Structure of Atu2422-GABA receptor in complex with proline

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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A conserved mechanism of GABA binding and antagonism is revealed by structure-function analysis of the periplasmic binding protein Atu2422 in Agrobacterium tumefaciens.

Planamente, S.Vigouroux, A.Mondy, S.Nicaise, M.Faure, D.Morera, S.

(2010) J Biol Chem 285: 30294-30303

  • DOI: https://doi.org/10.1074/jbc.M110.140715
  • Primary Citation of Related Structures:  
    3IP5, 3IP6, 3IP7, 3IP9, 3IPA, 3IPC

  • PubMed Abstract: 

    Bacterial periplasmic binding proteins (PBPs) and eukaryotic PBP-like domains (also called as Venus flytrap modules) of G-protein-coupled receptors are involved in extracellular GABA perception. We investigated the structural and functional basis of ligand specificity of the PBP Atu2422, which is implicated in virulence and transport of GABA in the plant pathogen Agrobacterium tumefaciens. Five high-resolution x-ray structures of Atu2422 liganded to GABA, Pro, Ala, and Val and of point mutant Atu2422-F77A liganded to Leu were determined. Structural analysis of the ligand-binding site revealed two essential residues, Phe(77) and Tyr(275), the implication of which in GABA signaling and virulence was confirmed using A. tumefaciens cells expressing corresponding Atu2422 mutants. Phe(77) restricts ligand specificity to α-amino acids with a short lateral chain, which act as antagonists of GABA signaling in A. tumefaciens. Tyr(275) specifically interacts with the GABA γ-amino group. Conservation of these two key residues in proteins phylogenetically related to Atu2422 brought to light a subfamily of PBPs in which all members could bind GABA and short α-amino acids. This work led to the identification of a fingerprint sequence and structural features for defining PBPs that bind GABA and its competitors and revealed their occurrence among host-interacting proteobacteria.

  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter, substrate binding protein (Amino acid)356Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: AGR_C_4394Atu2422
Find proteins for Q7CX36 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q7CX36 
Go to UniProtKB:  Q7CX36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CX36
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PRO Binding MOAD:  3IP6 Kd: 250 (nM) from 1 assay(s)
PDBBind:  3IP6 Kd: 250 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.23α = 90
b = 43.02β = 109.66
c = 66.3γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    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