Crystal structure of DctP7, a Bordetella pertussis extracytoplasmic solute receptor binding pyroglutamic acid

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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Crystal Structures of two Bordetella pertussis Periplasmic Receptors Contribute to Defining a Novel Pyroglutamic Acid Binding DctP Subfamily.

Rucktooa, P.Antoine, R.Herrou, J.Huvent, I.Locht, C.Jacob-Dubuisson, F.Villeret, V.Bompard, C.

(2007) J Mol Biol 370: 93-106

  • DOI: https://doi.org/10.1016/j.jmb.2007.04.047
  • Primary Citation of Related Structures:  
    2PFY, 2PFZ

  • PubMed Abstract: 

    Gram-negative bacteria have developed several different transport systems for solute uptake. One of these, the tripartite ATP independent periplasmic transport system (TRAP-T), makes use of an extracytoplasmic solute receptor (ESR) which captures specific solutes with high affinity and transfers them to their partner permease complex located in the bacterial inner membrane. We hereby report the structures of DctP6 and DctP7, two such ESRs from Bordetella pertussis. These two proteins display a high degree of sequence and structural similarity and possess the "Venus flytrap" fold characteristic of ESRs, comprising two globular alpha/beta domains hinged together to form a ligand binding cleft. DctP6 and DctP7 both show a closed conformation due to the presence of one pyroglutamic acid molecule bound by highly conserved residues in their respective ligand binding sites. BLAST analyses have revealed that the DctP6 and DctP7 residues involved in ligand binding are strictly present in a number of predicted TRAP-T ESRs from other bacteria. In most cases, the genes encoding these TRAP-T systems are located in the vicinity of a gene coding for a pyroglutamic acid metabolising enzyme. Both the high degree of conservation of these ligand binding residues and the genomic context of these TRAP-T-coding operons in a number of bacterial species, suggest that DctP6 and DctP7 constitute the prototypes of a novel TRAP-T DctP subfamily involved in pyroglutamic acid transport.

  • Organizational Affiliation

    UMR 8161 CNRS Institut de Biologie de Lille, Laboratoire de Cristallographie Macromoléculaire, Université des Sciences et Technologies de Lille, Université de Lille 2, Institut Pasteur de Lille IFR142, Lille cedex, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative exported protein
A, B, C, D
301Bordetella pertussis Tohama IMutation(s): 6 
Gene Names: BP1891
Find proteins for Q7VXB1 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore Q7VXB1 
Go to UniProtKB:  Q7VXB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7VXB1
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Binding Affinity Annotations 
IDSourceBinding Affinity
PCA PDBBind:  2PFY Kd: 300 (nM) from 1 assay(s)
Binding MOAD:  2PFY Kd: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.84α = 90
b = 149.75β = 90
c = 169.58γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-06-12 
  • Deposition Author(s): Rucktooa, P.

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance