3FXB | pdb_00003fxb

Crystal structure of the ectoine-binding protein UehA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.262 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The crystal structure of UehA in complex with ectoine-A comparison with other TRAP-T binding proteins.

Lecher, J.Pittelkow, M.Zobel, S.Bursy, J.Bonig, T.Smits, S.H.Schmitt, L.Bremer, E.

(2009) J Mol Biology 389: 58-73

  • DOI: https://doi.org/10.1016/j.jmb.2009.03.077
  • Primary Citation Related Structures: 
    3FXB

  • PubMed Abstract: 

    Substrate-binding proteins or extracellular solute receptors (ESRs) are components of both ABC (ATP binding cassette) and TRAP-T (tripartite ATP-independent periplasmic transporter). The TRAP-T system UehABC from Silicibacter pomeroyi DSS-3 imports the compatible solutes ectoine and 5-hydroxyectoine as nutrients. UehA, the ESR of the UehABC operon, binds both ectoine and 5-hydroxyectoine with high affinity (K(d) values of 1.4+/-0.1 and 1.1+/-0.1 microM, respectively) and delivers them to the TRAP-T complex. The crystal structure of UehA in complex with ectoine was determined at 2.9-A resolution and revealed an overall fold common for all ESR proteins from TRAP systems determined so far. A comparison of the recently described structure of TeaA from Halomonas elongata and an ectoine-binding protein (EhuB) from an ABC transporter revealed a conserved ligand binding mode that involves both directed and cation-pi interactions. Furthermore, a comparison with other known TRAP-T ESRs revealed a helix that might act as a selectivity filter imposing restraints on the ESRs that fine-tune ligand recognition and binding and finally might determine the selection of the cognate substrate.


  • Organizational Affiliation
    • Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Germany.

Macromolecule Content 

  • Total Structure Weight: 73.27 kDa 
  • Atom Count: 4,882 
  • Modeled Residue Count: 620 
  • Deposited Residue Count: 652 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRAP dicarboxylate transporter, DctP subunit
A, B
326Ruegeria pomeroyi DSS-3Mutation(s): 0 
Gene Names: SPO1147
UniProt
Find proteins for Q5LUA7 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Explore Q5LUA7 
Go to UniProtKB:  Q5LUA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LUA7
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.262 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63α = 90
b = 61.3β = 102.6
c = 86.3γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary