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 
  • R-Value Observed: 0.195 

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:  
    4INO, 4INP, 4LS3

  • 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 of key enzymes, such as urease and hydrogenase ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nickel (II) ABC transporter, periplasmic nickel-binding proteinA, B334Helicobacter pylori G27Mutation(s): 1 
Gene Names: HPG27_1499
UniProt
Find proteins for B5Z9J2 (Helicobacter pylori (strain G27))
Explore B5Z9J2 
Go to UniProtKB:  B5Z9J2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5Z9J2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.37α = 90
b = 87.02β = 90
c = 105.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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