3O65

Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Josephin-Ubiquitin Complex: EVOLUTIONARY RESTRAINTS ON ATAXIN-3 DEUBIQUITINATING ACTIVITY.

Weeks, S.D.Grasty, K.C.Hernandez-Cuebas, L.Loll, P.J.

(2011) J.Biol.Chem. 286: 4555-4565

  • DOI: 10.1074/jbc.M110.177360

  • PubMed Abstract: 
  • The Josephin domain is a conserved cysteine protease domain found in four human deubiquitinating enzymes: ataxin-3, the ataxin-3-like protein (ATXN3L), Josephin-1, and Josephin-2. Josephin domains from these four proteins were purified and assayed fo ...

    The Josephin domain is a conserved cysteine protease domain found in four human deubiquitinating enzymes: ataxin-3, the ataxin-3-like protein (ATXN3L), Josephin-1, and Josephin-2. Josephin domains from these four proteins were purified and assayed for their ability to cleave ubiquitin substrates. Reaction rates differed markedly both among the different proteins and for different substrates with a given protein. The ATXN3L Josephin domain is a significantly more efficient enzyme than the ataxin-3 domain despite their sharing 85% sequence identity. To understand the structural basis of this difference, the 2.6 Å x-ray crystal structure of the ATXN3L Josephin domain in complex with ubiquitin was determined. Although ataxin-3 and ATXN3L adopt similar folds, they bind ubiquitin in different, overlapping sites. Mutations were made in ataxin-3 at selected positions, introducing the corresponding ATXN3L residue. Only three such mutations are sufficient to increase the catalytic activity of the ataxin-3 domain to levels comparable with that of ATXN3L, suggesting that ataxin-3 has been subject to evolutionary restraints that keep its deubiquitinating activity in check.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative ataxin-3-like protein
A, C, E, G
191Homo sapiensMutation(s): 0 
Gene Names: ATXN3L (ATX3L, MJDL)
EC: 3.4.19.12
Find proteins for Q9H3M9 (Homo sapiens)
Go to Gene View: ATXN3L
Go to UniProtKB:  Q9H3M9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, D, F, H
76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C, E, G
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
NEH
Query on NEH
B, D, F, H
NON-POLYMERC2 H7 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 159.150α = 90.00
b = 159.150β = 90.00
c = 146.290γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
XDSdata reduction
RESOLVEphasing
PHENIXphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description