Pseudo-DUBs as allosteric activators and molecular scaffolds of protein complexes

Abstract

The ubiquitin (Ub) proteasome system and Ub signalling networks are crucial to cell biology and disease development. Deubiquitylases (DUBs) control cell signalling by removing mono-Ub and polyubiquitin chains from substrates. DUBs take part in almost all processes that regulate cellular life and are frequently dysregulated in disease. We have catalogued 99 currently known DUBs in the human genome and sequence conservation analyses of catalytic residues suggest that 11 lack enzyme activity and are classed as pseudo-DUBs. These pseudoenzymes play important biological roles by allosterically activating catalytically competent DUBs as well as other active enzymes. Additionally, pseudoenzymes act as assembly scaffolds of macromolecular complexes. We discuss how pseudo-DUBs have lost their catalytic activity, their diverse mechanisms of action and their potential as therapeutic targets. Many known pseudo-DUBs play crucial roles in cell biology and it is likely that unstudied and overlooked pseudo-DUB genes will have equally important functions.

Emerging concepts in pseudoenzyme classification, evolution, and signaling

“…The kinase-pseudokinase pair is perhaps the most well-known example from this pseudoenzyme class (15). However, this recurring theme has recently been exemplified in the ubiquitin field, with the analysis of the BRCC36 isopeptidase complex (BRISC) and the BRCA1-A complex, in which the catalytically active JAMM (JAB1/MPN/Mov34 metalloenzyme) domain Lys 63 -specific deubiquitinase (DUB) BRCC36 is physically partnered with the pseudo-DUBs Abraxas1 and Abraxas2 (16). The BRISC complex permits cooperation between a newly discovered moonlighting function of the metabolic enzyme serine hydroxymethyltransferase 2 (SHMT2), the pseudo-DUB Abraxas2, and three tandem pseudo-ubiquitin E2 variants (UEV) domains of BRCC45 ( Fig.…”

“…The third category of pseudoenzymes possess distinct biological functions by operating as protein interaction scaffolds, generating (sub)cellular focal points that nucleate assembly of protein complexes, or regulating the localization of a binding partner. Examples Table 1, with the most profligate example to date being pre-mRNA processing-splicing factor 8 (PRPF8), which contains four pseudoenzyme domains (Table 1) that act as scaffolds for assembly of the enzymatic spliceosome complex (16,18). The further study of protein interactions made by pseudoenzyme domains ("pseudoenzyme interactomes") will provide interesting information about the role of these proteins in the cell.…”

Regulation of NFκB Signalling by Ubiquitination: A Potential Therapeutic Target in Head and Neck Squamous Cell Carcinoma?

“…The human genome encodes for eight E1 proteins (only two E1 proteins are involved in ubiquitination), around 50 E2 proteins, and over 700 E3 proteins, demonstrating the complexity of the ubiquitin system [ 41 ]. In addition, ubiquitin can be removed by deubiquitinating enzymes (DUBs), of which there has been around 100 characterized in 7 distinct families [ 42 ].…”

“…Ubiquitination is a reversible post-translational modification and can be removed by deubiquitinases (DUBs). Over 100 DUBs have currently been characterized in seven distinct families [ 42 ]: ubiquitin C-terminal hydrolases (UCHs), ubiquitin-specific proteases (USPs), ovarian tumor proteases (OTUs), the Machado-Josephin domain superfamily (MJD), the MINDY family, and the ZUFSP family members function as cysteine proteases, whereas JAB1/MPN/MOV34 metalloenzymes (JAMMs) are zinc-dependent metalloproteases [ 42 ]. These enzymes have different specificities; some cleave only one kind of ubiquitin linkage (e.g., OTULIN; M1 linkages) or multiple ubiquitin linkages (e.g., CYLD; primarily M1 and K63 linkages) [ 57 ].…”

Deubiquitinating Enzymes in Model Systems and Therapy: Redundancy and Compensation Have Implications

“…It is conceivable that if expressed and translated, the zebrafish USP15 would retain some nonenzymatic function attributable to other structural domains in the protein. In such a scenario, the zebrafish USP15 protein would act as a pseudo‐DUB, a pseudoenzyme, modulating protein–protein interactions in the manner ascribed to known pseudo‐DUBs such as USP39 and USP52, neither of which have protease activity . Although the hypothetical conversion of USP15 to a pseudo‐DUB cannot be excluded, it would be without precedent, so the more parsimonious explanation for zebrafish remains simple inactivation through genetic drift.…”