4INO

The crystal structure of Helicobacter pylori Ceue (HP1561)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Helicobacter pylori periplasmic receptor CeuE (HP1561) modulates its nickel affinity via organic metallophores.

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

(2014) Mol.Microbiol. 91: 724-735

  • DOI: 10.1111/mmi.12487
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In Gram-negative bacteria, nickel uptake is guaranteed by multiple and complex systems that operate at the membrane and periplasmic level. Helicobacter pylori employs other yet uncharacterized systems to import the nickel required for the maturation ...

    In Gram-negative bacteria, nickel uptake is guaranteed by multiple and complex systems that operate at the membrane and periplasmic level. Helicobacter pylori employs other yet uncharacterized systems to import the nickel required for the maturation of key enzymes, such as urease and hydrogenase. H. pylori CeuE protein (HP1561), previously annotated as the periplasmic component of an ATP-binding cassette (ABC)-type transporter apparatus responsible of haem/siderophores or other Fe(III)-complexes uptake, has been recently proposed to be on the contrary involved in nickel/cobalt acquisition. In this work, the crystal structure of H. pylori CeuE has been determined at 1.65 Å resolution using the single anomalous dispersion (SAD) method. It comprises two structurally similar globular domains, each consisting of a central five-stranded β-sheet surrounded by α-helices, an arrangement commonly classified as a Rossmann-like fold. Structurally, H. pylori CeuE belongs to the class III periplasmic substrate-binding protein. Both crystallographic data and fluorescence binding assays allow to exclude a role of the protein in the transport of Vitamin B12, enterobactin, haem and isolated Ni(2+) ions. On the contrary, the crystal structure and plasmon resonance studies about CeuE/Ni-(l-His)2 complex indicate that in H. pylori nickel transport is supported by CeuE protein and requires the presence of a natural nickelophore, analogously to what has been recently demonstrated for NikA from Escherichia coli.


    Organizational Affiliation

    Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131, Padua, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nickel (II) ABC transporter, periplasmic nickel-binding protein
A, B
334Helicobacter pylori (strain G27)Mutation(s): 1 
Find proteins for B5Z9J2 (Helicobacter pylori (strain G27))
Go to UniProtKB:  B5Z9J2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.370α = 90.00
b = 87.020β = 90.00
c = 105.900γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
MOSFLMdata reduction
AutoSolphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2014-02-26
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Experimental preparation
  • Version 1.4: 2019-07-17
    Type: Data collection, Refinement description