Journal: Life Sci Alliance / Year: 2023 Title: Structural insights into ubiquitin chain cleavage by ovarian tumor deubiquitinases. Authors: Sangwoo Kang / Gyuhee Kim / Minhyeong Choi / Minwoo Jeong / Gerbrand J van der Heden van Noort / Soung-Hun Roh / Donghyuk Shin / Abstract: Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. , a gram-negative intracellular bacterium, possesses an ...Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. , a gram-negative intracellular bacterium, possesses an ovarian tumor (OTU) family of deubiquitinases (Lot DUBs). Herein, we describe the molecular characteristics of Lot DUBs. We elucidated the structure of the LotA OTU1 domain and revealed that entire Lot DUBs possess a characteristic extended helical lobe that is not found in other OTU-DUBs. The structural topology of an extended helical lobe is the same throughout the Lot family, and it provides an S1' ubiquitin-binding site. Moreover, the catalytic triads of Lot DUBs resemble those of the A20-type OTU-DUBs. Furthermore, we revealed a unique mechanism by which LotA OTU domains cooperate together to distinguish the length of the chain and preferentially cleave longer K48-linked polyubiquitin chains. The LotA OTU1 domain itself cleaves K6-linked ubiquitin chains, whereas it is also essential for assisting the cleavage of longer K48-linked polyubiquitin chains by the OTU2 domain. Thus, this study provides novel insights into the structure and mechanism of action of Lot DUBs.
Organelle or cellular component: Deubiquitinase of LotA 7-544 apo state
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Supramolecule #1: Deubiquitinase of LotA 7-544 apo state
Supramolecule
Name: Deubiquitinase of LotA 7-544 apo state / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)
Organism: Legionella pneumophila (bacteria)
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.6 mg/mL
Buffer
pH: 7.6
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.
Details
This sample was monodisperse
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Electron microscopy
Microscope
TFS GLACIOS
Image recording
Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.04 e/Å2
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
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