5NC8

Shewanella denitrificans Kef CTD in AMP bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Adenosine Monophosphate Binding Stabilizes the KTN Domain of the Shewanella denitrificans Kef Potassium Efflux System.

Pliotas, C.Grayer, S.C.Ekkerman, S.Chan, A.K.N.Healy, J.Marius, P.Bartlett, W.Khan, A.Cortopassi, W.A.Chandler, S.A.Rasmussen, T.Benesch, J.L.P.Paton, R.S.Claridge, T.D.W.Miller, S.Booth, I.R.Naismith, J.H.Conway, S.J.

(2017) Biochemistry 56: 4219-4234

  • DOI: https://doi.org/10.1021/acs.biochem.7b00300
  • Primary Citation of Related Structures:  
    5NC8

  • PubMed Abstract: 

    Ligand binding is one of the most fundamental properties of proteins. Ligand functions fall into three basic types: substrates, regulatory molecules, and cofactors essential to protein stability, reactivity, or enzyme-substrate complex formation. The regulation of potassium ion movement in bacteria is predominantly under the control of regulatory ligands that gate the relevant channels and transporters, which possess subunits or domains that contain Rossmann folds (RFs). Here we demonstrate that adenosine monophosphate (AMP) is bound to both RFs of the dimeric bacterial Kef potassium efflux system (Kef), where it plays a structural role. We conclude that AMP binds with high affinity, ensuring that the site is fully occupied at all times in the cell. Loss of the ability to bind AMP, we demonstrate, causes protein, and likely dimer, instability and consequent loss of function. Kef system function is regulated via the reversible binding of comparatively low-affinity glutathione-based ligands at the interface between the dimer subunits. We propose this interfacial binding site is itself stabilized, at least in part, by AMP binding.


  • Organizational Affiliation

    Biomedical Sciences Research Complex, University of St Andrews , North Haugh, St Andrews KY16 9ST, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium efflux system protein
A, B
237Shewanella denitrificans OS217Mutation(s): 0 
Gene Names: Sden_0368
UniProt
Find proteins for Q12SB3 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Explore Q12SB3 
Go to UniProtKB:  Q12SB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12SB3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.6α = 90
b = 71.6β = 90
c = 140.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description