Structure of periplasmic binding protein BugD

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 

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Crystal Structure of Bordetella pertussis BugD Solute Receptor Unveils the Basis of Ligand Binding in a New Family of Periplasmic Binding Proteins

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

(2006) J Mol Biol 356: 1014-1026

  • DOI: https://doi.org/10.1016/j.jmb.2005.11.096
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Periplasmic binding proteins of a new family particularly well represented in Bordetella pertussis have been called Bug receptors. One B.pertussis Bug protein is part of a tripartite tricarboxylate transporter while the functions of the other 77 are unknown. We report the first structure of a Bug receptor, BugD. It adopts the characteristic Venus flytrap motif observed in other periplasmic binding proteins, with two globular domains bisected by a deep cleft. BugD displays a closed conformation resulting from the fortuitous capture of a ligand, identified from the electron density as an aspartate. The structure reveals a distinctive alpha carboxylate-binding motif, involving two water molecules that bridge the carboxylate oxygen atoms to the protein. Both water molecules are hydrogen bonded to a common carbonyl group from Ala14, and each forms a hydrogen bond with one carboxylate oxygen atom of the ligand. Additional hydrogen bonds are found between the ligand alpha carboxylate oxygen atoms and protein backbone amide groups and with a threonine hydroxyl group. This specific ligand-binding motif is highly conserved in Bug proteins, indicating that they may all be receptors of amino acids or other carboxylated solutes, with a similar binding mode. The present structure thus unveils the bases of ligand binding in this large family of periplasmic binding proteins, several hundred members of which have been identified in various bacterial species.

  • Organizational Affiliation

    CNRS-UMR8117 Institut de Biologie de Lille, Institut 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
A, B, C
312Bordetella pertussis Tohama IMutation(s): 10 
Gene Names: BP3440
Find proteins for Q7VTS1 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore Q7VTS1 
Go to UniProtKB:  Q7VTS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7VTS1
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.67α = 90
b = 76.42β = 90
c = 260.86γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance