structure analysis of ProX in complex with glycine betaine

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 

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Cation-pi Interactions as Determinants for Binding of the Compatible Solutes Glycine Betaine and Proline Betaine by the Periplasmic Ligand-binding Protein ProX from Escherichia coli

Schiefner, A.Breed, J.Bosser, L.Kneip, S.Gade, J.Holtmann, G.Diederichs, K.Welte, W.Bremer, E.

(2004) J Biol Chem 279: 5588-5596

  • DOI: https://doi.org/10.1074/jbc.M309771200
  • Primary Citation of Related Structures:  
    1R9L, 1R9Q

  • PubMed Abstract: 

    Compatible solutes such as glycine betaine and proline betaine are accumulated to exceedingly high intracellular levels by many organisms in response to high osmolarity to offset the loss of cell water. They are excluded from the immediate hydration shell of proteins and thereby stabilize their native structure. Despite their exclusion from protein surfaces, the periplasmic ligand-binding protein ProX from the Escherichia coli ATP-binding cassette transport system ProU binds the compatible solutes glycine betaine and proline betaine with high affinity and specificity. To understand the mechanism of compatible solute binding, we determined the high resolution structure of ProX in complex with its ligands glycine betaine and proline betaine. This crystallographic study revealed that cation-pi interactions between the positive charge of the quaternary amine of the ligands and three tryptophan residues forming a rectangular aromatic box are the key determinants of the high affinity binding of compatible solutes by ProX. The structural analysis was combined with site-directed mutagenesis of the ligand binding pocket to estimate the contributions of the tryptophan residues involved in binding.

  • Organizational Affiliation

    Fachbereich Biologie, Universität Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine betaine-binding periplasmic protein309Escherichia coliMutation(s): 0 
Gene Names: proX
Find proteins for P0AFM2 (Escherichia coli (strain K12))
Explore P0AFM2 
Go to UniProtKB:  P0AFM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFM2
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
BET PDBBind:  1R9L Kd: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.43α = 90
b = 53.9β = 90
c = 115.2γ = 90
Software Package:
Software NamePurpose
MAR345data 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: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations