6IDS

Crystal structure of Vibrio cholerae MATE transporter VcmN D35N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter.

Kusakizako, T.Claxton, D.P.Tanaka, Y.Maturana, A.D.Kuroda, T.Ishitani, R.Mchaourab, H.S.Nureki, O.

(2019) Structure 27: 293

  • DOI: 10.1016/j.str.2018.10.004
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Multidrug and toxic compound extrusion (MATE) transporters efflux toxic compounds using a Na + or H + gradient across the membrane. Although the structures of MATE transporters have been reported, the cation-coupled substrate ...

    Multidrug and toxic compound extrusion (MATE) transporters efflux toxic compounds using a Na + or H + gradient across the membrane. Although the structures of MATE transporters have been reported, the cation-coupled substrate transport mechanism remains controversial. Here we report crystal structures of VcmN, a Vibrio cholerae MATE transporter driven by the H + gradient. High-resolution structures in two distinct conformations associated with different pHs revealed that the rearrangement of the hydrogen-bonding network around the conserved Asp35 induces the bending of transmembrane helix 1, as in the case of the H + -coupled Pyrococcus furiosus MATE transporter. We also determined the crystal structure of the D35N mutant, which captured a unique conformation of TM1 facilitated by an altered hydrogen-bonding network. Based on the present results, we propose a common step in the transport cycle shared among prokaryotic H + -coupled MATE transporters.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: nureki@bs.s.u-tokyo.ac.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MATE family efflux transporter
A
441Vibrio choleraeMutation(s): 1 
Gene Names: CGT79_05080
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.468α = 90
b = 90.149β = 90
c = 102.257γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references