Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains

Nature. 2008 Sep 18;455(7211):358-62. doi: 10.1038/nature07254. Epub 2008 Aug 31.


Deubiquitinating enzymes (DUBs) remove ubiquitin from conjugated substrates to regulate various cellular processes. The Zn(2+)-dependent DUBs AMSH and AMSH-LP regulate receptor trafficking by specifically cleaving Lys 63-linked polyubiquitin chains from internalized receptors. Here we report the crystal structures of the human AMSH-LP DUB domain alone and in complex with a Lys 63-linked di-ubiquitin at 1.2 A and 1.6 A resolutions, respectively. The AMSH-LP DUB domain consists of a Zn(2+)-coordinating catalytic core and two characteristic insertions, Ins-1 and Ins-2. The distal ubiquitin interacts with Ins-1 and the core, whereas the proximal ubiquitin interacts with Ins-2 and the core. The core and Ins-1 form a catalytic groove that accommodates the Lys 63 side chain of the proximal ubiquitin and the isopeptide-linked carboxy-terminal tail of the distal ubiquitin. This is the first reported structure of a DUB in complex with an isopeptide-linked ubiquitin chain, which reveals the mechanism for Lys 63-linkage-specific deubiquitination by AMSH family members.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Catalysis
  • Conserved Sequence
  • Crystallography, X-Ray
  • Endopeptidases / chemistry
  • Endopeptidases / metabolism
  • Endosomal Sorting Complexes Required for Transport
  • Humans
  • Kinetics
  • Lysine / metabolism*
  • Mice
  • Models, Molecular
  • Peptide Hydrolases
  • Polyubiquitin / chemistry*
  • Polyubiquitin / genetics
  • Polyubiquitin / metabolism*
  • Protein Structure, Tertiary
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism
  • Structure-Activity Relationship
  • Substrate Specificity
  • Ubiquitin Thiolesterase / chemistry*
  • Ubiquitin Thiolesterase / genetics
  • Ubiquitin Thiolesterase / metabolism*


  • Endosomal Sorting Complexes Required for Transport
  • RPN11 protein, S cerevisiae
  • STAMBP protein, human
  • Saccharomyces cerevisiae Proteins
  • Polyubiquitin
  • Endopeptidases
  • Peptide Hydrolases
  • STAMBPL1 protein, human
  • Ubiquitin Thiolesterase
  • Lysine

Associated data

  • PDB/2ZNR
  • PDB/2ZNV