3HPE

Crystal structure of yceI (HP1286) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 

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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
  • Primary Citation of Related Structures:  
    3HPE

  • 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 virulence factors ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved hypothetical secreted proteinA, B164Helicobacter pyloriMutation(s): 3 
Gene Names: HP1286
Membrane Entity: Yes 
UniProt
Find proteins for Q1CRX8 (Helicobacter pylori (strain HPAG1))
Explore Q1CRX8 
Go to UniProtKB:  Q1CRX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1CRX8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERU
Query on ERU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(13Z)-docos-13-enamide
C22 H43 N O
UAUDZVJPLUQNMU-KTKRTIGZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.936α = 90
b = 61.312β = 92.88
c = 88.316γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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