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Relevant bibliographies by topics / Ubiquitin protease

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Academic literature on the topic 'Ubiquitin protease'

Author: Grafiati

Published: 4 May 2024

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Journal articles on the topic "Ubiquitin protease"

1

Yip, Matthew C. J., Nicholas O. Bodnar, and Tom A. Rapoport. "Ddi1 is a ubiquitin-dependent protease." Proceedings of the National Academy of Sciences 117, no. 14 (March 19, 2020): 7776–81. http://dx.doi.org/10.1073/pnas.1902298117.

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TheSaccharomyces cerevisiaeprotein Ddi1 and its homologs in higher eukaryotes have been proposed to serve as shuttling factors that deliver ubiquitinated substrates to the proteasome. Although Ddi1 contains both ubiquitin-interacting UBA and proteasome-interacting UBL domains, the UBL domain is atypical, as it binds ubiquitin. Furthermore, unlike other shuttling factors, Ddi1 and its homologs contain a conserved helical domain (helical domain of Ddi1, HDD) and a retroviral-like protease (RVP) domain. The RVP domain is probably responsible for cleavage of the precursor of the transcription factor Nrf1 in higher eukaryotes, which results in the up-regulation of proteasomal subunit genes. However, enzymatic activity of the RVP domain has not yet been demonstrated, and the function of Ddi1 remains poorly understood. Here, we show that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains (longer than about eight ubiquitins). The RVP domain is inactive in isolation, in contrast to its retroviral counterpart. Proteolytic activity of Ddi1 requires the HDD domain and is stimulated by the UBL domain, which mediates high-affinity interaction with the polyubiquitin chain. Compromising the activity of Ddi1 in yeast cells results in the accumulation of polyubiquitinated proteins. Aside from the proteasome, Ddi1 is the only known endoprotease that acts on polyubiquitinated substrates. Ddi1 and its homologs likely cleave polyubiquitinated substrates under conditions where proteasome function is compromised.

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Drag, Marcin, Jowita Mikolajczyk, Miklos Bekes, Francisca E. Reyes-Turcu, Jonathan A. Ellman, Keith D. Wilkinson, and Guy S. Salvesen. "Positional-scanning fluorigenic substrate libraries reveal unexpected specificity determinants of DUBs (deubiquitinating enzymes)." Biochemical Journal 415, no. 3 (October 15, 2008): 367–75. http://dx.doi.org/10.1042/bj20080779.

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DUBs (deubiquitinating enzymes) are a family of proteases responsible for the specific removal of ubiquitin attached to target proteins and thus control the free cellular pools of this molecule. DUB activity is usually assayed using full-length ubiquitin, and these enzymes generally show low activity towards small substrates that constitute the P4–P1 LRGG (Lys-Arg-Gly-Gly) C-terminal motif of ubiquitin. To gain insight into the C-terminal recognition region of ubiquitin by DUBs, we synthesized positional scanning libraries of fluorigenic tetrapeptides and tested them on three examples of human DUBs [OTU-1 (ovarian tumour 1), Iso-T (isopeptidase T) and UCH-L3 (ubiquitin C-terminal hydrolase L3)] and one viral ubiquitin-specific protease, namely PLpro (papain-like protease) from SARS (severe acute respiratory syndrome) virus. In most cases the results show flexibility in the P4 position, very high specificity for arginine in the P3 position and glycine in the P2 position, in accord with the sequence of the natural substrate, ubiquitin. Surprisingly, screening of the P2 position revealed that UCH-L3, in contrast with all the other tested DUBs, demonstrates substantial tolerance of alanine and valine at P2, and a parallel analysis using the appropriate mutation of the full-length ubiquitin confirms this. We have also used an optimal tetrapeptide substrate, acetyl-Lys-Arg-Gly-Gly-7-amino-4-methylcoumarin, to investigate the activation mechanism of DUBs by ubiquitin and elevated salt concentration. Together, our results reveal the importance of the dual features of (1) substrate specificity and (2) the mechanism of ubiquitin binding in determining deubiquitination by this group of proteases.

