9PH2 | pdb_00009ph2

Crystal structure of Bordetella pertussis DsbA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.202 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Literature

Structural and functional specialization of Bordetella pertussis DsbA for pertussis toxin folding.

Penning, S.Mitchell, L.Hong, Y.Cunliffe, T.Subedi, P.Wang, G.Hor, L.Totsika, M.Paxman, J.J.Heras, B.

(2026) Protein Sci 35: e70421-e70421

  • DOI: https://doi.org/10.1002/pro.70421
  • Primary Citation of Related Structures:  
    9PH2

  • PubMed Abstract: 

    Disulphide bonds (Dsbs) are essential for the folding, stability, and function of many secreted and membrane-associated proteins in bacteria. In Gram-negative species, these bonds are introduced by the Dsb enzyme family, with DsbA acting as the primary thiol oxidase. While DsbA proteins share a conserved thioredoxin (TRX)-like fold, emerging evidence highlights substantial structural and functional divergence among pathogenic homologues. Here, we present the high-resolution crystal structure and functional characterization of BperDsbA, a DsbA homologue from Bordetella pertussis, the causative agent of whooping cough. BperDsbA adopts a canonical TRX fold with a CPHC active site and a threonine-containing cis-proline loop, but displays striking deviations from prototypical DsbAs. Notably, it contains a highly destabilizing catalytic Dsb, resulting in one of the most oxidizing redox potentials recorded for a DsbA enzyme. Surface electrostatic analysis reveals an unusual distribution of positive and negative charge around the active site, in contrast to the broadly hydrophobic catalytic surfaces of other DsbAs. Functionally, BperDsbA shows limited substrate promiscuity and selectively catalyzes the oxidative folding of a pertussis toxin-derived peptide, supporting a model of substrate specialization. Together, these findings suggest that BperDsbA has evolved unique redox and structural features to support virulence factor maturation in B. pertussis. This work expands our understanding of the mechanistic diversity of DsbA enzymes and highlights their potential as pathogen-specific targets for anti-virulence therapeutics.


  • Organizational Affiliation
    • Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, School of Agriculture, Biomedicine and Environment La Trobe University, Bundoora, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein
A, B
179Bordetella pertussisMutation(s): 0 
Gene Names: dsbANCTC10911_00456
UniProt
Find proteins for A0A0E8D8H5 (Bordetella pertussis)
Explore A0A0E8D8H5 
Go to UniProtKB:  A0A0E8D8H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E8D8H5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.785α = 90
b = 37.298β = 104.593
c = 57.111γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP250102263
Australian Research Council (ARC)AustraliaDP210100673
Australian Research Council (ARC)AustraliaDP190101613
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1143638
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1144046

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release