5GVI

Zebrafish USP30 in complex with Lys6-linked diubiquitin

Summary for 5GVI

• Entry DOI: 10.2210/pdb5gvi/pdb
• Descriptor: Ubiquitin carboxyl-terminal hydrolase 30, ubiquitin, ZINC ION, ... (5 entities in total)
• Functional Keywords: complex, mitophagy, hydrolase-signaling protein complex, hydrolase/signaling protein
• Biological source: Danio rerio (Zebrafish); More
• Cellular location: Ubiquitin: Cytoplasm : P62983 P62983
• Total number of polymer chains: 3
• Total formula weight: 67355.39

Authors

Sato, Y.,Fukai, S. (deposition date: 2016-09-05, release date: 2017-09-13, Last modification date: 2024-10-09)

Primary citation

Sato, Y.,Okatsu, K.,Saeki, Y.,Yamano, K.,Matsuda, N.,Kaiho, A.,Yamagata, A.,Goto-Ito, S.,Ishikawa, M.,Hashimoto, Y.,Tanaka, K.,Fukai, S.
Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30
Nat. Struct. Mol. Biol., 24:911-919, 2017

PubMed Abstract: Parkin ubiquitin (Ub) ligase (also known as PARK2) ubiquitinates damaged mitochondria for their clearance and quality control. USP30 deubiquitinase opposes parkin-mediated Ub-chain formation on mitochondria by preferentially cleaving Lys6-linked Ub chains. Here, we report the crystal structure of zebrafish USP30 in complex with a Lys6-linked diubiquitin (diUb or Ub) at 1.87-Å resolution. The distal Ub-recognition mechanism of USP30 is similar to those of other USP family members, whereas Phe4 and Thr12 of the proximal Ub are recognized by a USP30-specific surface. Structure-based mutagenesis showed that the interface with the proximal Ub is critical for the specific cleavage of Lys6-linked Ub chains, together with the noncanonical catalytic triad composed of Cys-His-Ser. The structural findings presented here reveal a mechanism for Lys6-linkage-specific deubiquitination.

PubMed: 28945247
DOI: 10.1038/nsmb.3469

Experimental method

X-RAY DIFFRACTION (1.87 Å)