3L1L

Structure of Arg-bound Escherichia coli AdiC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of substrate recognition and transport by an amino acid antiporter

Gao, X.Zhou, L.Jiao, X.Lu, F.Yan, C.Zeng, X.Wang, J.Shi, Y.

(2010) Nature 463: 828-832

  • DOI: 10.1038/nature08741
  • Primary Citation of Related Structures:  
    3L1L

  • PubMed Abstract: 
  • In extremely acidic environments, enteric bacteria such as Escherichia coli rely on the amino acid antiporter AdiC to expel protons by exchanging intracellular agmatine (Agm(2+)) for extracellular arginine (Arg(+)). AdiC is a representative member of ...

    In extremely acidic environments, enteric bacteria such as Escherichia coli rely on the amino acid antiporter AdiC to expel protons by exchanging intracellular agmatine (Agm(2+)) for extracellular arginine (Arg(+)). AdiC is a representative member of the amino acid-polyamine-organocation (APC) superfamily of membrane transporters. The structure of substrate-free AdiC revealed a homodimeric assembly, with each protomer containing 12 transmembrane segments and existing in an outward-open conformation. The overall folding of AdiC is similar to that of the Na(+)-coupled symporters. Despite these advances, it remains unclear how the substrate (arginine or agmatine) is recognized and transported by AdiC. Here we report the crystal structure of an E. coli AdiC variant bound to Arg at 3.0 A resolution. The positively charged Arg is enclosed in an acidic binding chamber, with the head groups of Arg hydrogen-bonded to main chain atoms of AdiC and the aliphatic portion of Arg stacked by hydrophobic side chains of highly conserved residues. Arg binding induces pronounced structural rearrangement in transmembrane helix 6 (TM6) and, to a lesser extent, TM2 and TM10, resulting in an occluded conformation. Structural analysis identified three potential gates, involving four aromatic residues and Glu 208, which may work in concert to differentially regulate the upload and release of Arg and Agm.


    Organizational Affiliation

    Ministry of Education Protein Science Laboratory, Tsinghua University, Beijing 100084, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginine/agmatine antiporterA445Escherichia coli O157:H7Mutation(s): 2 
Gene Names: adiCZ5717ECs5097
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Amino Acid/Polyamine/Organocation (APC) Superfamily
Protein: 
AdiC Arginine:Agmatine Antiporter (N22A, L123W mutant) with bound Arginine
Find proteins for P60063 (Escherichia coli O157:H7)
Explore P60063 
Go to UniProtKB:  P60063
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNG
Query on BNG

Download CCD File 
A
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
ARG
Query on ARG

Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.69α = 90
b = 127.17β = 90
c = 157.5γ = 90
Software Package:
Software NamePurpose
BSSdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary