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 
  • R-Value Observed: 0.192 

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:  
    3TMO, 3TMP

  • 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 single residue, Ser177, is both necessary and sufficient to activate the enzyme ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OTU domain-containing protein 5A, C, E, G184Homo sapiensMutation(s): 0 
Gene Names: DUBA, OTUD5
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96G74 (Homo sapiens)
Explore Q96G74 
Go to UniProtKB:  Q96G74
PHAROS:  Q96G74
GTEx:  ENSG00000068308 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96G74
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CB, D, F, H76Homo sapiensMutation(s): 0 
Gene Names: UBC, ubiquitin aldehyde
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Protein Feature View
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  • Reference Sequence
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 
  • R-Value Observed: 0.192 
  • 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
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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