2Q88 | pdb_00002q88

Crystal structure of EhuB in complex with ectoine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the ligand-binding protein EhuB from Sinorhizobium meliloti reveals substrate recognition of the compatible solutes ectoine and hydroxyectoine.

Hanekop, N.Hoing, M.Sohn-Bosser, L.Jebbar, M.Schmitt, L.Bremer, E.

(2007) J Mol Biology 374: 1237-1250

  • DOI: https://doi.org/10.1016/j.jmb.2007.09.071
  • Primary Citation Related Structures: 
    2Q88, 2Q89

  • PubMed Abstract: 

    In microorganisms, members of the binding-protein-dependent ATP-binding cassette transporter superfamily constitute an important class of transport systems. Some of them are involved in osmoprotection under hyperosmotic stress by facilitating the uptake of "compatible solutes". Currently, the molecular mechanisms used by these transport systems to recognize compatible solutes are limited to transporters specific for glycine betaine and proline betaine. Therefore, this study reports a detailed analysis of the molecular principles governing substrate recognition in the Ehu system from Sinorhizobium meliloti, which is responsible for the uptake of the compatible solutes ectoine and hydroxyectoine. To contribute to a broader understanding of the molecular interactions underlying substrate specificity, our study focused on the substrate-binding protein EhuB because this protein binds the ligand selectively, delivers it to the translocation machinery in the membrane and is thought to be responsible for substrate specificity. The crystal structures of EhuB, in complex with ectoine and hydroxyectoine, were determined at a resolution of 1.9 A and 2.3 A, respectively, and allowed us to assign the structural principles of substrate recognition and binding. Based on these results, site-directed mutagenesis of amino acids involved in ligand binding was employed to address their individual contribution to complex stability. A comparison with the crystal structures of other binding proteins specific for compatible solutes revealed common principles of substrate recognition, but also important differences that might be an adaptation to the nature of the ligand and to the demands on protein affinity imposed by the environment.


  • Organizational Affiliation
    • Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany.

Macromolecule Content 

  • Total Structure Weight: 27.76 kDa 
  • Atom Count: 2,043 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 257 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative ABC transporter amino acid-binding protein257Sinorhizobium melilotiMutation(s): 0 
UniProt
Find proteins for Q92WC8 (Rhizobium meliloti (strain 1021))
Explore Q92WC8 
Go to UniProtKB:  Q92WC8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92WC8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.365α = 90
b = 57.365β = 90
c = 161.883γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary