3SXP

Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859) from Helicobacter pylori.

Shaik, M.M.Zanotti, G.Cendron, L.

(2011) Biochim Biophys Acta 1814: 1641-1647

  • DOI: 10.1016/j.bbapap.2011.09.006
  • Primary Citation of Related Structures:  
    3SXP

  • PubMed Abstract: 
  • Helicobacter pylori, the human pathogen that affects about half of the world population and that is responsible for gastritis, gastric ulcer and adenocarcinoma and MALT lymphoma, owes much of the integrity of its outer membrane on lipopolysaccharides (LPSs) ...

    Helicobacter pylori, the human pathogen that affects about half of the world population and that is responsible for gastritis, gastric ulcer and adenocarcinoma and MALT lymphoma, owes much of the integrity of its outer membrane on lipopolysaccharides (LPSs). Together with their essential structural role, LPSs contribute to the bacterial adherence properties, as well as they are well characterized for the capability to modulate the immuno-response. In H. pylori the core oligosaccharide, one of the three main domains of LPSs, shows a peculiar structure in the branching organization of the repeating units, which displayed further variability when different strains have been compared. We present here the crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859, rfaD), the last enzyme in the pathway that produces L-glycero-D-manno-heptose starting from sedoheptulose-7-phosphate, a crucial compound in the synthesis of the core oligosaccharide. In a recent study, a HP0859 knockout mutant has been characterized, demonstrating a severe loss of lipopolysaccharide structure and a significant reduction of adhesion levels in an infection model to AGS cells, if compared with the wild type strain, in good agreement with its enzymatic role. The crystal structure reveals that the enzyme is a homo-pentamer, and NAD is bound as a cofactor in a highly conserved pocket. The substrate-binding site of the enzyme is very similar to that of its orthologue in Escherichia coli, suggesting also a similar catalytic mechanism.


    Related Citations: 
    • The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist
      Deacon, A.M., Ni, Y.S., Coleman, W.G., Ealick, S.E.
      (2000) Structure 8: 453

    Organizational Affiliation

    Department of Biological Chemistry, University of Padua, Padua, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-L-glycero-D-mannoheptose-6-epimeraseA, B, C, D, E362Helicobacter pylori G27Mutation(s): 1 
Gene Names: hp0859HPG27_813
EC: 5.1.3.20
UniProt
Find proteins for B5Z7L9 (Helicobacter pylori (strain G27))
Explore B5Z7L9 
Go to UniProtKB:  B5Z7L9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.94α = 90
b = 106.77β = 108.35
c = 152.22γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary