6D57 | pdb_00006d57

Campylobacter jejuni ferric uptake regulator S1 metalated


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.229 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6D57

This is version 1.2 of the entry. See complete history

Literature

Functional insights into the interplay between DNA interaction and metal coordination in ferric uptake regulators.

Sarvan, S.Charih, F.Askoura, M.Butcher, J.Brunzelle, J.S.Stintzi, A.Couture, J.F.

(2018) Sci Rep 8: 7140-7140

  • DOI: https://doi.org/10.1038/s41598-018-25157-6
  • Primary Citation Related Structures: 
    6D57

  • PubMed Abstract: 

    Ferric uptake regulators (Fur) are a family of transcription factors coupling gene regulatory events to metal concentration. Recent evidence has expanded the mechanistic repertoires employed by Fur to activate or repress gene expression in the presence or absence of regulatory metals. However, the mechanistic basis underlying this extended repertoire has remained largely unexplored. In this study, we used an extensive set of mutations to demonstrate that Campylobacter jejuni Fur (CjFur) employs the same surface to positively and negatively control gene expression regardless of the presence or absence of metals. Moreover, the crystal structure determination of a CjFur devoid of any regulatory metals shows that subtle reorientation of the transcription factor DNA binding domain negatively impacts DNA binding, gene expression and gut colonization in chickens. Overall, these results highlight the versatility of the CjFur DNA binding domain in mediating all gene regulatory events controlled by the metalloregulator and that the full metalation of CjFur is critical to the Campylobacter jejuni life cycle in vivo.


  • Organizational Affiliation
    • Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.

Macromolecule Content 

  • Total Structure Weight: 37.6 kDa 
  • Atom Count: 2,811 
  • Modeled Residue Count: 295 
  • Deposited Residue Count: 322 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferric uptake regulation protein
A, B
161Campylobacter jejuniMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A1E7PHN7 (Campylobacter jejuni)
Explore A0A1E7PHN7 
Go to UniProtKB:  A0A1E7PHN7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1E7PHN7
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A],
O [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OHI
Query on OHI
A, B
L-PEPTIDE LINKINGC6 H7 N3 O3HIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.229 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.742α = 90
b = 84.363β = 90
c = 123.626γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references, Derived calculations, Structure summary