3TMP

The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Phosphorylation-dependent activity of the deubiquitinase DUBA.

Huang, O.W., Ma, X., Yin, J., Flinders, J., Maurer, T., Kayagaki, N., Phung, Q., Bosanac, I., Arnott, D., Dixit, V.M., Hymowitz, S.G., Starovasnik, M.A., Cochran, A.G.

(2012) Nat.Struct.Mol.Biol. 19: 171-175

  • DOI: 10.1038/nsmb.2206
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Addition and removal of ubiquitin or ubiquitin chains to and from proteins is a tightly regulated process that contributes to cellular signaling and protein stability. Here we show that phosphorylation of the human deubiquitinase DUBA (OTUD5) at a si ...

    Addition and removal of ubiquitin or ubiquitin chains to and from proteins is a tightly regulated process that contributes to cellular signaling and protein stability. Here we show that phosphorylation of the human deubiquitinase DUBA (OTUD5) at a single residue, Ser177, is both necessary and sufficient to activate the enzyme. The crystal structure of the ubiquitin aldehyde adduct of active DUBA reveals a marked cooperation between phosphorylation and substrate binding. An intricate web of interactions involving the phosphate and the C-terminal tail of ubiquitin cause DUBA to fold around its substrate, revealing why phosphorylation is essential for deubiquitinase activity. Phosphoactivation of DUBA represents an unprecedented mode of protease regulation and a clear link between two major cellular signal transduction systems: phosphorylation and ubiquitin modification.

    Organizational Affiliation: 

    Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OTU domain-containing protein 5
A, C, E, G
184Homo sapiensMutation(s): 0 
Gene Names: OTUD5
EC: 3.4.19.12
Find proteins for Q96G74 (Homo sapiens)
Go to Gene View: OTUD5
Go to UniProtKB:  Q96G74
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, C, E, G
L-PEPTIDE LINKINGC3 H8 N O6 PSER
GLZ
Query on GLZ
B, D, F, H
L-PEPTIDE LINKINGC2 H5 N OGLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 59.532α = 90.26
b = 65.296β = 93.53
c = 65.843γ = 99.28
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Database references