Crystal structure of Eremococcus coleocola manganese transporter in complex with an aromatic bis-isothiourea substituted compound

Experimental Data Snapshot

  • Resolution: 3.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 

wwPDB Validation   3D Report Full Report

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Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds.

Manatschal, C.Pujol-Gimenez, J.Poirier, M.Reymond, J.L.Hediger, M.A.Dutzler, R.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.51913
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In humans, the divalent metal ion transporter-1 (DMT1) mediates the transport of ferrous iron across the apical membrane of enterocytes. Hence, its inhibition could be beneficial for the treatment of iron overload disorders. Here we characterize the interaction of aromatic bis-isothiourea-substituted compounds with human DMT1 and its prokaryotic homologue EcoDMT. Both transporters are inhibited by a common competitive mechanism with potencies in the low micromolar range. The crystal structure of EcoDMT in complex with a brominated derivative defines the binding of the inhibitor to an extracellular pocket of the transporter in direct contact with residues of the metal ion coordination site, thereby interfering with substrate loading and locking the transporter in its outward-facing state. Mutagenesis and structure-activity relationships further support the observed interaction mode and reveal species-dependent differences between pro- and eukaryotic transporters. Together, our data provide the first detailed mechanistic insight into the pharmacology of SLC11/NRAMP transporters.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Divalent metal cation transporter MntH494Eremococcus coleocola ACS-139-V-Col8Mutation(s): 0 
Gene Names: mntHHMPREF9257_1603
Membrane Entity: Yes 
Find proteins for E4KPW4 (Eremococcus coleocola ACS-139-V-Col8)
Explore E4KPW4 
Go to UniProtKB:  E4KPW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4KPW4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NJZ (Subject of Investigation/LOI)
Query on NJZ

Download Ideal Coordinates CCD File 
B [auth A][3-bromanyl-5-(carbamimidoylsulfanylmethyl)phenyl]methyl carbamimidothioate
C10 H13 Br N4 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.01α = 90
b = 81.65β = 107.43
c = 95.59γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release