1XD3

Crystal structure of UCHL3-UbVME complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate

Misaghi, S.Galardy, P.J.Meester, W.J.N.Ovaa, H.Ploegh, H.L.Gaudet, R.

(2005) J Biol Chem 280: 1512-1520

  • DOI: 10.1074/jbc.M410770200
  • Primary Citation of Related Structures:  
    1XD3

  • PubMed Abstract: 
  • Ubiquitin C-terminal hydrolases (UCHs) comprise a family of small ubiquitin-specific proteases of uncertain function. Although no cellular substrates have been identified for UCHs, their highly tissue-specific expression patterns and the association ...

    Ubiquitin C-terminal hydrolases (UCHs) comprise a family of small ubiquitin-specific proteases of uncertain function. Although no cellular substrates have been identified for UCHs, their highly tissue-specific expression patterns and the association of UCH-L1 mutations with human disease strongly suggest a critical role. The structure of the yeast UCH Yuh1-ubiquitin aldehyde complex identified an active site crossover loop predicted to limit the size of suitable substrates. We report the 1.45 A resolution crystal structure of human UCH-L3 in complex with the inhibitor ubiquitin vinylmethylester, an inhibitor that forms a covalent adduct with the active site cysteine of ubiquitin-specific proteases. This structure confirms the predicted mechanism of the inhibitor and allows the direct comparison of a UCH family enzyme in the free and ligand-bound state. We also show the efficient hydrolysis by human UCH-L3 of a 13-residue peptide in isopeptide linkage with ubiquitin, consistent with considerable flexibility in UCH substrate size. We propose a model for the catalytic cycle of UCH family members which accounts for the hydrolysis of larger ubiquitin conjugates.


    Related Citations: 
    • Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family
      Borodovsky, A., Ovaa, H., Kolli, N., Gan-Erdene, T., Wilkinson, K.D., Ploegh, H.L., Kessler, B.M.
      (2002) Chem Biol 9: 1149
    • A novel active site-directed probe specific for deubiquitinating enzymes reveals proteasome association of USP14
      Borodovsky, A., Kessler, B.M., Casagrande, R., Overkleeft, H.S., Wilkinson, K.D., Ploegh, H.L.
      (2001) EMBO J 20: 5187
    • 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
    • Structural basis for the specificity of ubiquitin C-terminal hydrolases
      Johnston, S.C., Riddle, S.M., Cohen, R.E., Hill, C.P.
      (1999) EMBO J 18: 3877

    Organizational Affiliation

    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin Carboxyl-terminal esterase L3AC230Homo sapiensMutation(s): 0 
Gene Names: UCHL3
EC: 3.4.19.12
Find proteins for P15374 (Homo sapiens)
Explore P15374 
Go to UniProtKB:  P15374
NIH Common Fund Data Resources
PHAROS  P15374
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBC proteinBD75Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GVE
Query on GVE

Download CCD File 
B, D
METHYL 4-AMINOBUTANOATE
C5 H11 N O2
KVQGGLZHHFGHPU-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.11α = 86.12
b = 49.29β = 75.03
c = 67.62γ = 76.78
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance