Crystal structure of Vibrio cholerae MATE transporter VcmN D35N mutant

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

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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: https://doi.org/10.1016/j.str.2018.10.004
  • Primary Citation of Related Structures:  
    6IDP, 6IDR, 6IDS

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MATE family efflux transporter441Vibrio choleraeMutation(s): 1 
Gene Names: CGT79_05080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references