Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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This is version 1.2 of the entry. See complete history


Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis.

King, J.D.Harmer, N.J.Preston, A.Palmer, C.M.Rejzek, M.Field, R.A.Blundell, T.L.Maskell, D.J.

(2007) J Mol Biol 374: 749-763

  • DOI: https://doi.org/10.1016/j.jmb.2007.09.055
  • Primary Citation of Related Structures:  
    2PZJ, 2PZK, 2PZL, 2PZM, 2Q1S, 2Q1T, 2Q1U, 2Q1W

  • PubMed Abstract: 

    The pathogenic bacteria Bordetella parapertussis and Bordetella bronchiseptica express a lipopolysaccharide O antigen containing a polymer of 2,3-diacetamido-2,3-dideoxy-l-galacturonic acid. The O-antigen cluster contains three neighbouring genes that encode proteins belonging to the short-chain dehydrogenase/reductase (SDR) family, wbmF, wbmG and wbmH, and we aimed to elucidate their individual functions. Mutation and complementation implicate each gene in O-antigen expression but, as their putative sugar nucleotide substrates are not currently available, biochemical characterisation of WbmF, WbmG and WbmH is impractical at the present time. SDR family members catalyse a wide range of chemical reactions including oxidation, reduction and epimerisation. Because they typically share low sequence conservation, however, catalytic function cannot be predicted from sequence analysis alone. In this context, structural characterisation of the native proteins, co-crystals and small-molecule soaks enables differentiation of the functions of WbmF, WbmG and WbmH. These proteins exhibit typical SDR architecture and coordinate NAD. In the substrate-binding domain, all three enzymes bind uridyl nucleotides. WbmG contains a typical SDR catalytic TYK triad, which is required for oxidoreductase function, but the active site is devoid of additional acid-base functionality. Similarly, WbmH possesses a TYK triad, but an otherwise feature-poor active site. Consequently, 3,5-epimerase function can probably be ruled out for these enzymes. The WbmF active site contains conserved 3,5-epimerase features, namely, a positionally conserved cysteine (Cys133) and basic side chain (His90 or Asn213), but lacks the serine/threonine component of the SDR triad and therefore may not act as an oxidoreductase. The data suggest a pathway for synthesis of the O-antigen precursor UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid and illustrate the usefulness of structural data in predicting protein function.

  • Organizational Affiliation

    Department of Veterinary Medicine, Madingley Road, University of Cambridge, Cambridge CB3 0ES, UK. jking01@uoguelph.ca

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative nucleotide sugar epimerase/ dehydratase377Bordetella bronchisepticaMutation(s): 0 
Gene Names: BbLPS1.16wbmF
Find proteins for O87989 (Bordetella bronchiseptica)
Explore O87989 
Go to UniProtKB:  O87989
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87989
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
C21 H27 N7 O14 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.884α = 90
b = 77.875β = 108.17
c = 59.226γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description