About: Chapter Sixteen Profiling DUBs and Ubl-specific proteases with activity-based probes

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Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Chapter Sixteen Profiling DUBs and Ubl-specific proteases with activity-based probes
Creator	Kikkert, Marjolein Ovaa, Huib Geurink, Paul Knaap, Robert Mulder, Monique Van Der Heden Van Noort, Gerbrand
Source	Elsevier; Medline; PMC
abstract	Abstract Protein (poly-)ubiquitination is a posttranslational modification that plays a key role in almost all cellular processes. It involves the installment of either single ubiquitin (Ub) moieties or one of eight different polyUb linkage types, each giving a distinct cellular outcome. Deubiquitinating enzymes (DUBs) reverse Ub signaling by disassembly of one or multiple poly-Ub chain types and their malfunction is often associated with human disease. The Ub system displays significant crosstalk with structurally homologous ubiquitin-like proteins (Ubls), including SUMO, Nedd8, and ISG15. This can be seen with the existence of heterogeneous chains made from Ub–Ubl mixtures as well as the proteolytic cross reactivity displayed by several DUBs toward other Ubl systems. In addition, numerous pathogens have been found to encode Ub(l)-ligases and deconjugating enzymes in order to facilitate infection and fight the host immune response. Studying the activity of DUBs and Ubl-specific proteases, both human as well as pathogen-derived, gives fundamental insights into their physiological roles. Activity-based probes (ABPs) have proven to be valuable tools to achieve this, as they report on enzyme activities by making a (often irreversible) covalent complex, rather than on their relative abundance. In this chapter, we explain the potential of ABPs to assess substrate preferences, structural features, and activity of Ub and Ubl deconjugating enzymes. We further demonstrate the practical use of ABPs to (1) characterize the activity of viral proteases toward Ub and Ubls and (2) to gain more insight in the structural determinants of substrate preference of DUBs.
has issue date	2019-12-31(xsd:dateTime)
bibo:doi	10.1016/bs.mie.2018.12.037
bibo:pmid	30850060
has license	els-covid
sha1sum (hex)	ae0294a3bf36a8f845194ac63d10b1b9d264d5a0
schema:url	https://doi.org/10.1016/bs.mie.2018.12.037
resource representing a document's title	Chapter Sixteen Profiling DUBs and Ubl-specific proteases with activity-based probes
has PubMed Central identifier	PMC7112362
has PubMed identifier	30850060
schema:publication	Methods in Enzymology
resource representing a document's body	covid:ae0294a3bf36a8f845194ac63d10b1b9d264d5a0#body_text
is schema:about of	named entity 'disease' named entity 'Enzymology' named entity 'ACTIVITY' named entity 'SINGLE' named entity 'UBIQUITIN' named entity 'DISASSEMBLY' named entity 'ISG15' named entity 'INCLUDING' named entity 'ENZYMOLOGY' named entity 'CELLULAR' named entity 'SIGNIFICANT' named entity 'ONE OF' named entity 'KEY' named entity 'ASSOCIATED WITH' named entity 'SEEN' named entity 'REVERSE' named entity 'SYSTEM' named entity 'UBL' named entity 'PLAYS' named entity 'SIGNALING' named entity 'MALFUNCTION' named entity 'DEUBIQUITINATING ENZYMES' named entity 'OUTCOME' named entity 'PROTEINS' named entity 'THEIR' named entity 'DIFFERENT' named entity 'LIKE' named entity 'DISTINCT' named entity 'IS A' named entity 'TYPES' named entity 'SPECIFIC' named entity 'PROTEASES' named entity 'MULTIPLE' named entity 'PROBES' named entity 'HUMAN DISEASE' named entity 'CHAIN' named entity 'DISPLAYS' named entity 'POSTTRANSLATIONAL MODIFICATION' named entity 'SUMO' named entity 'POLY' named entity 'ALMOST ALL' named entity 'CELLULAR PROCESSES' named entity 'NEDD8' named entity 'LINKAGE' named entity 'VOLUME' named entity 'BASED' named entity 'GIVING' named entity 'METHODS' named entity 'HOMOLOGOUS' named entity 'PROTEIN ' named entity 'ROLE' named entity 'CROSSTALK' named entity 'EITHER' named entity 'enzymes' named entity 'signaling' named entity 'structurally' named entity 'installment' named entity 'Protein' named entity 'plays' named entity 'structurally homologous' named entity 'ubiquitin' named entity 'proteases' named entity 'enzyme' named entity 'OTUs' named entity 'USP18' named entity 'enzyme' named entity 'lyophilized' named entity 'active site' named entity 'proteases' named entity 'cysteine proteases' named entity 'C-terminal' named entity 'biological role' named entity 'cleavage' named entity 'cell lysate' named entity 'mechanisms of action' named entity 'binding sites'

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