2PZH

YbgC thioesterase (Hp0496) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and enzymatic characterization of HP0496, a YbgC thioesterase from Helicobacter pylori.

Angelini, A.Cendron, L.Goncalves, S.Zanotti, G.Terradot, L.

(2008) Proteins 72: 1212-1221

  • DOI: 10.1002/prot.22014
  • Primary Citation of Related Structures:  
    2PZH

  • PubMed Abstract: 
  • YbgC proteins are bacterial acyl-CoA thioesterases associated with the Tol-Pal system. This system is important for cell envelope integrity and is part of the cell division machinery. In E. coli, YbgC associates with the cell membrane and is part of ...

    YbgC proteins are bacterial acyl-CoA thioesterases associated with the Tol-Pal system. This system is important for cell envelope integrity and is part of the cell division machinery. In E. coli, YbgC associates with the cell membrane and is part of a protein network involved in lipid biogenesis. In the human pathogen Helicobacter pylori, a putative homologue of YbgC, named HP0496, was found to interact with the cytotoxin CagA by two different studies. We have determined its crystal structure and characterized its enzymatic activity. The structure of HP0496 shows that it is a member of the hot-dog family of proteins, with a epsilongamma tetrameric arrangement. Finally, enzymatic assays performed with the purified protein showed that HP0496 is an acyl-CoA thioesterase that favors long-chain substrates.


    Related Citations: 
    • The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases
      Dillon, S.C., Bateman, A.
      (2004) BMC Bioinformatics 59: 109
    • The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3
      Benning, M.M., Wesemberg, G., Liu, R., Taylor, K.L., Dunway-Mariano, D., Holden, H.M.
      (1998) J Biol Chem 273: 33572

    Organizational Affiliation

    Macromolecular Crystallography Group, European Synchrotron Radiation Facility, B.P. 220, 6 rue Jules Horowitz, F-38043 Grenoble Cedex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical protein HP_0496A, B, C, D135Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP0496ybgCHP_0496
EC: 3.1.2
Find proteins for P94842 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P94842 
Go to UniProtKB:  P94842
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.86α = 90
b = 99.206β = 90
c = 107.288γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance