4D1B

STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORTER, IN A CLOSED CONFORMATION WITH BENZYL-HYDANTOIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.15252/embj.201387557
  • Primary Citation of Related Structures:  

  • 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 sol ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDANTOIN TRANSPORT PROTEIN
A
495Microbacterium liquefaciensMutation(s): 0 
Gene Names: hyuP
Find proteins for D6R8X8 (Microbacterium liquefaciens)
Go to UniProtKB:  D6R8X8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
5FH
Query on 5FH

Download SDF File 
Download CCD File 
A
(5S)-5-benzylimidazolidine-2,4-dione
C10 H10 N2 O2
DBOMTIHROGSFTI-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.283 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.614α = 90.00
b = 106.742β = 90.00
c = 107.852γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references