Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.21 kDa 
• Atom Count: 1764 
• Residue Count: 206 
• Unique protein chains: 1

1UCH

DEUBIQUITINATING ENZYME UCH-L3 (HUMAN) AT 1.8 ANGSTROM RESOLUTION

• DOI: 10.2210/pdb1UCH/pdb

• Classification: CYSTEINE PROTEASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-10-06 Released: 1998-01-28 
• Deposition Author(s): Johnston, S.C., Larsen, C.N., Cook, W.J., Wilkinson, K.D., Hill, C.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.294 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 

Literature

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

• PubMed: 9233788 
• DOI: 10.1093/emboj/16.13.3787
• Primary Citation of Related Structures:  
  1UCH


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN C-TERMINAL HYDROLASE UCH-L3	A	230	Homo sapiens	Mutation(s): 0  Gene Names: UCHL3 EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
Find proteins for P15374 (Homo sapiens) Explore P15374  Go to UniProtKB:  P15374
NIH Common Fund Data Resources
PHAROS:  P15374 GTEx:  ENSG00000118939

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 48.6	α = 90
b = 60.9	β = 90
c = 81.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-10-06 
• Released Date: 1998-01-28 
Deposition Author(s): Johnston, S.C., Larsen, C.N., Cook, W.J., Wilkinson, K.D., Hill, C.P.

Revision History 

• 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