8J4C | pdb_00008j4c

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

PDB DOI: https://doi.org/10.2210/pdb8J4C/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Winmispira thermophila DSM 6578, Corynebacterium pollutisoli
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-04-19 Released: 2024-03-27
Deposition Author(s): Ikei, M., Miyazaki, R., Monden, K., Naito, Y., Takeuchi, A., Takahashi, Y.S., Tanaka, Y., Ichikawa, M., Tsukazaki, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.34 Å
R-Value Free:
0.311 (Depositor), 0.311 (DCC)
R-Value Work:
0.265 (Depositor), 0.265 (DCC)
R-Value Observed:
0.269 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

PubMed: 38656967 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pbio.3002601
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 106.67 kDa
Atom Count: 6,675
Modeled Residue Count: 816
Deposited Residue Count: 920
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spirochaeta thermophila YeeE(TsuA)-YeeD(TsuB),UPF0033 domain-containing protein, SirA-like domain-containing protein (chimera)	A [auth B], B [auth A]	460	Winmispira thermophila DSM 6578, Corynebacterium pollutisoli	Mutation(s): 1 Gene Names: Spith_0734, SAMN06295981_0228, Spith_0735 Membrane Entity: Yes
UniProt
Find proteins for G0GAP6 (Winmispira thermophila (strain ATCC 700085 / DSM 6578 / Z-1203)) Explore G0GAP6 Go to UniProtKB: G0GAP6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0GAP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B] E [auth B] F [auth B] G [auth B] H [auth B] D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
THJ (Subject of Investigation/LOI) Query on THJ Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain C [auth B] MOL2 format, chain O [auth A] MOL2 format, chain C [auth B] mmCIF format, chain O [auth A] mmCIF format, chain C [auth B]	C [auth B], O [auth A]	THIOSULFATE O₃ S₂ DHCDFWKWKRSZHF-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain O [auth A] Interactions & Density Focus chain C [auth B] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.34 Å
R-Value Free: 0.311 (Depositor), 0.311 (DCC)
R-Value Work: 0.265 (Depositor), 0.265 (DCC)
R-Value Observed: 0.269 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.98	α = 90
b = 102.44	β = 90
c = 186.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

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