The structure of the CYLD USP domain explains its specificity for Lys63-linked polyubiquitin and reveals a B box module

Mol Cell. 2008 Feb 29;29(4):451-64. doi: 10.1016/j.molcel.2007.12.018.


The tumor suppressor CYLD antagonizes NF-kappaB and JNK signaling by disassembly of Lys63-linked ubiquitin chains synthesized in response to cytokine stimulation. Here we describe the crystal structure of the CYLD USP domain, revealing a distinctive architecture that provides molecular insights into its specificity toward Lys63-linked polyubiquitin. We identify regions of the USP domain responsible for this specificity and demonstrate endodeubiquitinase activity toward such chains. Pathogenic truncations of the CYLD C terminus, associated with the hypertrophic skin tumor cylindromatosis, disrupt the USP domain, accounting for loss of CYLD catalytic activity. A small zinc-binding B box domain, similar in structure to other crossbrace Zn-binding folds--including the RING domain found in E3 ubiquitin ligases--is inserted within the globular core of the USP domain. Biochemical and functional characterization of the B box suggests a role as a protein-interaction module that contributes to determining the subcellular localization of CYLD.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Cell Line
  • Crystallography, X-Ray
  • Deubiquitinating Enzyme CYLD
  • Genes, Tumor Suppressor
  • Humans
  • JNK Mitogen-Activated Protein Kinases / antagonists & inhibitors
  • JNK Mitogen-Activated Protein Kinases / metabolism
  • Lysine / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • NF-kappa B / metabolism
  • Neoplasms / genetics
  • Polyubiquitin / chemistry
  • Polyubiquitin / genetics
  • Polyubiquitin / metabolism*
  • Protein Structure, Tertiary*
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Sequence Alignment
  • Signal Transduction / physiology
  • Substrate Specificity
  • Tumor Suppressor Proteins / chemistry*
  • Tumor Suppressor Proteins / classification
  • Tumor Suppressor Proteins / genetics
  • Tumor Suppressor Proteins / metabolism*
  • Ubiquitin Thiolesterase / chemistry
  • Ubiquitin Thiolesterase / genetics
  • Ubiquitin-Specific Peptidase 7
  • Zinc / metabolism


  • NF-kappa B
  • Recombinant Fusion Proteins
  • Tumor Suppressor Proteins
  • Polyubiquitin
  • JNK Mitogen-Activated Protein Kinases
  • CYLD protein, human
  • Deubiquitinating Enzyme CYLD
  • USP7 protein, human
  • Ubiquitin Thiolesterase
  • Ubiquitin-Specific Peptidase 7
  • Zinc
  • Lysine

Associated data

  • PDB/2VHF