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 

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

  • 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: 
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin Carboxyl-terminal esterase L3
A, C
230Homo sapiensMutation(s): 0 
Gene Names: UCHL3
EC: 3.4.19.12
Find proteins for P15374 (Homo sapiens)
Go to Gene View: UCHL3
Go to UniProtKB:  P15374
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBC protein
B, D
75Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GVE
Query on GVE

Download SDF File 
Download CCD File 
B, D
METHYL 4-AMINOBUTANOATE
C5 H11 N O2
KVQGGLZHHFGHPU-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 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.110α = 86.12
b = 49.290β = 75.03
c = 67.620γ = 76.78
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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