6S5B

Non-square conformation of KtrA R16K mutant ring with bound ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.052 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.7554/eLife.50661
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RCK domains regulate the activity of K <sup>+ </sup> channels and transporters in eukaryotic and prokaryotic organisms by responding to ions or nucleotides. The mechanisms of RCK activation by Ca <sup>2+ </sup> in the eukaryotic BK and bacterial MthK ...

    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

    Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ktr system potassium uptake protein A
A, B, C, D, E, F, G, H
222Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: ktrA (yuaA)
Find proteins for O32080 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O32080
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.052 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.818α = 90.00
b = 137.429β = 90.00
c = 202.617γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2020-01-08
    Type: Initial release