8YXV | pdb_00008yxv

Toxin-antitoxin complex from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.259 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural and Functional Insight Into YefM-YoeB Complex of Toxin-Antitoxin System From Streptococcus pneumoniae.

Kim, D.H.Lee, Y.C.Jin, C.Kang, S.M.Kang, S.J.Kang, H.S.Lee, B.J.

(2025) J Cell Biochem 126: e30672-e30672

  • DOI: https://doi.org/10.1002/jcb.30672
  • Primary Citation of Related Structures:  
    8YXV, 8YZG

  • PubMed Abstract: 

    Streptococcus pneumonia is a Gram-positive and facultative anaerobic bacterium that causes a number of diseases, including otitis media, community-acquired pneumonia, sepsis, and meningitis. With the emergence of antibiotic-resistant strains, there is an urgent need to develop antibiotics with a novel mechanism. The toxin-antitoxin (TA) system, which is primarily found in prokaryotes, consists of a toxin and its equivalent antitoxin genes. The YefM-YoeB module is a Type II TA system, where the YoeB toxin functions as a putative mRNA interferase upon activation, while the YefM antitoxin acts as a transcription repressor by binding to its promoter region along with YoeB. In this study, we determined the crystal structure of the YefM-YoeB complex from S. pneumoniae TIGR4 to comprehend the binding mechanism of the TA system. Furthermore, an in vitro ribonuclease activity assay was conducted to identify the ribonuclease activity of the YoeB toxin. Additionally, furthermore, the oligomeric state of the YefM-YoeB complex in solution was investigated, and a DNA-binding mode was proposed. These structural and functional insights into the YefM-YoeB complex could provide valuable information for the development of novel antibiotics targeting S. pneumonia-associated diseases.


  • Organizational Affiliation

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin75Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: SP_1741
UniProt
Find proteins for A0A0H2UR92 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2UR92 
Go to UniProtKB:  A0A0H2UR92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UR92
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative mRNA interferase YoeBB [auth F],
E,
H [auth K],
K [auth L]
84Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: SP_1740
UniProt
Find proteins for A0A0H2URH3 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2URH3 
Go to UniProtKB:  A0A0H2URH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2URH3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.782α = 90
b = 63.402β = 128.8
c = 149.556γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release