6S5D

Square conformation of KtrA R16A mutant ring with bound ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.

Teixeira-Duarte, C.M.Fonseca, F.Morais Cabral, J.H.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.50661
  • Primary Citation of Related Structures:  
    6S2J, 6S5B, 6S5C, 6S5D, 6S5E, 6S5G, 6S5N, 6S5O, 6S7R

  • PubMed Abstract: 

    RCK domains regulate the activity of K + channels and transporters in eukaryotic and prokaryotic organisms by responding to ions or nucleotides. The mechanisms of RCK activation by Ca 2+ in the eukaryotic BK and bacterial MthK K + channels are well understood. However, the molecular details of activation in nucleotide-dependent RCK domains are not clear. Through a functional and structural analysis of the mechanism of ATP activation in KtrA, a RCK domain from the B. subtilis KtrAB cation channel, we have found that activation by nucleotide requires binding of cations to an intra-dimer interface site in the RCK dimer. In particular, divalent cations are coordinated by the γ-phosphates of bound-ATP, tethering the two subunits and stabilizing the active state conformation. Strikingly, the binding site residues are highly conserved in many different nucleotide-dependent RCK domains, indicating that divalent cations are a general cofactor in the regulatory mechanism of many nucleotide-dependent RCK domains.


  • Organizational Affiliation

    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ktr system potassium uptake protein A
A, B
222Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: ktrAyuaABSU31090
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: 3.39 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.572α = 90
b = 121.572β = 90
c = 83.726γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BIA-BQM/29863/2017
Fundacao para a Ciencia e a TecnologiaPortugalPOCI-01-0145-FEDER-007274

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description