Structures of CYLD USP With Met1- Or Lys63-linked Diubiquitin Reveal Mechanisms for Dual Specificity

Nat Struct Mol Biol. 2015 Mar;22(3):222-9. doi: 10.1038/nsmb.2970. Epub 2015 Feb 16.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Conserved Sequence
  • Crystallography, X-Ray
  • HEK293 Cells
  • Humans
  • Kinetics
  • Models, Molecular
  • Protein Structure, Tertiary
  • Sequence Analysis, Protein
  • Signal Transduction
  • Tumor Suppressor Proteins / chemistry*
  • Tumor Suppressor Proteins / metabolism
  • Ubiquitin Thiolesterase / chemistry
  • Ubiquitin-Specific Peptidase 7
  • Ubiquitin-Specific Proteases / chemistry*
  • Ubiquitin-Specific Proteases / metabolism
  • Zebrafish Proteins / chemistry*
  • Zebrafish Proteins / metabolism

Substances

  • Tumor Suppressor Proteins
  • Zebrafish Proteins
  • USP7 protein, human
  • Ubiquitin Thiolesterase
  • Ubiquitin-Specific Peptidase 7
  • Ubiquitin-Specific Proteases

Associated data

  • PDB/3WXE
  • PDB/3WXF
  • PDB/3WXG