5J4I

Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2 Angstroem resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.207 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.

Ilgu, H.Jeckelmann, J.M.Gapsys, V.Ucurum, Z.de Groot, B.L.Fotiadis, D.

(2016) Proc.Natl.Acad.Sci.USA 113: 10358-10363

  • DOI: 10.1073/pnas.1605442113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pathogenic enterobacteria need to survive the extreme acidity of the stomach to successfully colonize the human gut. Enteric bacteria circumvent the gastric acid barrier by activating extreme acid-resistance responses, such as the arginine-dependent ...

    Pathogenic enterobacteria need to survive the extreme acidity of the stomach to successfully colonize the human gut. Enteric bacteria circumvent the gastric acid barrier by activating extreme acid-resistance responses, such as the arginine-dependent acid resistance system. In this response, l-arginine is decarboxylated to agmatine, thereby consuming one proton from the cytoplasm. In Escherichia coli, the l-arginine/agmatine antiporter AdiC facilitates the export of agmatine in exchange of l-arginine, thus providing substrates for further removal of protons from the cytoplasm and balancing the intracellular pH. We have solved the crystal structures of wild-type AdiC in the presence and absence of the substrate agmatine at 2.6-Å and 2.2-Å resolution, respectively. The high-resolution structures made possible the identification of crucial water molecules in the substrate-binding sites, unveiling their functional roles for agmatine release and structure stabilization, which was further corroborated by molecular dynamics simulations. Structural analysis combined with site-directed mutagenesis and the scintillation proximity radioligand binding assay improved our understanding of substrate binding and specificity of the wild-type l-arginine/agmatine antiporter AdiC. Finally, we present a potential mechanism for conformational changes of the AdiC transport cycle involved in the release of agmatine into the periplasmic space of E. coli.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland; Swiss National Centre of Competence in Research TransCure, University of Bern, CH-3012 Bern, Switzerland;,Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland; Swiss National Centre of Competence in Research TransCure, University of Bern, CH-3012 Bern, Switzerland; dimitrios.fotiadis@ibmm.unibe.ch.,Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginine/agmatine antiporter
A, B
453Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: adiC (aniC, yjdD, yjdE)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Amino Acid/Polyamine/Organocation (APC) Superfamily
Protein: 
AdiC Arginine:Agmatine Antiporter
Find proteins for P60061 (Escherichia coli (strain K12))
Go to UniProtKB:  P60061
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.207 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.739α = 90.00
b = 175.424β = 90.00
c = 73.148γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_162581

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2016-09-21
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence