2Q1T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2007.09.055
  • Primary Citation of Related Structures:  

  • 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 tha ...

    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.


    Related Citations: 
    • Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica.
      Harmer, N.J.,King, J.D.,Palmer, C.M.,Preston, A.,Maskell, D.J.,Blundell, T.L.
      (2007) Acta Crystallogr.,Sect.F 63: 711


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative nucleotide sugar epimerase/ dehydratase
A
377Bordetella bronchisepticaMutation(s): 0 
Gene Names: BbLPS1.16
Find proteins for O87989 (Bordetella bronchiseptica)
Go to UniProtKB:  O87989
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.442α = 90.00
b = 78.119β = 108.08
c = 59.262γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary