STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORTER with the inhibitor 5-(2-naphthylmethyl)-L-hydantoin.

Experimental Data Snapshot

  • Resolution: 3.70 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Molecular Mechanism of Ligand Recognition by Membrane Transport Protein, Mhp1.

Simmons, K.J.Jackson, S.M.Brueckner, F.Patching, S.G.Beckstein, O.Ivanova, E.Geng, T.Weyand, S.Drew, D.Lanigan, J.Sharples, D.J.Sansom, M.S.Iwata, S.Fishwick, C.W.Johnson, A.P.Cameron, A.D.Henderson, P.J.

(2014) EMBO J 33: 1831

  • DOI: https://doi.org/10.15252/embj.201387557
  • Primary Citation of Related Structures:  
    4D1A, 4D1B, 4D1C, 4D1D

  • PubMed Abstract: 

    The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1.

  • Organizational Affiliation

    School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYDANTOIN TRANSPORT PROTEIN495Microbacterium liquefaciensMutation(s): 0 
Membrane Entity: Yes 
Find proteins for D6R8X8 (Microbacterium liquefaciens)
Explore D6R8X8 
Go to UniProtKB:  D6R8X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6R8X8
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 3.70 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.6α = 90
b = 106.9β = 90
c = 106.8γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description