3IP5

Structure of Atu2422-GABA receptor in complex with alanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC transporter, substrate binding protein (Amino acid)A356Agrobacterium 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ALA
Query on ALA

Download CCD File 
A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ALAKd:  600   nM  Binding MOAD
ALAKd :  600   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.25α = 90
b = 38.94β = 95.68
c = 71.63γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance