Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution

EMBO J. 1997 Jul 1;16(13):3787-96. doi: 10.1093/emboj/16.13.3787.

Abstract

Ubiquitin C-terminal hydrolases catalyze the removal of adducts from the C-terminus of ubiquitin. We have determined the crystal structure of the recombinant human Ubiquitin C-terminal Hydrolase (UCH-L3) by X-ray crystallography at 1.8 A resolution. The structure is comprised of a central antiparallel beta-sheet flanked on both sides by alpha-helices. The beta-sheet and one of the helices resemble the well-known papain-like cysteine proteases, with the greatest similarity to cathepsin B. This similarity includes the UCH-L3 active site catalytic triad of Cys95, His169 and Asp184, and the oxyanion hole residue Gln89. Papain and UCH-L3 differ, however, in strand and helix connectivity, which in the UCH-L3 structure includes a disordered 20 residue loop (residues 147-166) that is positioned over the active site and may function in the definition of substrate specificity. Based upon analogy with inhibitor complexes of the papain-like enzymes, we propose a model describing the binding of ubiquitin to UCH-L3. The UCH-L3 active site cleft appears to be masked in the unliganded structure by two different segments of the enzyme (residues 9-12 and 90-94), thus implying a conformational change upon substrate binding and suggesting a mechanism to limit non-specific hydrolysis.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Crystallography, X-Ray
  • Drosophila melanogaster
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Papain / chemistry
  • Protein Structure, Secondary*
  • Recombinant Proteins / chemistry
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Thiolester Hydrolases / chemistry*
  • Ubiquitin Thiolesterase
  • Ubiquitins / metabolism

Substances

  • Recombinant Proteins
  • Ubiquitins
  • Thiolester Hydrolases
  • Ubiquitin Thiolesterase
  • Papain

Associated data

  • SWISSPROT/P09936
  • SWISSPROT/P15374
  • SWISSPROT/P35122
  • SWISSPROT/P35127