3HPE

Crystal structure of yceI (HP1286) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Helicobacter pylori acidic stress response factor HP1286 is a YceI homolog with new binding specificity.

Sisinni, L.Cendron, L.Favaro, G.Zanotti, G.

(2010) Febs J. 277: 1896-1905

  • DOI: 10.1111/j.1742-4658.2010.07612.x

  • PubMed Abstract: 
  • HP1286 from Helicobacter pylori is among the proteins that play a relevant role in bacterial colonization and persistence in the stomach. Indeed, it was demonstrated to be overexpressed under acidic stress conditions, together with other essential vi ...

    HP1286 from Helicobacter pylori is among the proteins that play a relevant role in bacterial colonization and persistence in the stomach. Indeed, it was demonstrated to be overexpressed under acidic stress conditions, together with other essential virulence factors. Here we describe its crystal structure, determined at 2.1 A resolution. The molecular model, a dimer characterized by two-fold symmetry, shows that HP1286 structurally belongs to the YceI-like protein family, which in turn is characterized by the lipocalin fold. The latter characterizes proteins possessing an internal cavity with the function of binding and/or transport of amphiphilic molecules. Surprisingly, a molecule of erucamide was found bound in the internal cavity of each monomer of recombinant HP1286, cloned and expressed in an Escherichia coli heterologous system. The shape and length of the cavity indicate that, at variance with other members of the family, HP-YceI has a binding specificity for amphiphilic compounds with a linear chain of about 22 carbon atoms. These features, along with the fact that the protein is secreted by the bacterium and is involved in adaptation to an acidic environment, suggest that its function could be that of sequestering specific fatty acids or amides from the environment, either to supply the bacterium with the fatty acids necessary for its metabolism, or to protect and detoxify it from the detergent-like antimicrobial activity of fatty acids that are eventually present in the external milieu.


    Related Citations: 
    • Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8.
      Handa, N.,Terada, T.,Doi-Katayama, Y.,Hirota, H.,Tame, J.R.,Park, S.Y.,Kuramitsu, S.,Shirouzu, M.,Yokoyama, S.
      (2005) Protein Sci. 14: 1004
    • Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II.
      Toms, A.V.,Haas, A.L.,Park, J.H.,Begley, T.P.,Ealick, S.E.
      (2005) Biochemistry 44: 2319


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Conserved hypothetical secreted protein
A, B
164Helicobacter pylori (strain HPAG1)N/A
Find proteins for Q1CRX8 (Helicobacter pylori (strain HPAG1))
Go to UniProtKB:  Q1CRX8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERU
Query on ERU

Download SDF File 
Download CCD File 
A, B
(13Z)-docos-13-enamide
Erucamide, erucylamide
C22 H43 N O
UAUDZVJPLUQNMU-KTKRTIGZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 30.936α = 90.00
b = 61.312β = 92.88
c = 88.316γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description