Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADP and UDP-GlcNAc

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 

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Structural Studies of FlaA1 from Helicobacter pylori Reveal the Mechanism for Inverting 4,6-Dehydratase Activity.

Ishiyama, N.Creuzenet, C.Miller, W.L.Demendi, M.Anderson, E.M.Harauz, G.Lam, J.S.Berghuis, A.M.

(2006) J Biol Chem 281: 24489-24495

  • DOI: https://doi.org/10.1074/jbc.M602393200
  • Primary Citation of Related Structures:  
    2GN4, 2GN6, 2GN8, 2GN9, 2GNA

  • PubMed Abstract: 

    FlaA1 from the human pathogen Helicobacter pylori is an enzyme involved in saccharide biosynthesis that has been shown to be essential for pathogenicity. Here we present five crystal structures of FlaA1 in the presence of substrate, inhibitors, and bound cofactor, with resolutions ranging from 2.8 to 1.9 A. These structures reveal that the enzyme is a novel member of the short-chain dehydrogenase/reductase superfamily. Additional electron microscopy studies show the enzyme to possess a hexameric doughnut-shaped quaternary structure. NMR analyses of "real time" enzyme-substrate reactions indicate that FlaA1 is a UDP-GlcNAc-inverting 4,6-dehydratase, suggesting that the enzyme catalyzes the first step in the biosynthetic pathway of a pseudaminic acid derivative, which is implicated in protein glycosylation. Guided by evidence from site-directed mutagenesis and computational simulations, a three-step reaction mechanism is proposed that involves Lys-133 functioning as both a catalytic acid and base.

  • Organizational Affiliation

    Department of Biochemistry and Department of Microbiology and Immunology, McGill University, Montreal, Quebec.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-GlcNAc C6 dehydratase
A, B
344Helicobacter pyloriMutation(s): 0 
Gene Names: HP0840
EC: 4.2.1
Find proteins for O25511 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25511 
Go to UniProtKB:  O25511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25511
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.846α = 90
b = 109.846β = 90
c = 107.978γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description