A family of unconventional deubiquitinases with modular chain specificity determinants

Thomas Hermanns,Christian Pichlo,Karsten Klopffleisch,Katharina F Witting,Kay Hofmann,Huib Ovaa,Ulrich Baumann,Ilka Woiwode

doi:10.1038/s41467-018-03148-5

Thomas Hermanns, Christian Pichlo + Show 6 more

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https://doi.org/10.1038/s41467-018-03148-5

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Deubiquitinating enzymes (DUBs) regulate ubiquitin signaling by trimming ubiquitin chains or removing ubiquitin from modified substrates. Similar activities exist for ubiquitin-related modifiers, although the enzymes involved are usually not related. Here, we report human ZUFSP (also known as ZUP1 and C6orf113) and fission yeast Mug105 as founding members of a DUB family different from the six known DUB classes. The crystal structure of human ZUFSP in covalent complex with propargylated ubiquitin shows that the DUB family shares a fold with UFM1- and Atg8-specific proteases, but uses a different active site more similar to canonical DUB enzymes. ZUFSP family members differ widely in linkage specificity through differential use of modular ubiquitin-binding domains (UBDs). While the minimalistic Mug105 prefers K48 chains, ZUFSP uses multiple UBDs for its K63-specific endo-DUB activity. K63 specificity, localization, and protein interaction network suggest a role for ZUFSP in DNA damage response.

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Deubiquitinating enzymes (DUBs) regulate ubiquitin signaling by trimming ubiquitin chains or removing ubiquitin from modified substrates
ubiquitin-like modifiers (UBLs) proteases typically belong to families distinct from DUBs7: SUMO and NEDD8 are cleaved by members of the SENP/ULP family, UFM1 is cleaved by the UFM1-specific protease (UFSP) family, while the autophagy modifiers ATG8 and ATG12 are cleaved by members of the autophagin (ATG4) family[8,9]
Hypothesizing that ZUFSP might be an active protease with a rearranged active site, we analyzed ZUFSP family members from a wide range of species and identified two highly conserved histidine residues, with His-491 being the best candidate for completing the active site of human ZUFSP (Supplementary Fig. 1)

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Deubiquitinating enzymes (DUBs) regulate ubiquitin signaling by trimming ubiquitin chains or removing ubiquitin from modified substrates. There are several ubiquitin-like modifiers (UBLs), which require proteases for processing their immature precursors and/ or for their deconjugation Despite their mechanistic similarities, UBL proteases typically belong to families distinct from DUBs7: SUMO and NEDD8 are cleaved by members of the SENP/ULP family, UFM1 is cleaved by the UFSP family, while the autophagy modifiers ATG8 and ATG12 are cleaved by members of the autophagin (ATG4) family[8,9]. Many DUBs and UBL proteases harbor domains or motifs for recognizing the modifier to be cleaved, or the substrate from which the modifier is removed This trend is pronounced for DUBs, where the presence of multiple ubiquitinbinding domains (UBDs) can confer specificity for ubiquitin chains of a particular linkage type[10]. A comparison of ZUFSP and Mug[105] offers unique insights into the mechanism of how the evolutionary loss (or gain) of non-catalytic ubiquitin-binding domains can profoundly change the specificity of a deubiquitinase

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