3WXF

Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.

Sato, Y.Goto, E.Shibata, Y.Kubota, Y.Yamagata, A.Goto-Ito, S.Kubota, K.Inoue, J.Takekawa, M.Tokunaga, F.Fukai, S.

(2015) Nat.Struct.Mol.Biol. 22: 222-229

  • DOI: 10.1038/nsmb.2970
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,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.,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.,Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, C
312Danio rerioMutation(s): 2 
Gene Names: cylda
Find proteins for E7FEV5 (Danio rerio)
Go to UniProtKB:  E7FEV5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, D
148Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.628α = 77.66
b = 65.372β = 89.04
c = 69.846γ = 89.46
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-07-30 
  • Released Date: 2015-02-11 
  • Deposition Author(s): Sato, Y., Fukai, S.

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Refinement description, Source and taxonomy
  • Version 1.2: 2020-01-01
    Type: Database references