Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

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This is version 1.3 of the entry. See complete history


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

Johnston, S.C.Larsen, C.N.Cook, W.J.Wilkinson, K.D.Hill, C.P.

(1997) EMBO J 16: 3787-3796

  • DOI: https://doi.org/10.1093/emboj/16.13.3787
  • Primary Citation of Related Structures:  

  • PubMed 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.

  • Organizational Affiliation

    Biochemistry Department, University of Utah, Salt Lake City 84132, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN C-TERMINAL HYDROLASE UCH-L3230Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P15374 (Homo sapiens)
Explore P15374 
Go to UniProtKB:  P15374
PHAROS:  P15374
GTEx:  ENSG00000118939 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15374
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.6α = 90
b = 60.9β = 90
c = 81.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Other