5CRC

Structure of the SdeA DUB Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.853 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination.

Sheedlo, M.J.Qiu, J.Tan, Y.Paul, L.N.Luo, Z.Q.Das, C.

(2015) Proc.Natl.Acad.Sci.USA 112: 15090-15095

  • DOI: 10.1073/pnas.1514568112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Manipulation of the host's ubiquitin network is emerging as an important strategy for counteracting and repurposing the posttranslational modification machineries of the host by pathogens. Ubiquitin E3 ligases encoded by infectious agents are well kn ...

    Manipulation of the host's ubiquitin network is emerging as an important strategy for counteracting and repurposing the posttranslational modification machineries of the host by pathogens. Ubiquitin E3 ligases encoded by infectious agents are well known, as are a variety of viral deubiquitinases (DUBs). Bacterial DUBs have been discovered, but little is known about the structure and mechanism underlying their ubiquitin recognition. In this report, we found that members of the Legionella pneumophila SidE effector family harbor a DUB module important for ubiquitin dynamics on the bacterial phagosome. Structural analysis of this domain alone and in complex with ubiquitin vinyl methyl ester (Ub-VME) reveals unique molecular contacts used in ubiquitin recognition. Instead of relying on the Ile44 patch of ubiquitin, as commonly used in eukaryotic counterparts, the SdeADub module engages Gln40 of ubiquitin. The architecture of the active-site cleft presents an open arrangement with conformational plasticity, permitting deubiquitination of three of the most abundant polyubiquitin chains, with a distinct preference for Lys63 linkages. We have shown that this preference enables efficient removal of Lys63 linkages from the phagosomal surface. Remarkably, the structure reveals by far the most parsimonious use of molecular contacts to achieve deubiquitination, with less than 1,000 Å(2) of accessible surface area buried upon complex formation with ubiquitin. This type of molecular recognition appears to enable dual specificity toward ubiquitin and the ubiquitin-like modifier NEDD8.


    Organizational Affiliation

    Department of Chemistry, Purdue University, West Lafayette, IN 47907;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SdeA
A, B
193Legionella pneumophilaMutation(s): 0 
Find proteins for Q6RCR0 (Legionella pneumophila)
Go to UniProtKB:  Q6RCR0
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.853 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.280 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.542α = 90.00
b = 63.340β = 90.00
c = 136.508γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references
  • Version 1.2: 2015-12-16
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Author supporting evidence, Database references, Derived calculations