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Gardner, Richard G., Zara W. Nelson, and Daniel E. Gottschling. "Ubp10/Dot4p Regulates the Persistence of Ubiquitinated Histone H2B: Distinct Roles in Telomeric Silencing and General Chromatin." Molecular and Cellular Biology 25, no. 14 (July 2005): 6123–39. http://dx.doi.org/10.1128/mcb.25.14.6123-6139.2005.

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ABSTRACT We previously discovered that the ubiquitin protease Ubp10/Dot4p is important for telomeric silencing through its interaction with Sir4p. However, the mechanism of Ubp10p action was unknown. We now provide evidence that Ubp10p removes ubiquitin from histone H2B; cells with UBP10 deleted have increased steady-state levels of H2B ubiquitination. As a consequence, ubp10Δ cells also have increased steady-state levels of histone H3 Lys4 and Lys79 methylation. Consistent with its role in silencing, Ubp10p is preferentially localized to silent chromatin where its ubiquitin protease activity maintains low levels of H3 Lys4 and Lys79 methylation to allow optimal Sir protein binding to telomeres and global telomeric silencing. The ubiquitin protease Ubp8p has also been shown to remove ubiquitin from H2B, and ubp8Δ cells have increased steady-state levels of H2B ubiquitination similar to those in ubp10Δ cells. Unlike ubp10Δ cells, however, ubp8Δ cells do not have increased steady-state levels of H3 Lys4 and Lys79 methylation, nor is telomeric silencing affected. Despite their separate functions in silencing and SAGA-mediated transcription, respectively, deletion of both UBP10 and UBP8 results in a synergistic increase in the steady-state levels of H2B ubiquitination and in the number of genes with altered expression, indicating that Ubp10p and Ubp8p likely overlap in some of their target chromatin regions. We propose that Ubp10p and Ubp8p are the only ubiquitin proteases that normally remove monoubiquitin from histone H2B and, while there are regions of the genome to which each is specifically targeted, both combine to regulate the global balance of H2B ubiquitination.

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Schairer, Rebekka, Gareth Hall, Ming Zhang, Richard Cowan, Roberta Baravalle, Frederick W. Muskett, Peter J. Coombs, et al. "Allosteric activation of MALT1 by its ubiquitin-binding Ig3 domain." Proceedings of the National Academy of Sciences 117, no. 6 (January 24, 2020): 3093–102. http://dx.doi.org/10.1073/pnas.1912681117.

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The catalytic activity of the protease MALT1 is required for adaptive immune responses and regulatory T (Treg)-cell development, while dysregulated MALT1 activity can lead to lymphoma. MALT1 activation requires its monoubiquitination on lysine 644 (K644) within the Ig3 domain, localized adjacent to the protease domain. The molecular requirements for MALT1 monoubiquitination and the mechanism by which monoubiquitination activates MALT1 had remained elusive. Here, we show that the Ig3 domain interacts directly with ubiquitin and that an intact Ig3-ubiquitin interaction surface is required for the conjugation of ubiquitin to K644. Moreover, by generating constitutively active MALT1 mutants that overcome the need for monoubiquitination, we reveal an allosteric communication between the ubiquitination site K644, the Ig3-protease interaction surface, and the active site of the protease domain. Finally, we show that MALT1 mutants that alter the Ig3-ubiquitin interface impact the biological response of T cells. Thus, ubiquitin binding by the Ig3 domain promotes MALT1 activation by an allosteric mechanism that is essential for its biological function.

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Vertegaal, Alfred C. O. "SUMO chains: polymeric signals." Biochemical Society Transactions 38, no. 1 (January 19, 2010): 46–49. http://dx.doi.org/10.1042/bst0380046.

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Ubiquitin and ubiquitin-like proteins are conjugated to a wide variety of target proteins that play roles in all biological processes. Target proteins are conjugated to ubiquitin monomers or to ubiquitin polymers that form via all seven internal lysine residues of ubiquitin. The fate of these target proteins is controlled in a chain architecture-dependent manner. SUMO (small ubiquitin-related modifier) shares the ability of ubiquitin to form chains via internal SUMOylation sites. Interestingly, a SUMO-binding site in Ubc9 is important for SUMO chain synthesis. Similar to ubiquitin–polymer cleavage by USPs (ubiquitin-specific proteases), SUMO chain formation is reversible. SUMO polymers are cleaved by the SUMO proteases SENP6 [SUMO/sentrin/SMT3 (suppressor of mif two 3)-specific peptidase 6], SENP7 and Ulp2 (ubiquitin-like protease 2). SUMO chain-binding proteins including ZIP1, SLX5/8 (synthetic lethal of unknown function 5/8), RNF4 (RING finger protein 4) and CENP-E (centromere-associated protein E) have been identified that interact non-covalently with SUMO chains, thereby regulating target proteins that are conjugated to SUMO multimers. SUMO chains play roles in replication, in the turnover of SUMO targets by the proteasome and during mitosis and meiosis. Thus signalling via polymers is an exciting feature of the SUMO family.

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Fieulaine, Sonia, Martin D. Witte, Christopher S. Theile, Maya Ayach, Hidde L. Ploegh, Isabelle Jupin, and Stéphane Bressanelli. "Turnip yellow mosaic virus protease binds ubiquitin suboptimally to fine-tune its deubiquitinase activity." Journal of Biological Chemistry 295, no. 40 (July 30, 2020): 13769–83. http://dx.doi.org/10.1074/jbc.ra120.014628.

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Single-stranded, positive-sense RNA viruses assemble their replication complexes in infected cells from a multidomain replication polyprotein. This polyprotein usually contains at least one protease, the primary function of which is to process the polyprotein into mature proteins. Such proteases also may have other functions in the replication cycle. For instance, cysteine proteases (PRO) frequently double up as ubiquitin hydrolases (DUB), thus interfering with cellular processes critical for virus replication. We previously reported the crystal structures of such a PRO/DUB from Turnip yellow mosaic virus (TYMV) and of its complex with one of its PRO substrates. Here we report the crystal structure of TYMV PRO/DUB in complex with ubiquitin. We find that PRO/DUB recognizes ubiquitin in an unorthodox way: It interacts with the body of ubiquitin through a split recognition motif engaging both the major and the secondary recognition patches of ubiquitin (Ile44 patch and Ile36 patch, respectively, including Leu8, which is part of the two patches). However, the contacts are suboptimal on both sides. Introducing a single-point mutation in TYMV PRO/DUB aimed at improving ubiquitin-binding led to a much more active DUB. Comparison with other PRO/DUBs from other viral families, particularly coronaviruses, suggests that low DUB activities of viral PRO/DUBs may generally be fine-tuned features of interaction with host factors.

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Mielech, Anna M., Xufang Deng, Yafang Chen, Eveline Kindler, Dorthea L. Wheeler, Andrew D. Mesecar, Volker Thiel, Stanley Perlman, and Susan C. Baker. "Murine Coronavirus Ubiquitin-Like Domain Is Important for Papain-Like Protease Stability and Viral Pathogenesis." Journal of Virology 89, no. 9 (February 18, 2015): 4907–17. http://dx.doi.org/10.1128/jvi.00338-15.

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ABSTRACTUbiquitin-like domains (Ubls) now are recognized as common elements adjacent to viral and cellular proteases; however, their function is unclear. Structural studies of the papain-like protease (PLP) domains of coronaviruses (CoVs) revealed an adjacent Ubl domain in severe acute respiratory syndrome CoV, Middle East respiratory syndrome CoV, and the murine CoV, mouse hepatitis virus (MHV). Here, we tested the effect of altering the Ubl adjacent to PLP2 of MHV on enzyme activity, viral replication, and pathogenesis. Using deletion and substitution approaches, we identified sites within the Ubl domain, residues 785 to 787 of nonstructural protein 3, which negatively affect protease activity, and valine residues 785 and 787, which negatively affect deubiquitinating activity. Using reverse genetics, we engineered Ubl mutant viruses and found that AM2 (V787S) and AM3 (V785S) viruses replicate efficiently at 37°C but generate smaller plaques than wild-type (WT) virus, and AM2 is defective for replication at higher temperatures. To evaluate the effect of the mutation on protease activity, we purified WT and Ubl mutant PLP2 and found that the proteases exhibit similar specific activities at 25°C. However, the thermal stability of the Ubl mutant PLP2 was significantly reduced at 30°C, thereby reducing the total enzymatic activity. To determine if the destabilizing mutation affects viral pathogenesis, we infected C57BL/6 mice with WT or AM2 virus and found that the mutant virus is highly attenuated, yet it replicates sufficiently to elicit protective immunity. These studies revealed that modulating the Ubl domain adjacent to the PLP reduces protease stability and viral pathogenesis, revealing a novel approach to coronavirus attenuation.IMPORTANCEIntroducing mutations into a protein or virus can have either direct or indirect effects on function. We asked if changes in the Ubl domain, a conserved domain adjacent to the coronavirus papain-like protease, altered the viral protease activity or affected viral replication or pathogenesis. Our studies using purified wild-type and Ubl mutant proteases revealed that mutations in the viral Ubl domain destabilize and inactivate the adjacent viral protease. Furthermore, we show that a CoV encoding the mutant Ubl domain is unable to replicate at high temperature or cause lethal disease in mice. Our results identify the coronavirus Ubl domain as a novel modulator of viral protease stability and reveal manipulating the Ubl domain as a new approach for attenuating coronavirus replication and pathogenesis.

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Békés, Miklós, Wioletta Rut, Paulina Kasperkiewicz, Monique P. C. Mulder, Huib Ovaa, Marcin Drag, Christopher D. Lima, and Tony T. Huang. "SARS hCoV papain-like protease is a unique Lys48 linkage-specific di-distributive deubiquitinating enzyme." Biochemical Journal 468, no. 2 (May 22, 2015): 215–26. http://dx.doi.org/10.1042/bj20141170.

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We compare processing proteases from two human coronaviruses - the severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) hCoVs - with respect to their activities and substrate specificities for ubiquitin (Ub)-like signaling molecules, Ub and ISG15 (interferon stimulated gene 15); and doing so, we uncover a unique mode of polyUb recognition by the SARS protease.

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Gilchrist, Catherine A., Douglas A. Gray, and Rohan T. Baker. "A Ubiquitin-specific Protease That Efficiently Cleaves the Ubiquitin-Proline Bond." Journal of Biological Chemistry 272, no. 51 (December 19, 1997): 32280–85. http://dx.doi.org/10.1074/jbc.272.51.32280.

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Luna‐Vargas, Mark P. A., Alex C. Faesen, Willem J. van Dijk, Michael Rape, Alexander Fish, and Titia K. Sixma. "Ubiquitin‐specific protease 4 is inhibited by its ubiquitin‐like domain." EMBO reports 12, no. 4 (March 18, 2011): 365–72. http://dx.doi.org/10.1038/embor.2011.33.

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Dissertations / Theses on the topic "Ubiquitin protease"

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Thorne, Christopher Mark Cornelius. "Characterisation of ubiquitin specific protease 33." Thesis, University of Liverpool, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.548811.

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Groll, Michael. "Strukturelle und funktionelle Zusammenhänge und Unterschiede archaebakterieller und eukaryontischer 20S-Proteasome." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2005. http://dx.doi.org/10.18452/13957.

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In eukaryotes protein degradation is performed by the ubiquitin-proteasome system. The 26S proteasome, a 2.5MDa large multimeric molecular machine, consists of more than 30 subunits and represents the core component of this proteolytic pathway. The complex is assembled from a proteolytically active 20S proteasome and two 19S regulator cap complexes. So far crystal structure, topology and enzymatic mechanism have only been elucidated for the 20S proteasome core particle (CP). CPs are assembled from four stacked rings of seven subunits each, following an alpha7beta7beta7alpha7-stochiometry. The strict established order of the proteasomal assembly and maturation is essential to prevent uncontrolled and premature protein degradation in the cell. CPs belong to the class of Ntn-hydrolases. Peptide hydrolysis is performed inside a central cavity at the active sites of the beta-type subunits, with Ogam of the hydroxyl group of the N-terminal threonine acting as the nucleophile. Release of the proteolytically active threonine through N-O-Acetyl rearrangement is the last step of the proteasomal assembly. Compartmentalisation of CPs is an important way to regulate substrate access to the central cavity as well as release of the generated oligopeptides. The activity of eukaryotic CPs are controlled by an unique mechanism: docking of regulatory complexes, like Blm3, PA28 or 19S, causes a conformational change of the N-terminal residues of the latent alpha-subunits, resulting in an activation of the proteolytically active sites. Archaebacterial CPs lack such regulatory gating mechanism. The controlled degradation of proteins by the proteasome dominates a variety of biological essential processes, like metabolic adaptation, apoptosis, inflammation, immune and stress response, as well as cell proliferation and cell differentiation. Selective and specific natural and synthetic inhibitors of CPs might find their practical application in treatment of cancer or inflammatory diseases.

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Blanchette, Paola. "Functional analysis of Unp, a mammalian ubiquitin protease." Thesis, University of Ottawa (Canada), 2002. http://hdl.handle.net/10393/6281.

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The murine Unp gene encodes a ubiquitously expressed protein that fractionates with the nuclear fraction (hence its name ubiquitous nuclear protein) (Gupta, K., Copeland, N. G., Gilbert, D. J., Jenkins, N. A., and Gray, D. A. (1993). Oncogene 8, 2307-10). It possesses proprieties of an oncogene, such as the ability to promote tumours in a nude mouse assay (Gupta, K., Chevrette, M., and Gray, D. A. (1994). Oncogene 9, 1729--31), and its human homologue, USP4 (previously known as Unph), was shown to be over expressed in certain types of human lung tumours (Gray, D. A., Inazawa, J., Gupta, K., Wong, A., Ueda, R., and Takahashi, T. (1995). Oncogene 10, 2179--83). Although very little was known about this protein's normal function, even less on its mechanism of tumorigenicity, the predicted protein sequence gave some clues on its function. It possesses the two conserved domains present in all ubiquitin specific proteases, and the two motifs common to viral oncoproteins through which they interact with the retinoblastoma gene product pRb. In addition to these features it also possesses a region that resembles a nuclear localisation signal. A mutational approach was taken in combination with ubiquitin cleavage assays and binding assays to study Unp's function. With these, it was confirmed that Unp is a ubiquitin specific protease, its ability to cleave ubiquitin dependent on the conserved cysteine, and may be dependent on Unp phosphorylation status. Unp is a phosphoprotein, being phosphorylated on serine residue(s). It is capable of binding to pRb's hypophosphorylated as well as the hyperphosphorylated forms, a binding that is dependent on an intact conserved motif 2 (CR2). It is also capable of binding to the other pocket proteins, p107 and p130, although with different requirements of conserved regions that for pRb. With these and other results obtained, a model is proposed linking Unp's activity as a deubiquitinating enzyme and its interactions with the pocket proteins with its role as an oncogene. The data obtained also supports the newer view that ubiquitin specific proteases, have a role in the specific regulation of protein levels and not just as general ubiquitin recycling enzymes as previously believed.

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Tibbo, Emma. "Cell cycle aspects of the Unp ubiquitin protease." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/nq21019.pdf.

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Albrecht, Brian Keith. "A concise total synthesis of the TMC-95A and TMC-95B proteasome inhibitors." Access citation, abstract and download form; downloadable file 12.48 Mb, 2004. http://wwwlib.umi.com/dissertations/fullcit/3131652.

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MASSA, FILOMENA. "THE UBIQUITIN-SPECIFIC PROTEASE USP14 CONTROLS CILIOGENESIS AND THE HEDGEHOG PATHWAY." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/562686.

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Primary cilia are microtubule-based organelles on the apical surface of mammalian cells, and play a crucial role in vertebrate development and tissue homeostasis. Consequently, ciliary defects are associated with human disorders called ciliopathies. This organelle represents an organizing center for signaling pathways. In particular, in vertebrates, the Hedgehog (Hh) pathway controls embryonic development and adult homeostasis using the primary cilium to transduce its signal. Hh components localize to cilia and Kif7, a key player in cilia structure and length, controls the ciliary localization of Hh signaling molecules. Phenotypes associated to Hh signaling impairment are often observed in ciliopathies. Recent studies established a link between ciliary proteins and the Ubiquitin proteasome system (UPS) pathway, however much remains to be understood. The main role of the UPS is to mark proteins for degradation although it also functions in a wide variety of cellular processes. The aim of my PhD project was to investigate the association between cilioproteins and proteasomal functions, with particular emphasis on the cilia- associated OFD1 protein, which is responsible for the rare OFD type I syndrome. The results obtained demonstrate that OFD1 controls proteasomal complex composition through direct binding with proteasomal components (see Liu et al. in appendix). Our results also demonstrate a role for Usp14, a deubiquitinating enzyme, in the control of ciliogenesis, cilia length and proper activation of the Hh pathway. We propose a new mechanism by which cilia maintenance and the Hh pathway are regulated by Usp14 via modulation of Kif7 proteasomal degradation (manuscript in preparation). This mechanism may be relevant not only in ciliopathies but also in other pathological conditions associated to Hedgehog signaling defects. Overall our results provide new insight into the spectrum of action of the UPS and may provide novel opportunities for therapeutic intervention in pathological conditions associated to cilia dysfunction.

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Boehringer, Jonas. "Substrate recognition by the proteasome." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.669968.

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The ubiquitin proteasome system targets proteins to the proteasome where they are degraded. Substrate recognition and processing prior to degradation take place at the 19S regulatory particle of the proteasome. A polyubiquitin chain, linked through isopeptide bonds formed between the C-terminal G76 and K48, is the signal responsible for delivery to the proteasome. Because chains linked via any of the seven lysine residues of ubiquitin exist in vivo and encode signals unrelated to protein degradation it is crucial for cells to avoid crosstalk between these different pathways. Several ubiquitin receptors related to proteasomal degradation have been identified but the selectivity between the different ubiquitin chains has not been assessed quantitatively while avoiding artefacts attributed to GST-dimerisation. By employing isothermal titration calorimetry, analytical ultracentrifugation and nuclear magnetic resonance, discrimination between K48- and K63-linked diubiquitin was established for the S. pombe proteasomal receptor Rpn10 and the shuttle protein Rhp23. The same methods allowed us to propose a discriminatory model for Rpn10. The crystal structures of the 19S regulatory particle subunits Rpn101-193 and Rpn121-224 have been determined and possible protein-protein interaction sites were identified by surface conservation and electrostatics analysis. Rpn12 surface residues were identified that had a negative effect on Rpn10-binding. This interaction was studied by surface plasmon resonance, fluorescence anisotropy and nuclear magnetic resonance. These experiments revealed a binding site on Rpn10 that is exclusively occupied by either ubiquitin or Rpn12 and for the first time demonstrated the interaction of a ubiquitin interacting motif with a protein other than ubiquitin.

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Fischer, Susanne. "Untersuchungen zur Funktion der Ubiquitin spezifischen Protease nonstop im visuellen System von Drosophila melanogaster." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=961831448.

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Sharif, Azar. "Structural characterization of the polycomb repressor complex 1 binding partner ubiquitin specific protease 11." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/39355.

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Ubiquitin Specific Protease 11 (USP11), USP4 and USP15 are highly conserved and are characterised by an N-terminal 'domain present in ubiquitin specific proteases' (DUSP) and 'ubiquitin-like' (UBL) domains. This DUSP-UBL (DU) domain is thought to be involved in substrate recognition. It was shown that USP11 co-purifies with human Polycomb Repressive Complex type 1 (PRC1) and regulates the stability of the E3 ligase component of PRC1 (Maertens et al, 2010). PRC1 repress transcription from the INK4a tumour suppressor locus. Hence knockdown of USP11 in primary human fibroblasts causes de-repression of INK4a, followed by a senescence-like proliferative arrest. In this project we aimed to map the interaction between USP11 and PRC1 components (BMI1, RING2, MEL18 and CBX8). We used two methods to investigate their interactions; yeast two-hybrid and in vitro pull down. Unexpectedly, we could not confirm a direct interaction between USP11 and any PRC1 component. We hypothesize that the lack of post-translation modifications, the presence of fusion tags and/or the need of a multi-subunit PRC1 complex might be needed to observe a high affinity interaction. We also aimed to map the interaction between three PRC1 components; RING2, BMI1 and RYBP, with the ultimate aim of solving the X-ray structure of the complex. The main obstacle in this project was to express, extract and purify these proteins at high levels in bacterial culture. Preliminary data suggests that RYBP and BMI1 do not interact directly. Here we report the 3.6 Å resolution X-ray structure of the human USP11 DU. The sequence linking the DUSP and UBL domains, the DU finger, could not be assigned in the electron density map due to low resolution. Comparison with the related USP4 DU crystal structure reveals that the structures are mostly conserved.

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Nunes, Gonçalo Pedro da Silva. "The role of Ubiquitin Specific Protease 7 on Latency Associated Nuclear Antigen DNA binding." Master's thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Quimica e Biológica António Xavier, 2018. http://hdl.handle.net/10362/130062.

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Dissertation presented to obtain the Master degree in Biochemistry for Health
The implications of USP7 (Ubiquitin Specific Protease 7, deubiquitinating enzyme involved in several crucial molecular pathways) interactions with LANA (Latency Associated Nuclear Antigen protein, that facilitates the tethering of viral γ-Herpesvirus episomes into the host’s DNA and promotes its replication) has multiple health consequences, since USP7 is a protein that has an essential role it the regulation of many cellular functions, like the p53-mdm2 pathway, that regulates cellular apoptosis and prevents cancer.
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Books on the topic "Ubiquitin protease"

1

P, Zwickl, and Baumeister W. 1946-, eds. The Proteasome-ubiquitin protein degradation pathway. Berlin: Springer, 2002.

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Patterson, Cam, and Douglas M. Cyr. Ubiquitin-Proteasome Protocols. New Jersey: Humana Press, 2005. http://dx.doi.org/10.1385/1592598951.

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Cam, Patterson, and Cyr Douglas M, eds. Ubiquitin-proteasome protocols. Totowa, N.J: Humana Press, 2005.

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Mayor, Thibault, and Gary Kleiger, eds. The Ubiquitin Proteasome System. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8706-1.

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Zwickl, Peter, and Wolfgang Baumeister, eds. The Proteasome — Ubiquitin Protein Degradation Pathway. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-59414-4.

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Dohmen, R. Jürgen, and Martin Scheffner, eds. Ubiquitin Family Modifiers and the Proteasome. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-474-2.

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J, Ciechanover Aaron, and Masucci Maria G, eds. The ubiquitin-proteasome proteolytic system: From classical biochemistry to human diseases. Singapore: World Scientific, 2002.

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name, No. The ubiquitin-proteasome proteolytic system: From classical biochemistry to human diseases. Singapore: World Scientific, 2002.

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Di, Napoli Mario, and Wójcik Cezary 1968-, eds. The ubiquitin proteasome system in the central nervous system: From physiology to pathology : 2008 update. Hauppauge, NY: Nova Science, 2009.

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(Editor), Peter Zwickl, and Wolfgang Baumeister (Editor), eds. The Proteasome-Ubiquitin Protein Degradation Pathway. Springer, 2002.

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Book chapters on the topic "Ubiquitin protease"

1

Hough, Ronald F., Gregory W. Pratt, and Martin Rechsteiner. "Ubiquitin/ATP-Dependent Protease." In Ubiquitin, 101–34. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_5.

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Basu, Bhaskar, Seemana Bhattacharya, Gouranga Saha, and Mrinal K. Ghosh. "USP7 (Ubiquitin-Specific Protease 7)." In Encyclopedia of Signaling Molecules, 5849–54. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-67199-4_101812.

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Komada, Masayuki, Martin Reincke, and Marily Theodoropoulou. "USP8 (Ubiquitin-Specific Protease 8)." In Encyclopedia of Signaling Molecules, 5855–62. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-67199-4_101955.

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Basu, Bhaskar, Seemana Bhattacharya, Gouranga Saha, and Mrinal K. Ghosh. "USP7 (Ubiquitin-Specific Protease 7)." In Encyclopedia of Signaling Molecules, 1–7. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4614-6438-9_101812-1.

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Komada, Masayuki, Martin Reincke, and Marily Theodoropoulou. "USP8 (Ubiquitin-Specific Protease 8)." In Encyclopedia of Signaling Molecules, 1–9. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4614-6438-9_101955-1.

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Mao, Youdong. "Structure, Dynamics and Function of the 26S Proteasome." In Subcellular Biochemistry, 1–151. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-58971-4_1.

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Abstract:

AbstractThe 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal “processor” for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.

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Brooks, Christopher L., and Wei Gu. "Herpesvirus-Associated Ubiquitin-Specific Protease De-ubiquitinase." In Encyclopedia of Cancer, 1–5. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-27841-9_2690-2.

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Brooks, Christopher L., and Wei Gu. "Herpesvirus-Associated Ubiquitin-Specific Protease De-ubiquitinase." In Encyclopedia of Cancer, 2059–63. Berlin, Heidelberg: Springer Berlin Heidelberg, 2017. http://dx.doi.org/10.1007/978-3-662-46875-3_2690.

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Brooks, Christopher L., and Wei Gu. "Herpesvirus-Associated Ubiquitin-Specific Protease De-ubiquitinase." In Encyclopedia of Cancer, 1684–88. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-16483-5_2690.

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Knobeloch, Klaus-Peter. "Ubiquitin/Proteasome." In Encyclopedia of Molecular Pharmacology, 1529–35. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-57401-7_282.

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Conference papers on the topic "Ubiquitin protease"

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Reverdy, Céline, Susan Conrath, Roman Lopez, Cécile Planquette, Vincent Collura, Philippe Guedat, Rémi Delansorne, Laurent Daviet, and Frédéric Colland. "Abstract 2642: Identification and characterization of selective inhibitors of ubiquitin specific protease 7." 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.am10-2642.

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Mustachio, Lisa Maria, Fadzai Chinyengetere, Yun Lu, Shanhu Hu, Masanori Kawakami, Laura J. Tafe, Alexey Danilov, et al. "Abstract 1782: The ubiquitin protease UBP43 is a target for KRAS mutant lung cancers." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-1782.

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Sun, Xiao-Xin, Xia He, Li Yin, Rosalie Sears, and Mushui Dai. "Abstract LB-074: The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc." 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-074.

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Guo, Yongli, Fadzai Chinyengetere, Andrey V. Dolinko, Alexandra Lopez-Aguiar, Fabrizio Galimberti, Tian Ma, Qing Feng, et al. "Abstract 1655: The ubiquitin protease UBP43 is a target for lung cancer therapy and prevention." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-1655.

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Kim, Jayoung, Massimo F. Loda, and Michael R. Freeman. "Abstract 2188: The ubiquitin-specific protease USP2a targets cyclin A1: A potential role in bladder cancer." 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.am2012-2188.

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James, Godwin. "Ubiquitin Specific Protease 5, an interactor of PWO1 and Polycomb group proteins that regulates Arabidopsis development." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1052939.

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Henrich, Ian, Rob Young, Laura Quick, Xiaoke Wang, Andre Oliveira, and Margaret Chou. "Abstract PR08: Ubiquitin-specific protease 6 (USP6) oncogene confers sensitivity of Ewing sarcoma to interferon cytotoxicity." In Abstracts: Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1557-3265.sarcomas17-pr08.

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Sharma, Nidhi, Qianzheng Zhu, Qi-En Wang, and Altaf A. Wani. "Abstract 1785: Ubiquitin specific protease 3 is a regulator of histone ubiquitination required for maintenance of genomic stability." 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.am2013-1785.

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Mustachio, Lisa Maria, Yun Lu, Laura J. Tafe, Angeline S. Andrew, Vincent Memoli, Jaime Rodriguez-Canales, Pamela A. Villalobos, et al. "Abstract 1255: Loss of the ubiquitin protease USP18 represses KRAS mutant lung cancer tumorigenicity in mice by destabilizing KRAS protein." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-1255.

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Duex, Jason E., Benjamin Kefas, Benjamin Purow, and Alexander Sorkin. "Abstract 4691: Inhibition of ubiquitin specific protease Usp18 reduces cancer cell proliferation by down regulating multiple proto-oncogenes including EGFR." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4691.

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