Crystal Structure of ETDA-treated BdbD (Reduced)

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Crystal Structure and Biophysical Properties of Bacillus subtilis BdbD: AN OXIDIZING THIOL:DISULFIDE OXIDOREDUCTASE CONTAINING A NOVEL METAL SITE

Crow, A.Lewin, A.Hecht, O.Carlsson Moller, M.Moore, G.R.Hederstedt, L.Le Brun, N.E.

(2009) J Biol Chem 284: 23719-23733

  • DOI: https://doi.org/10.1074/jbc.M109.005785
  • Primary Citation of Related Structures:  
    3EU3, 3EU4, 3GH9, 3GHA

  • PubMed Abstract: 

    BdbD is a thiol:disulfide oxidoreductase (TDOR) from Bacillus subtilis that functions to introduce disulfide bonds in substrate proteins/peptides on the outside of the cytoplasmic membrane and, as such, plays a key role in disulfide bond management. Here we demonstrate that the protein is membrane-associated in B. subtilis and present the crystal structure of the soluble part of the protein lacking its membrane anchor. This reveals that BdbD is similar in structure to Escherichia coli DsbA, with a thioredoxin-like domain with an inserted helical domain. A major difference, however, is the presence in BdbD of a metal site, fully occupied by Ca(2+), at an inter-domain position some 14 A away from the CXXC active site. The midpoint reduction potential of soluble BdbD was determined as -75 mV versus normal hydrogen electrode, and the active site N-terminal cysteine thiol was shown to have a low pK(a), consistent with BdbD being an oxidizing TDOR. Equilibrium unfolding studies revealed that the oxidizing power of the protein is based on the instability introduced by the disulfide bond in the oxidized form. The crystal structure of Ca(2+)-depleted BdbD showed that the protein remained folded, with only minor conformational changes. However, the reduced form of Ca(2+)-depleted BdbD was significantly less stable than reduced Ca(2+)-containing protein, and the midpoint reduction potential was shifted by approximately -20 mV, suggesting that Ca(2+) functions to boost the oxidizing power of the protein. Finally, we demonstrate that electron exchange does not occur between BdbD and B. subtilis ResA, a low potential extra-cytoplasmic TDOR.

  • Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disulfide bond formation protein D202Bacillus subtilisMutation(s): 0 
Gene Names: bdbDBSU33480yvgV
Find proteins for O32218 (Bacillus subtilis (strain 168))
Explore O32218 
Go to UniProtKB:  O32218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32218
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.55α = 90
b = 43.63β = 107.4
c = 54.58γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BP3model building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description