title: Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
abstract: The tumor suppressor CYLD belongs to a ubiquitin (Ub)-specific protease (USP) family and specifically cleaves Met1- and Lys63-linked polyubiquitin chains to suppress inflammatory signaling pathways. Here, we report crystal structures representing the catalytic states of zebrafish CYLD for Met1- and Lys63-linked Ub chains and two distinct precatalytic states for Met1-linked chains. In both catalytic states, the distal Ub is bound to CYLD in a similar manner, and the scissile bond is located close to the catalytic residue, whereas the proximal Ub is bound in a manner specific to Met1- or Lys63-linked chains. Further structure-based mutagenesis experiments support the mechanism by which CYLD specifically cleaves both Met1- and Lys63-linked chains and provide insight into tumor-associated mutations of CYLD. This study provides new structural insight into the mechanisms by which USP family deubiquitinating enzymes recognize and cleave Ub chains with specific linkage types.
authors: 1] Life Science Division, Synchrotron Radiation Research Organization, University of Tokyo, Tokyo, Japan. [2] Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan. [3] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.
authors: Yusuke
authors: Y
authors: Sato
authors: Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.
authors: Eiji
authors: E
authors: Goto
authors: Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
authors: Yuri
authors: Y
authors: Shibata
authors: Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
authors: Yuji
authors: Y
authors: Kubota
authors: 1] Life Science Division, Synchrotron Radiation Research Organization, University of Tokyo, Tokyo, Japan. [2] Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan. [3] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.
authors: Atsushi
authors: A
authors: Yamagata
authors: 1] Life Science Division, Synchrotron Radiation Research Organization, University of Tokyo, Tokyo, Japan. [2] Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan. [3] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.
authors: Sakurako
authors: S
authors: Goto-Ito
authors: 1] Life Science Division, Synchrotron Radiation Research Organization, University of Tokyo, Tokyo, Japan. [2] Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan. [3] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.
authors: Keiko
authors: K
authors: Kubota
authors: 1] Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan. [2] Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
authors: Jun-ichiro
authors: J
authors: Inoue
authors: Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
authors: Mutsuhiro
authors: 0000000280273847
authors: M
authors: Takekawa
authors: Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.
authors: Fuminori
authors: F
authors: Tokunaga
authors: 1] Life Science Division, Synchrotron Radiation Research Organization, University of Tokyo, Tokyo, Japan. [2] Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan. [3] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan. [4] Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.
authors: Shuya
authors: S
authors: Fukai
mesh_terms: D001665:Binding Sites; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D057809:HEK293 Cells; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D015398:Signal Transduction; D025521:Tumor Suppressor Proteins / Q000737:chemistry* / Q000378:metabolism; D043222:Ubiquitin Thiolesterase / Q000737:chemistry; D000076084:Ubiquitin-Specific Peptidase 7; D064570:Ubiquitin-Specific Proteases / Q000737:chemistry* / Q000378:metabolism; D029961:Zebrafish Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D025521:Tumor Suppressor Proteins; D029961:Zebrafish Proteins; C464569:USP7 protein, human; D043222:Ubiquitin Thiolesterase; D000076084:Ubiquitin-Specific Peptidase 7; D064570:Ubiquitin-Specific Proteases