A family of unconventional deubiquitinases with modular chain specificity determinants

Nature Communications
Thomas HermannsKay Hofmann

Abstract

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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Datasets Mentioned

BETA
PXD008731

Methods Mentioned

BETA
ubiquitination
pull-down
co-immunoprecipitation
electrophoretic mobility shift
deubiquitination
affinity purification
size exclusion chromatography
electrophoresis
ion
X-ray

Software Mentioned

Coot
ray detector XDS
MaxQuant
GraphPad
Prism
phenix
SeqLogo
Andromeda

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