The two-domain elevator-type mechanism of zinc-transporting ZIP proteins

Abstract

Zinc is essential for all organisms and yet detrimental at elevated levels. Hence, homeostasis of this metal is tightly regulated. The Zrt/Irt-like proteins (ZIPs) represent the only zinc importers in metazoans. Mutations in human ZIPs cause serious disorders, but the mechanism by which ZIPs transfer zinc remains elusive. Hitherto, structural information is only available for a model member, BbZIP, and as a single, ion-bound conformation, precluding mechanistic insights. Here, we elucidate an inward-open metal-free BbZIP structure, differing substantially in the relative positions of the two separate domains of ZIPs. With accompanying coevolutional analyses, mutagenesis, and uptake assays, the data point to an elevator-type transport mechanism, likely shared within the ZIP family, unifying earlier functional data. Moreover, the structure reveals a previously unknown ninth transmembrane segment that is important for activity in vivo. Our findings outline the mechanistic principles governing ZIP-protein transport and enhance the molecular understanding of ZIP-related disorders.

Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter

“…α0a associates with α4 via hydrophobic interactions and α3 via hydrogen bonds (Supplementary Fig. 9d ), which provides a reasonable structural explanation of hyperactivation of the transporter upon α0a deletion which would otherwise limit the movement of the transport domain relative to the scaffold domain 82 . Remarkably, although the method of generating the OFC model in this work (repeat-swap homology modeling) is different from the approach used in that report (manually adjusting the position of the transport domain relative to the scaffold domain to eliminate the mismatch between the predicted contacting residues and the structure in the IFC), the two OFC models are consistent in that the transport site is lifted toward the extracellular space by ~8 Å upon the IFC-to-OFC transition (Fig.…”

Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter

“…Lastly, the amphipathic helix (α0a, residue 7-21) solved in our structure was missed in 7Z6N. α0a associates with α4 via hydrophobic interactions and α3 via hydrogen bonds ( Figure S9d ), which provides a reasonable structural explanation of hyperactivation of the transporter upon α0a deletion which would otherwise limit the movement of the transport domain relative to the scaffold domain 82 . Remarkably, although the method of generating the OFC model in this work (repeat-swap homology modeling) is different from the approach used in that report (manually adjusting the position of the transport domain relative to the scaffold domain to eliminate the mismatch between the predicted contacting residues and the structure in the IFC), the two OFC models are consistent in that the transport site is lifted toward the extracellular space by ~8 Å upon the IFC-to-OFC transition ( Figure 6 ).…”

“…While this manuscript was under revision, an independent study reported a structure of BbZIP in the metal-free state similarly crystallized at low pH (PDB ID: 7Z6N, referred to as 7Z6N hereafter) 82 . Contrast and comparison of two structures provide additional insights into the elevator-type transport mechanism ( Figure S9 ).…”

A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2

“…The movement of the substrate-binding site across the membrane, and the presence of two “barriers” and two “gates” that form upon the conformational transition, indicates that the ZIP protein family members could act through moving barriers with two gates, as envisioned in the comprehensive work of Garaeva and Slotboom (2020) for the elevator-type mechanism taking place in bile acid transporter ASBT. During the revision of the present work, we became aware of a recently published manuscript describing an elevator-type mechanism for BbZIP ( Wiuf et al, 2022 ). Thus, the transport mechanism here hypothesized is fully supported by the study of Wiuf et al (2022) .…”

“…During the revision of the present work, we became aware of a recently published manuscript describing an elevator-type mechanism for BbZIP ( Wiuf et al, 2022 ). Thus, the transport mechanism here hypothesized is fully supported by the study of Wiuf et al (2022) . In conclusion, the availability of structural models for all members of the hZIP family of metal transporters will be a valuable aid in the experimental characterization of the functional details of metal transport.…”