4BOZ

Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis.

Mevissen, T.E.T., Hospenthal, M.K., Geurink, P.P., Elliott, P.R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., Freund, S.M.V., Ovaa, H., Komander, D.

(2013) Cell 154: 169

  • DOI: 10.1016/j.cell.2013.05.046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the ...

    Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1' and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates.

    Organizational Affiliation: 

    Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN THIOESTERASE OTU1
A, D
183Homo sapiensMutation(s): 1 
Gene Names: YOD1 (DUBA8, HIN7, OTUD2)
EC: 3.4.19.12
Find proteins for Q5VVQ6 (Homo sapiens)
Go to Gene View: YOD1
Go to UniProtKB:  Q5VVQ6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-C
B, C, 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 174.790α = 90.00
b = 44.220β = 91.41
c = 84.950γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release