RCSB PDB - 8K1R: YeeE(TsuA)-YeeD(TsuB) complex for thiosulfate uptake

 8K1R

YeeE(TsuA)-YeeD(TsuB) complex for thiosulfate uptake


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition.

Ikei, M.Miyazaki, R.Monden, K.Naito, Y.Takeuchi, A.Takahashi, Y.S.Tanaka, Y.Murata, K.Mori, T.Ichikawa, M.Tsukazaki, T.

(2024) PLoS Biol 22: e3002601-e3002601

  • DOI: https://doi.org/10.1371/journal.pbio.3002601
  • Primary Citation of Related Structures:  
    8J4C, 8K1R

  • PubMed Abstract: 

    Uptake of thiosulfate ions as an inorganic sulfur source from the environment is important for bacterial sulfur assimilation. Recently, a selective thiosulfate uptake pathway involving a membrane protein YeeE (TsuA) in Escherichia coli was characterized. YeeE-like proteins are conserved in some bacteria, archaea, and eukaryotes. However, the precise function of YeeE, along with its potential partner protein in the thiosulfate ion uptake pathway, remained unclear. Here, we assessed selective thiosulfate transport via Spirochaeta thermophila YeeE in vitro and characterized E. coli YeeD (TsuB) as an adjacent and essential protein for YeeE-mediated thiosulfate uptake in vivo. We further showed that S. thermophila YeeD possesses thiosulfate decomposition activity and that a conserved cysteine in YeeD was modified to several forms in the presence of thiosulfate. Finally, the crystal structures of S. thermophila YeeE-YeeD fusion proteins at 3.34-Å and 2.60-Å resolutions revealed their interactions. The association was evaluated by a binding assay using purified S. thermophila YeeE and YeeD. Based on these results, a model of the sophisticated uptake of thiosulfate ions by YeeE and YeeD is proposed.


  • Organizational Affiliation

    Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spirochaeta thermophila YeeE(TsuA)-YeeD(TsuB),UPF0033 domain-containing protein, SirA-like domain-containing protein (chimera)A [auth B],
B [auth A]
460Spirochaeta thermophila DSM 6578Corynebacterium pollutisoliMutation(s): 2 
Gene Names: Spith_0734SAMN06295981_0228Spith_0735
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
C [auth B]
D [auth B]
E [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.58α = 90
b = 101.75β = 90
c = 182.76γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted OLCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--
Japan Science and TechnologyJapan--
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Database references, Structure summary