7V5Y

Crystal structure of hexameric complex of Sa2YoeB-Sa2YefM toxin-antitoxin from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


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Literature

The two paralogous copies of the YoeB-YefM toxin-antitoxin module in Staphylococcus aureus differ in DNA binding and recognition patterns.

Xue, L.Khan, M.H.Yue, J.Zhu, Z.Niu, L.

(2022) J Biol Chem 298: 101457-101457

  • DOI: 10.1016/j.jbc.2021.101457
  • Primary Citation of Related Structures:  
    7V5Y, 7V5Z, 7V6W

  • PubMed Abstract: 
  • Toxin-antitoxin (TA) systems are ubiquitous regulatory modules for bacterial growth and cell survival following stress. YefM-YoeB, the most prevalent type II TA system, is present in a variety of bacterial species. In Staphylococcus aureus, the YefM-YoeB system exists as two independent paralogous copies ...

    Toxin-antitoxin (TA) systems are ubiquitous regulatory modules for bacterial growth and cell survival following stress. YefM-YoeB, the most prevalent type II TA system, is present in a variety of bacterial species. In Staphylococcus aureus, the YefM-YoeB system exists as two independent paralogous copies. Our previous research resolved crystal structures of the two oligomeric states (heterotetramer and heterohexamer-DNA ternary complex) of the first paralog as well as the molecular mechanism of transcriptional autoregulation of this module. However, structural details reflecting molecular diversity in both paralogs have been relatively unexplored. To understand the molecular mechanism of how Sa 2 YoeB and Sa 2 YefM regulate their own transcription and how each paralog functions independently, we solved a series of crystal structures of the Sa 2 YoeB-Sa 2 YefM. Our structural and biochemical data demonstrated that both paralogous copies adopt similar mechanisms of transcriptional autoregulation. In addition, structural analysis suggested that molecular diversity between the two paralogs might be reflected in the interaction profile of YefM and YoeB and the recognition pattern of promoter DNA by YefM. Interaction analysis revealed unique conformational and activating force effected by the interface between Sa 2 YoeB and Sa 2 YefM. In addition, the recognition pattern analysis demonstrated that residues Thr 7 and Tyr 14 of Sa 2 YefM specifically recognizes the flanking sequences (G and C) of the promoter DNA. Together, these results provide the structural insights into the molecular diversity and independent function of the paralogous copies of the YoeB-YefM TA system.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China. Electronic address: lwniu@ustc.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AntitoxinC [auth A],
A [auth B],
D [auth C],
B [auth D]
85Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: SAOUHSC_02757
UniProt
Find proteins for Q2FVF7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FVF7 
Go to UniProtKB:  Q2FVF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FVF7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative mRNA interferase YoeBE, F88Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: SAOUHSC_02756
UniProt
Find proteins for Q2FVF8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FVF8 
Go to UniProtKB:  Q2FVF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FVF8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.989α = 90
b = 66.984β = 105.21
c = 82.361γ = 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 Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references