2F5X

Structure of periplasmic binding protein BugD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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:  
    2F5X

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BugD
A, B, C
312Bordetella pertussis Tohama IMutation(s): 10 
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CCP4data scaling
SHARPphasing

Structure Validation

View Full Validation Report



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