disease and therapeutic potential for future drug development.
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Song, Jie, and Maréne Landström. "Lys63-Linked Polyubiquitination of Transforming Growth Factor β Type I Receptor (TβRI) Specifies Oncogenic Signaling." In Ubiquitin - Proteasome Pathway. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.93065.

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Transforming growth factor β (TGFβ) is a multifunctional cytokine with potent regulatory effects on cell fate during embryogenesis, in the normal adult organism, and in cancer cells. In normal cells, the signal from the TGFβ ligand is transduced from the extracellular space to the cell nucleus by transmembrane serine–threonine kinase receptors in a highly specific manner. The dimeric ligand binding to the TGFβ Type II receptor (TβRII) initiates the signal and then recruits the TGFβ Type I receptor (TβRI) into the complex, which activates TβRI. This causes phosphorylation of receptor-activated Smad proteins Smad2 and Smad3 and promotes their nuclear translocation and transcriptional activity in complex with context-dependent transcription factors. In several of our most common forms of cancer, this pathway is instead regulated by polyubiquitination of TβRI by the E3 ubiquitin ligase TRAF6, which is associated with TβRI. The activation of TRAF6 promotes the proteolytic cleavage of TβRI, liberating its intracellular domain (TβRI-ICD). TβRI-ICD enters the cancer cell nucleus in a manner dependent on the endosomal adaptor proteins APPL1/APPL2. Nuclear TβRI-ICD promotes invasion by cancer cells and is recognized as acting distinctly and differently from the canonical TGFβ-Smad signaling pathway occurring in normal cells.
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"Molecular Investigation of Protein–Protein Interaction Candidates Related to the Mammalian Brain." In Cheminformatics and Bioinformatics at the Interface with Systems Biology, 81–107. Royal Society of Chemistry, 2023. http://dx.doi.org/10.1039/9781839166037-00081.

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The traditional protein–protein interaction (PPI) system is a mathematical depiction to accumulate valuable knowledge regarding cell physiology in normal and disease states still lacking some mechanistic approaches to biological processes. The mapping protein composition of the PPI system/network provides structural details of PPIs and their mutual exclusion interactions. However, the information revealed by high-throughput screening (HTS) PPI data is a collection of numerous false positives and negatives that could be addressed initially in experiments. The integrated PPI information and its next-generation sequencing technology collections with other genome-wide statistics, i.e. phenotype and expression profile facts, are widely used in understanding novel biological insights. Through this, we obtain a detailed integration analysis to reveal the function of proteins and many other aspects that help in understanding the complexity of the mammalian brain. For example, hereditary Parkinson’s disease and its extensive PPI processes are currently used for the determination of the mechanism of action of Parkinson’s disease. This is done with the localization of E3 ubiquitin ligase, and the activity involved becomes modulated with its interaction partners. These techniques are able to uncover the slightest alterations of the molecular pathogenesis of the specified disease. A new research paradigm corresponding to the protein interactions and detailed structural knowledge on the interacting surfaces of proteins helps in predicting the genotype–phenotype relationship. The main goal of this chapter is to emphasize the importance of examining substitute conformations of proteins in structural PPI networks, which enhances our capability to analyze protein interactions more accurately.
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Sandmann, Alexander, and Nico Dissmeyer. "In vitro autoubiquitination activity of E3 ubiquitin ligases of the N-degron pathway." In Methods in Enzymology. Elsevier, 2023. http://dx.doi.org/10.1016/bs.mie.2023.02.014.

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Conference papers on the topic "E3 LIGASE ACTIVITY"

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Lin, Huan-Yu, Shiu-Ting Lin, Mei-June Wang, and Jeou-Yuan Chen. "Abstract 1699: Suppressor of cytokine signaling 6 (SOCS6) promotes mitochondrial fission through E3 ubiquitin ligase complex activity." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-1699.

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Shin, Jun-Wan, and Young-Joon Surh. "Abstract B67: Curcumin induces stabilization of Nrf2 protein by decreasing the activity of Cullin3-Rbx1 E3 ubiquitin ligase." In Abstracts: AACR International Conference on Frontiers in Cancer Prevention Research‐‐ Oct 22-25, 2011; Boston, MA. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1940-6207.prev-11-b67.

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Shukla, Shirish, Felicia Gray, Weijiang Ying, Hyoje Cho, Qingjie Zhao, Hongzhi Miao, Hongzhi Miao, et al. "Abstract 50: Small molecule Ring1B-Bmi1 inhibitor attenuates PRC1 E3 ligase activity and targets leukemia stem cells self-renewal." In Abstracts: Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1557-3265.hemmal17-50.

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Qian, Tingting, Jeong-Yeon Lee, Hyun-Jun Kim, and Gu Kong. "Abstract LB-96: Id1 enhances RING1b E3 ubiquitin ligase activity through the Mel-18/Bmi-1 polycomb group complex." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-lb-96.

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Qi, Jianfei, Manisha Tripathi, Natasha Sahgal, Ladan Fazil, Susan Ettinger, William J. Placzek, Giuseppina Claps, et al. "Abstract 5456: The E3 ubiquitin ligase Siah2 regulates the androgen receptor activity and contributes to castration-resistant prostate cancer." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-5456.

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Yu, Yonghui, Jinyi Liu, Dongyun Zhang, Wenjing Luo, Jianxiu Yu, Jingxia Li, Xinhai Zhang, Jingyuan Chen, and Chuanshu Huang. "Abstract 4312: E3 ligase activity of XIAP RING domain is required for XIAP-mediated cancer cell migration but not for its RhoGDI binding activity." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-4312.

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Shukla, Shirish, Qingjie Zhao, Weijang Ying, Felicia Gray, Kelly Vandenberg, George Lund, Bohdan Boytsov, Shihan He, Jolanta Grembecka, and Tomasz Cierpicki. "Abstract 3520: Small molecule inhibitors of ring1B-Bmi1 E3 ligase target polycomb repressive complex 1 activity and regulate cell proliferation." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-3520.

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Banh, Robert S., Caterina Iorio, Richard Marcotte, Yang Xu, Dan Cojocari, Anas Abdel Rahman, Judy Pawling, et al. "Abstract LB-302: PTP1B regulates the Moyamoya disease-associated E3 ligase, RNF213 and cellular dioxygenase activity to allow breast tumor survival in hypoxia." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-lb-302.

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Sosin, Angela M., Angelika M. Burger, Dajun Yang, Ramzi M. Mohammad, and Ayad Al-Katib. "Abstract 4516: A new class of MDM2 inhibitors cause growth inhibition and stabilize wt p53 in lymphoma cells but do not interfere with MDM2 E3 ligase activity." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-4516.

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Zhao, Hongling, Vineeth Sukrithan, Niloy Iqbal, Cari Nicholas, Yingjiao Xue, Joseph Locker, Juntao Zou, Liang Zhu, and Edward L. Schwartz. "Abstract 1060: Genetic and pharmacologic inhibition of Skp2, an E3 ubiquitin ligase and RB1-target, has antitumor activity in RB1-deficient human and mouse small cell lung cancer (SCLC)." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-1060.

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