Isolated globin domain of the Bordetella pertussis globin-coupled sensor

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structural and Functional Characterization of the Globin-Coupled Sensors ofAzotobacter vinelandiiandBordetella pertussis.

Germani, F.Nardini, M.De Schutter, A.Cuypers, B.Berghmans, H.Van Hauwaert, M.L.Bruno, S.Mozzarelli, A.Moens, L.Van Doorslaer, S.Bolognesi, M.Pesce, A.Dewilde, S.

(2020) Antioxid Redox Signal 32: 378-395

  • DOI: https://doi.org/10.1089/ars.2018.7690
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aims: Structural and functional characterization of the globin-coupled sensors (GCSs) from Azotobacter vinelandii ( Av GReg) and Bordetella pertussis ( Bpe GReg). Results: Ultraviolet/visible and resonance Raman spectroscopies confirm the presence in Av GReg and Bpe GReg of a globin domain capable of reversible gaseous ligand binding. In Av GReg, an influence of the transmitter domain on the heme proximal region of the globin domain can be seen, and k ' CO is higher than for other GCSs. The O 2 binding kinetics suggests the presence of an open and a closed conformation. As for Bpe GReg, the fully oxygenated Av GReg show a very high diguanylate cyclase activity. The carbon monoxide rebinding to Bpe GReg indicates that intra- and intermolecular interactions influence the ligand binding. The globin domains of both proteins ( Av GReg globin domain and Bpe GRegGb with cysteines (Cys16, 45, 114, 154) mutated to serines [ Bpe GReg-Gb*]) share the same GCS fold, a similar proximal but a different distal side structure. They homodimerize through a G-H helical bundle as in other GCSs. However, Bpe GReg-Gb* shows also a second dimerization mode. Innovation: This article extends our knowledge on the GCS proteins and contributes to a better understanding of the GCSs role in the formation of bacterial biofilms. Conclusions: Av GReg and Bpe GReg conform to the GCS family, share a similar overall structure, but they have different properties in terms of the ligand binding. In particular, Av GReg shows an open and a closed conformation that in the latter form will very tightly bind oxygen. Bpe GReg has only one closed conformation. In both proteins, it is the fully oxygenated GCS form that catalyzes the production of the second messenger.

  • Organizational Affiliation

    Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
177Bordetella pertussis Tohama IMutation(s): 4 
Find proteins for Q7VTL8 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore Q7VTL8 
Go to UniProtKB:  Q7VTL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7VTL8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C34 H32 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.96α = 90
b = 86.72β = 93.34
c = 41.82γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgiumG.0247.09N

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Database references
  • Version 1.3: 2020-09-23
    Changes: Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description