6WEF | pdb_00006wef

Copper-bound D92H variant of Campylobacter jejuni P19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.299 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.270 (Depositor), 0.275 (DCC) 
  • R-Value Observed: 
    0.272 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6WEF

This is version 1.1 of the entry. See complete history

Literature

A copper site is required for iron transport by the periplasmic proteins P19 and FetP.

Chan, A.C.K.Lin, H.Koch, D.Grass, G.Nies, D.H.Murphy, M.E.P.

(2020) Metallomics 12: 1530-1541

  • DOI: https://doi.org/10.1039/d0mt00130a
  • Primary Citation Related Structures: 
    5I0V, 5I0W, 5I0X, 5I0Y, 6WED, 6WEE, 6WEF

  • PubMed Abstract: 

    Campylobacter jejuni is a leading cause of food-borne gastrointestinal disease in humans and uropathogenic Escherichia coli is a leading cause of urinary tract infections. Both human pathogens harbour a homologous iron uptake system (termed cjFetM-P19 in C. jejuni and ecFetM-FetP in E. coli). Although these systems are important for growth under iron limitation, the mechanisms by which these systems function during iron transport remain undefined. The copper ions bound to P19 and FetP, the homologous periplasmic proteins, are coordinated in an uncommon penta-dentate manner involving a Met-Glu-His3 motif and exhibit positional plasticity. Here we demonstrate the function of the Met and Glu residues in modulating copper binding and controlling copper positioning through site-directed variants, binding assays, and crystal structures. Growth of C. jejuni strains with these p19 variants is impaired under iron limited conditions as compared to the wild-type strain. Additionally, an acidic residue-rich secondary site is required for binding iron and function in vivo. Finally, western blot analyses demonstrate direct and specific interactions between periplasmic P19 and FetP with the large periplasmic domain of their respective inner membrane transporters cjFetM and ecFetM.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Canada. michael.murphy@ubc.ca.

Macromolecule Content 

  • Total Structure Weight: 213.55 kDa 
  • Atom Count: 15,461 
  • Modeled Residue Count: 1,901 
  • Deposited Residue Count: 1,908 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein159Campylobacter jejuni subsp. jejuni 81-176Mutation(s): 1 
Gene Names: CJJ81176_1650
UniProt
Find proteins for A0A0H3PA01 (Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176))
Explore A0A0H3PA01 
Go to UniProtKB:  A0A0H3PA01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3PA01
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth G]
HA [auth I]
JA [auth J]
O [auth D]
P [auth D]
CA [auth G],
HA [auth I],
JA [auth J],
O [auth D],
P [auth D],
R [auth A],
S [auth A],
U [auth B],
W [auth E],
Y [auth F],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
BA [auth G],
EA [auth H],
FA [auth H],
LA [auth K]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
(Subject of Investigation/LOI)

Query on CU



Download:Ideal Coordinates CCD File
AA [auth G]
DA [auth H]
GA [auth I]
IA [auth J]
KA [auth K]
AA [auth G],
DA [auth H],
GA [auth I],
IA [auth J],
KA [auth K],
M [auth C],
MA [auth L],
N [auth D],
Q [auth A],
T [auth B],
V [auth E],
X [auth F]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.299 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.270 (Depositor), 0.275 (DCC) 
  • R-Value Observed: 0.272 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.455α = 90
b = 132.455β = 90
c = 104.585γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description