6L8E

Crystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system.

Xue, L.Yue, J.Ke, J.Khan, M.H.Wen, W.Sun, B.Zhu, Z.Niu, L.

(2020) Nucleic Acids Res 48: 10527-10541

  • DOI: 10.1093/nar/gkaa706
  • Primary Citation of Related Structures:  
    6L8E, 6L8F, 7CUA

  • PubMed Abstract: 
  • YoeB-YefM, the widespread type II toxin-antitoxin (TA) module, binds to its own promoter to autoregulate its transcription: repress or induce transcription under normal or stress conditions, respectively. It remains unclear how YoeB-YefM regulates its transcription depending on the YoeB to YefM TA ratio ...

    YoeB-YefM, the widespread type II toxin-antitoxin (TA) module, binds to its own promoter to autoregulate its transcription: repress or induce transcription under normal or stress conditions, respectively. It remains unclear how YoeB-YefM regulates its transcription depending on the YoeB to YefM TA ratio. We find that YoeB-YefM complex from S.aureus exists as two distinct oligomeric assemblies: heterotetramer (YoeB-YefM2-YoeB) and heterohexamer (YoeB-YefM2-YefM2-YoeB) with low and high DNA-binding affinities, respectively. Structures of the heterotetramer alone and heterohexamer bound to promoter DNA reveals that YefM C-terminal domain undergoes disorder to order transition upon YoeB binding, which allosterically affects the conformation of N-terminal DNA-binding domain. At TA ratio of 1:2, unsaturated binding of YoeB to the C-terminal regions of YefM dimer forms an optimal heterohexamer for DNA binding, and two YefM dimers with N-terminal domains dock into the adjacent major grooves of DNA to specifically recognize the 5'-TTGTACAN6AGTACAA-3' palindromic sequence, resulting in transcriptional repression. In contrast, at TA ratio of 1:1, binding of two additional YoeB molecules onto the heterohexamer induces the completely ordered conformation of YefM and disassembles the heterohexamer into two heterotetramers, which are unable to bind the promoter DNA optimally due to steric clashes, hence derepresses TA operon transcription.


    Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YefM AntitoxinA, B, C, D, I, J, K, L83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: SAOUHSC_02692
UniProt
Find proteins for Q2G285 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G285 
Go to UniProtKB:  Q2G285
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
YoeB toxinE, F, M, N88Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: SAOUHSC_02691
UniProt
Find proteins for Q2G286 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G286 
Go to UniProtKB:  Q2G286
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (26-mer)G, O26synthetic construct
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (26-mer)H, P26synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.352α = 90
b = 151.352β = 90
c = 183.778γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-11-06 
  • Released Date: 2020-09-02 
  • Deposition Author(s): Yue, J., Xue, L.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaU1632124 to L.N.

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references