2PZH

YbgC thioesterase (Hp0496) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 

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

  • 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 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
    • The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases
      Dillon, S.C.,Bateman, A.
      (2004) BMC Bioinformatics 59: 109


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein HP_0496
A, C, D, B
135Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ybgC
EC: 3.1.2.-
Find proteins for P94842 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P94842
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.860α = 90.00
b = 99.206β = 90.00
c = 107.288γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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