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TitleZinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.
Journal, issue, pagesJ Gen Physiol, Vol. 153, Issue 8, Year 2021
Publish dateAug 2, 2021
AuthorsMaria Lopez-Redondo / Shujie Fan / Akiko Koide / Shohei Koide / Oliver Beckstein / David L Stokes /
PubMed AbstractYiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a ...YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle.
External linksJ Gen Physiol / PubMed:34254979 / PubMed Central
MethodsEM (single particle)
Resolution3.42 - 4.0 Å
Structure data

23092

7kzx

EMDB-23092, PDB-7kzx:
Cryo-EM structure of YiiP-Fab complex in Apo state
Method: EM (single particle) / Resolution: 4.0 Å

23093

7kzz

EMDB-23093, PDB-7kzz:
Cryo-EM structure of YiiP-Fab complex in Holo state
Method: EM (single particle) / Resolution: 3.42 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • shewanella oneidensis (bacteria)
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / Zinc / transporter / cation diffusion facilitator / holo state / inward-facing state / Zinc transport

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