8POO

Low resolution structure of inactive conformation of the Ktr cation channel in presence of ATP and c-di-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.77 Å
  • R-Value Free: 0.426 
  • R-Value Work: 0.405 
  • R-Value Observed: 0.407 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

c-di-AMP determines the hierarchical organization of bacterial RCK proteins.

Rocha, R.Jorge, J.M.P.Teixeira-Duarte, C.M.Figueiredo-Costa, I.R.Cereija, T.B.Ferreira-Teixeira, P.F.Herzberg, C.Stulke, J.Morais-Cabral, J.H.

(2024) Proc Natl Acad Sci U S A 121: e2318666121-e2318666121

  • DOI: https://doi.org/10.1073/pnas.2318666121
  • Primary Citation of Related Structures:  
    8POO

  • PubMed Abstract: 

    In bacteria, intracellular K + is involved in the regulation of membrane potential, cytosolic pH, and cell turgor as well as in spore germination, environmental adaptation, cell-to-cell communication in biofilms, antibiotic sensitivity, and infectivity. The second messenger cyclic-di-AMP (c-di-AMP) has a central role in modulating the intracellular K + concentration in many bacterial species, controlling transcription and function of K + channels and transporters. However, our understanding of how this regulatory network responds to c-di-AMP remains poor. We used the RCK (Regulator of Conductance of K + ) proteins that control the activity of Ktr channels in Bacillus subtilis as a model system to analyze the regulatory function of c-di-AMP with a combination of in vivo and in vitro functional and structural characterization. We determined that the two RCK proteins (KtrA and KtrC) are neither physiologically redundant or functionally equivalent. KtrC is the physiologically dominant RCK protein in the regulation of Ktr channel activity. In explaining this hierarchical organization, we found that, unlike KtrA, KtrC is very sensitive to c-di-AMP inactivation and lack of c-di-AMP regulation results in RCK protein toxicity, most likely due to unregulated K + flux. We also found that KtrC can assemble with KtrA, conferring c-di-AMP regulation to the functional KtrA/KtrC heteromers and potentially compensating KtrA toxicity. Altogether, we propose that the central role of c-di-AMP in the control of the K + machinery, by modulating protein levels through gene transcription and by regulating protein activity, has determined the evolutionary selection of KtrC as the dominant RCK protein, shaping the hierarchical organization of regulatory components of the K + machinery.


  • Organizational Affiliation

    Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ktr system potassium uptake protein BA [auth I],
B [auth J],
C [auth A],
D [auth B]
445Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ktrByubGBSU31100
Membrane Entity: Yes 
UniProt
Find proteins for O32081 (Bacillus subtilis (strain 168))
Explore O32081 
Go to UniProtKB:  O32081
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32081
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ktr system potassium uptake protein AE [auth C],
F [auth D],
G [auth E],
H [auth G]
288Bacillus subtilis subsp. subtilis str. 168Mutation(s): 2 
Gene Names: ktrAyuaABSU31090
Membrane Entity: Yes 
UniProt
Find proteins for O32080 (Bacillus subtilis (strain 168))
Explore O32080 
Go to UniProtKB:  O32080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32080
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.77 Å
  • R-Value Free: 0.426 
  • R-Value Work: 0.405 
  • R-Value Observed: 0.407 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.795α = 90
b = 143.686β = 112.372
c = 160.669γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugal--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release