6LEP

Crystal structure of thiosulfate transporter YeeE inactive mutant - C91A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake.

Tanaka, Y.Yoshikaie, K.Takeuchi, A.Ichikawa, M.Mori, T.Uchino, S.Sugano, Y.Hakoshima, T.Takagi, H.Nonaka, G.Tsukazaki, T.

(2020) Sci Adv 6: eaba7637-eaba7637

  • DOI: https://doi.org/10.1126/sciadv.aba7637
  • Primary Citation of Related Structures:  
    6LEO, 6LEP

  • PubMed Abstract: 

    We have demonstrated that a bacterial membrane protein, YeeE, mediates thiosulfate uptake. Thiosulfate is used for cysteine synthesis in bacteria as an inorganic sulfur source in the global biological sulfur cycle. The crystal structure of YeeE at 2.5-Å resolution reveals an unprecedented hourglass-like architecture with thiosulfate in the positively charged outer concave side. YeeE is composed of loops and 13 helices including 9 transmembrane α helices, most of which show an intramolecular pseudo 222 symmetry. Four characteristic loops are buried toward the center of YeeE and form its central region surrounded by the nine helices. Additional electron density maps and successive molecular dynamics simulations imply that thiosulfate can remain temporally at several positions in the proposed pathway. We propose a plausible mechanism of thiosulfate uptake via three important conserved cysteine residues of the loops along the pathway.


  • Organizational Affiliation

    Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulf_transp domain-containing protein339Spirochaeta thermophilaMutation(s): 1 
Gene Names: Spith_0734
Membrane Entity: Yes 
UniProt
Find proteins for G0GAP6 (Spirochaeta thermophila (strain ATCC 700085 / DSM 6578 / Z-1203))
Explore G0GAP6 
Go to UniProtKB:  G0GAP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0GAP6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.91α = 90
b = 94.61β = 90
c = 101.51γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP19K06526, JP19K22395, JP19H05639

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description