Structure of a periplasmic transporter

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 

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Structural analysis of Bordetella pertussis BugE solute receptor in a bound conformation

Huvent, I.Belrhali, H.Antoine, R.Bompard, C.Locht, C.Jacob-Dubuisson, F.Villeret, V.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1375-1381

  • DOI: https://doi.org/10.1107/S0907444906032653
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Bug proteins form a large family of periplasmic solute-binding receptors present in a number of bacterial species. Here, the crystal structure of Bordetella pertussis BugE, a member of the Bug family coded by the gene BP0250, is reported. It adopts the Venus flytrap architecture of periplasmic binding proteins, with two domains separated by a deep cleft. BugE has a bound ligand, identified as a glutamate. The structure of B. pertussis BugD, which is an aspartic acid transporter, has recently been reported. These structures reveal high conservation of the Bug architecture, despite limited sequence identity. They share a common carboxylate-binding motif defined by two strand-beta-turn-alpha-helix motifs, also involving two water molecules to bridge the carboxylate O atoms to the protein. The two water molecules are hydrogen bonded to a common main-chain carbonyl group. Although the features of the carboxylate-binding motif are totally conserved, the ligand in BugE is bound by its side-chain carboxylate group rather than by its alpha-carboxylate as in BugD. This specific ligand-binding motif is highly conserved in Bug proteins and the BugE structure suggests that the cavity of the Bug proteins might also accommodate carboxylated solutes other than amino acids. The vast expansion of the Bug family in several bacterial genera is likely to be explained by the possible diversity of ligands. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far.

  • Organizational Affiliation

    UMR8161 CNRS, Institut de Biologie de Lille, Institute Pasteur de Lille, 1 rue du Professeur Calmette, BP245, 59021 Lille CEDEX, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative exported protein314Bordetella pertussisMutation(s): 8 
Find proteins for Q7W0A0 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore Q7W0A0 
Go to UniProtKB:  Q7W0A0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7W0A0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.829α = 90
b = 53.829β = 90
c = 422.66γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance