7O82

The L-arginine/agmatine antiporter from E. coli at 1.7 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding.

Ilgu, H.Jeckelmann, J.M.Kalbermatter, D.Ucurum, Z.Lemmin, T.Fotiadis, D.

(2021) BMC Biol 19: 179-179

  • DOI: https://doi.org/10.1186/s12915-021-01102-4
  • Primary Citation of Related Structures:  
    7O82

  • PubMed Abstract: 

    The L-arginine/agmatine transporter AdiC is part of the arginine-dependent extreme acid resistance system of the bacterium Escherichia coli and its pathogenic varieties such as strain E. coli O157:H7. At the present time, there is a lack of knowledge concerning the role of water molecules and networks for the structure and function of AdiC, and solute transporters in general. The structure of the L-arginine/agmatine transporter AdiC was determined at 1.7 Å resolution by X-ray crystallography. This high resolution allowed for the identification of numerous water molecules buried in the structure. In combination with molecular dynamics (MD) simulations, we demonstrate that water molecules play an important role for stabilizing the protein and key residues, and act as placeholders for atoms of the AdiC substrates L-arginine and agmatine. MD simulations unveiled flexibility and restrained mobility of gating residues W202 and W293, respectively. Furthermore, a water-filled cavity was identified at the dimer interface of AdiC. The two monomers formed bridging interactions through water-mediated hydrogen bonds. The accessibility and presence of water molecules in this cavity was confirmed with MD simulations. Point mutations disrupting the interfacial water network validated the importance of water molecules for dimer stabilization. This work gives new insights into the role and importance of water molecules in the L-arginine/agmatine transporter AdiC for protein stabilization and substrate-binding site shaping and as placeholders of substrate atoms. Furthermore, and based on the observed flexibility and restrained mobility of gating residues, a mechanistic role of the gate flexibility in the transport cycle was proposed. Finally, we identified a water-filled cavity at the dimeric interface that contributes to the stability of the amino acid transporter oligomer.


  • Organizational Affiliation

    Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012, Bern, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine/agmatine antiporter
A, B
453Escherichia coli O157:H7Mutation(s): 0 
Gene Names: adiCZ5717ECs5097
Membrane Entity: Yes 
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BNG
Query on BNG

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B],
I [auth B]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
F [auth A],
P [auth B]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
OCT
Query on OCT

Download Ideal Coordinates CCD File 
G [auth A]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX
Query on HEX

Download Ideal Coordinates CCD File 
E [auth A]
K [auth B]
L [auth B]
M [auth B]
N [auth B]
E [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.708α = 90
b = 175.592β = 90
c = 73.275γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_184980

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description