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 

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: 10.1016/j.jmb.2005.11.096

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BugD
A, B, C
312Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)Mutation(s): 0 
Find proteins for Q7VTS1 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Go to UniProtKB:  Q7VTS1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ASP
Query on ASP

Download SDF File 
Download CCD File 
A, B, C
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.670α = 90.00
b = 76.420β = 90.00
c = 260.860γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SHARPphasing
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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