5AYO

Crystal structure of a bacterial homologue of iron transporter ferroportin in inward-facing state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin

Taniguchi, R.Kato, H.E.Font, J.Deshpande, C.N.Wada, M.Ito, K.Ishitani, R.Jormakka, M.Nureki, O.

(2015) Nat Commun 6: 8545-8545

  • DOI: 10.1038/ncomms9545
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In vertebrates, the iron exporter ferroportin releases Fe(2+) from cells into plasma, thereby maintaining iron homeostasis. The transport activity of ferroportin is suppressed by the peptide hormone hepcidin, which exhibits upregulated expression in ...

    In vertebrates, the iron exporter ferroportin releases Fe(2+) from cells into plasma, thereby maintaining iron homeostasis. The transport activity of ferroportin is suppressed by the peptide hormone hepcidin, which exhibits upregulated expression in chronic inflammation, causing iron-restrictive anaemia. However, due to the lack of structural information about ferroportin, the mechanisms of its iron transport and hepcidin-mediated regulation remain largely elusive. Here we report the crystal structures of a putative bacterial homologue of ferroportin, BbFPN, in both the outward- and inward-facing states. Despite undetectable sequence similarity, BbFPN adopts the major facilitator superfamily fold. A comparison of the two structures reveals that BbFPN undergoes an intra-domain conformational rearrangement during the transport cycle. We identify a substrate metal-binding site, based on structural and mutational analyses. Furthermore, the BbFPN structures suggest that a predicted hepcidin-binding site of ferroportin is located within its central cavity. Thus, BbFPN may be a valuable structural model for iron homeostasis regulation by ferroportin.


    Organizational Affiliation

    Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Solute carrier family 39 (Iron-regulated transporter)A440Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: slc39Bd2019
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
Ferroportin (FPN) Fe2+ transporter (SLC40A1) analog, outward-facing conformation
Find proteins for Q6MLJ0 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100))
Explore Q6MLJ0 
Go to UniProtKB:  Q6MLJ0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.53α = 90
b = 70.68β = 90
c = 101.79γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations