7ETR

Crystal structure of SO_1444-SO_1445 complex from Shewanella oneidensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.289 

wwPDB Validation   3D Report Full Report


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Literature

Insights into the Neutralization and DNA Binding of Toxin-Antitoxin System ParE SO-CopA SO by Structure-Function Studies.

Zhou, J.Du, X.J.Liu, Y.Gao, Z.Q.Geng, Z.Dong, Y.H.Zhang, H.

(2021) Microorganisms 9

  • DOI: https://doi.org/10.3390/microorganisms9122506
  • Primary Citation of Related Structures:  
    7ETR

  • PubMed Abstract: 

    ParE SO -CopA SO is a new type II toxin-antitoxin (TA) system in prophage CP4So that plays an essential role in circular CP4So maintenance after the excision in Shewanella oneidensis . The toxin ParE SO severely inhibits cell growth, while CopA SO functions as an antitoxin to neutralize ParE SO toxicity through direct interactions. However, the molecular mechanism of the neutralization and autoregulation of the TA operon transcription remains elusive. In this study, we determined the crystal structure of a ParE SO -CopA SO complex that adopted an open V-shaped heterotetramer with the organization of ParE SO -(CopA SO ) 2 -ParE SO . The structure showed that upon ParE SO binding, the intrinsically disordered C-terminal domain of CopA SO was induced to fold into a partially ordered conformation that bound into a positively charged and hydrophobic groove of ParE SO . Thermodynamics analysis showed the DNA-binding affinity of CopA SO was remarkably higher than that of the purified TA complex, accompanied by the enthalpy change reversion from an exothermic reaction to an endothermic reaction. These results suggested ParE SO acts as a de-repressor of the TA operon transcription at the toxin:antitoxin level of 1:1. Site-directed mutagenesis of ParE SO identified His91 as the essential residue for its toxicity by cell toxicity assays. Our structure-function studies therefore elucidated the transcriptional regulation mechanism of the ParE SO -CopA SO pair, and may help to understand the regulation of CP4So maintenance in S. oneidensis .


  • Organizational Affiliation

    Institute of Health Sciences and School of Life Science, Anhui University, Hefei 230601, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator CopG family
A, B
102Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_1445
UniProt
Find proteins for Q8EGZ2 (Shewanella oneidensis (strain MR-1))
Explore Q8EGZ2 
Go to UniProtKB:  Q8EGZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EGZ2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin module of toxin-antitoxin system RelE/StbE family
C, D
97Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: SO_1444
UniProt
Find proteins for Q8EGZ3 (Shewanella oneidensis (strain MR-1))
Explore Q8EGZ3 
Go to UniProtKB:  Q8EGZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EGZ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.289 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.404α = 90
b = 85.404β = 90
c = 110.918γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaU1732113, 31670059

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release