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



Entry History 

Deposition Data

Revision History 

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