Structure of AdiC(N101A) in the open-to-out Arg+ bound conformation

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Molecular basis of substrate-induced permeation by an amino acid antiporter.

Kowalczyk, L.Ratera, M.Paladino, A.Bartoccioni, P.Errasti-Murugarren, E.Valencia, E.Portella, G.Bial, S.Zorzano, A.Fita, I.Orozco, M.Carpena, X.Vazquez-Ibar, J.L.Palacin, M.

(2011) Proc Natl Acad Sci U S A 108: 3935-3940

  • DOI: https://doi.org/10.1073/pnas.1018081108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Transporters of the amino acid, polyamine and organocation (APC) superfamily play essential roles in cell redox balance, cancer, and aminoacidurias. The bacterial L-arginine/agmatine antiporter, AdiC, is the main APC structural paradigm and shares the "5 + 5 inverted repeat" fold found in other families like the Na(+)-coupled neurotransmitter transporters. The available AdiC crystal structures capture two states of its transport cycle: the open-to-out apo and the outward-facing Arg(+)-bound occluded. However, the role of Arg(+) during the transition between these two states remains unknown. Here, we report the crystal structure at 3.0 Å resolution of an Arg(+)-bound AdiC mutant (N101A) in the open-to-out conformation, completing the picture of the major conformational states during the transport cycle of the 5 + 5 inverted repeat fold-transporters. The N101A structure is an intermediate state between the previous known AdiC conformations. The Arg(+)-guanidinium group in the current structure presents high mobility and delocalization, hampering substrate occlusion and resulting in a low translocation rate. Further analysis supports that proper coordination of this group with residues Asn101 and Trp293 is required to transit to the occluded state, providing the first clues on the molecular mechanism of substrate-induced fit in a 5 + 5 inverted repeat fold-transporter. The pseudosymmetry found between repeats in AdiC, and in all fold-related transporters, restraints the conformational changes, in particular the transmembrane helices rearrangements, which occur during the transport cycle. In AdiC these movements take place away from the dimer interface, explaining the independent functioning of each subunit.

  • Organizational Affiliation

    Institute for Research in Biomedicine, 08028 Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AdiC arginine:agmatine antiporter
A, B
445Escherichia coliMutation(s): 1 
Gene Names: adiCB21_03947
Membrane Entity: Yes 
Find proteins for P60061 (Escherichia coli (strain K12))
Explore P60061 
Go to UniProtKB:  P60061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60061
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.071α = 90
b = 77.204β = 106.79
c = 104.451γ = 90
Software Package:
Software NamePurpose
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description