2G45

Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The Ubiquitin Binding Domain ZnF UBP Recognizes the C-Terminal Diglycine Motif of Unanchored Ubiquitin.

Reyes-Turcu, F.E., Horton, J.R., Mullally, J.E., Heroux, A., Cheng, X., Wilkinson, K.D.

(2006) Cell 124: 1197-1208

  • DOI: 10.1016/j.cell.2006.02.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Ubiquitin binding proteins regulate the stability, function, and/or localization of ubiquitinated proteins. Here we report the crystal structures of the zinc-finger ubiquitin binding domain (ZnF UBP) from the deubiquitinating enzyme isopeptidase T (I ...

    Ubiquitin binding proteins regulate the stability, function, and/or localization of ubiquitinated proteins. Here we report the crystal structures of the zinc-finger ubiquitin binding domain (ZnF UBP) from the deubiquitinating enzyme isopeptidase T (IsoT, or USP5) alone and in complex with ubiquitin. Unlike other ubiquitin binding domains, this domain contains a deep binding pocket where the C-terminal diglycine motif of ubiquitin is inserted, thus explaining the specificity of IsoT for an unmodified C terminus on the proximal subunit of polyubiquitin. Mutations in the domain demonstrate that it is required for optimal catalytic activation of IsoT. This domain is present in several other protein families, and the ZnF UBP domain from an E3 ligase also requires the C terminus of ubiquitin for binding. These data suggest that binding the ubiquitin C terminus may be necessary for the function of other proteins.

    Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 5
A, D
129Homo sapiensMutation(s): 0 
Gene Names: USP5 (ISOT)
EC: 3.4.19.12
Find proteins for P45974 (Homo sapiens)
Go to Gene View: USP5
Go to UniProtKB:  P45974
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, E
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.229 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 68.074α = 90.00
b = 68.074β = 90.00
c = 225.345γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
CNSrefinement
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance