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TitleEnergy coupling and stoichiometry of Zn/H antiport by the prokaryotic cation diffusion facilitator YiiP.
Journal, issue, pagesElife, Vol. 12, Year 2023
Publish dateOct 31, 2023
AuthorsAdel Hussein / Shujie Fan / Maria Lopez-Redondo / Ian Kenney / Xihui Zhang / Oliver Beckstein / David L Stokes /
PubMed AbstractYiiP from Shewanella oneidensis is a prokaryotic Zn/H antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for ...YiiP from Shewanella oneidensis is a prokaryotic Zn/H antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn to 2-3 H depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn.
External linksElife / PubMed:37906094 / PubMed Central
MethodsEM (single particle)
Resolution3.46 - 4.03 Å
Structure data

28881

8f6e

EMDB-28881, PDB-8f6e:
Cryo-EM structure of a Zinc-loaded wild-type YiiP-Fab complex
Method: EM (single particle) / Resolution: 3.8 Å

28882

8f6f

EMDB-28882, PDB-8f6f:
Cryo-EM structure of a Zinc-loaded D51A mutant of the YiiP-Fab complex
Method: EM (single particle) / Resolution: 3.6 Å

28883

8f6h

EMDB-28883, PDB-8f6h:
Cryo-EM structure of a Zinc-loaded asymmetrical TMD D70A mutant of the YiiP-Fab complex
Method: EM (single particle) / Resolution: 3.9 Å

28884

8f6i

EMDB-28884, PDB-8f6i:
Cryo-EM structure of a Zinc-loaded symmetrical D70A mutant of the YiiP-Fab complex
Method: EM (single particle) / Resolution: 4.03 Å

28885

8f6j

EMDB-28885, PDB-8f6j:
Cryo-EM structure of a Zinc-loaded D287A mutant of the YiiP-Fab complex
Method: EM (single particle) / Resolution: 3.7 Å

28886

8f6k

EMDB-28886, PDB-8f6k:
Cryo-EM structure of a Zinc-loaded H263A/D287A mutant of the YiiP-Fab complex
Method: EM (single particle) / Resolution: 3.46 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • shewanella oneidensis (bacteria)
  • homo sapiens (human)
  • shewanella oneidensis mr-1 (bacteria)
KeywordsTRANSPORT PROTEIN / Zinc transporter / cation diffusion facilitator / membrane protein

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