3TMO | pdb_00003tmo

The catalytic domain of human deubiquitinase DUBA

• PDB DOI: https://doi.org/10.2210/pdb3TMO/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-31 Released: 2012-01-11 
• Deposition Author(s): Yin, J., Bosanac, I., Ma, X., Hymowitz, S., Starovasnik, M., Cochran, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.276 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

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

• PubMed: 22245969 
• DOI: https://doi.org/10.1038/nsmb.2206
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.6 kDa 
• Atom Count: 1,213 
• Modeled Residue Count: 141 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OTU domain-containing protein 5	A	184	Homo sapiens	Mutation(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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.276 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.658	α = 90
b = 66.658	β = 90
c = 82.218	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Yin, J., Bosanac, I., Ma, X., Hymowitz, S., Starovasnik, M., Cochran, A.

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2012-02-29
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary