Water molecules mediate zinc mobility in the bacterial zinc diffusion channel ZIPB

Evolution, classification, and mechanisms of transport, activity regulation, and substrate specificity of ZIP metal transporters

The Zrt/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent d-block metal transporters that play central roles in the uptake, secretion, excretion, and distribution of several essential and toxic metals in living organisms. The past few years has witnessed rapid progress in the molecular basis of these membrane transport proteins. In this critical review, we summarize the research progress at the molecular level of the ZIP family and discuss the future prospects. Furthermore, an evolutionary path for the unique ZIP fold and a new classification of the ZIP family are proposed based on the presented structural and sequence analyses.

Metalation and activation of Zn2+ enzymes via early secretory pathway-resident ZNT proteins

Zinc (Zn2+), an essential trace element, binds to various proteins, including enzymes, transcription factors, channels, and signaling molecules and their receptors, to regulate their activities in a wide range of physiological functions. Zn2+ proteome analyses have indicated that approximately 10% of the proteins encoded by the human genome have potential Zn2+ binding sites. Zn2+ binding to the functional site of a protein (for enzymes, the active site) is termed Zn2+ metalation. In eukaryotic cells, approximately one-third of proteins are targeted to the endoplasmic reticulum; therefore, a considerable number of proteins mature by Zn2+ metalation in the early secretory pathway compartments. Failure to capture Zn2+ in these compartments results in not only the inactivation of enzymes (apo-Zn2+ enzymes), but also their elimination via degradation. This process deserves attention because many Zn2+ enzymes that mature during the secretory process are associated with disease pathogenesis. However, how Zn2+ is mobilized via Zn2+ transporters, particularly ZNTs, and incorporated in enzymes has not been fully elucidated from the cellular perspective and much less from the biophysical perspective. This review focuses on Zn2+ enzymes that are activated by Zn2+ metalation via Zn2+ transporters during the secretory process. Further, we describe the importance of Zn2+ metalation from the physiopathological perspective, helping to reveal the importance of understanding Zn2+ enzymes from a biophysical perspective.

Structural mechanism of intracellular autoregulation of zinc uptake in ZIP transporters

Zinc is an essential micronutrient that supports all living organisms through regulating numerous biological processes. However, the mechanism of uptake regulation by intracellular Zn2+ status remains unclear. Here we report a cryo-electron microscopy structure of a ZIP-family transporter from Bordetella bronchiseptica at 3.05 Å resolution in an inward-facing, inhibited conformation. The transporter forms a homodimer, each protomer containing nine transmembrane helices and three metal ions. Two metal ions form a binuclear pore structure, and the third ion is located at an egress site facing the cytoplasm. The egress site is covered by a loop, and two histidine residues on the loop interact with the egress-site ion and regulate its release. Cell-based Zn2+ uptake and cell growth viability assays reveal a negative regulation of Zn2+ uptake through sensing intracellular Zn2+ status using a built-in sensor. These structural and biochemical analyses provide mechanistic insight into the autoregulation of zinc uptake across membranes.

High-resolution structure of a mercury cross-linked ZIP metal transporter reveals delicate motions and metal relay for regulated zinc transport

Zrt-/Irt-like protein (ZIP) divalent metal transporters play a central role in maintaining trace element homeostasis. The prototypical ZIP from Bordetella bronchiseptica (BbZIP) is an elevator-type transporter, but the dynamic motions and detailed transport mechanism remain to be elucidated. Here, we report a high-resolution crystal structure of a mercury-crosslinked BbZIP variant at 1.95 Å, revealing an upward rotation of the transport domain in the new inward-facing conformation and a water-filled metal release channel that is divided into two parallel pathways by the previously disordered cytoplasmic loop. Mutagenesis and transport assays indicated that the newly identified high-affinity metal binding site in the primary pathway acts as a "metal sink" to reduce the transport rate. The discovery of a hinge motion around an extracellular axis allowed us to propose a sequential hinge-elevator-hinge movement of the transport domain to achieve alternating access. These findings provide key insights into the transport mechanisms and activity regulation.

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

The Zrt-/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent metal transporters critically involved in maintaining systemic and cellular homeostasis of zinc, iron, and manganese. Here, we present a study on a prokaryotic ZIP from Bordetella bronchiseptica (BbZIP) by combining structural biology, evolutionary covariance, computational modeling, and a variety of biochemical assays to tackle the issue of the transport mechanism which has not been established for the ZIP family. The apo state structure in an inward-facing conformation revealed a disassembled transport site, altered inter-helical interactions, and importantly, a rigid body movement of a 4-transmembrane helix (TM) bundle relative to the other TMs. The computationally generated and biochemically validated outward-facing conformation model revealed a slide of the 4-TM bundle, which carries the transport site(s), by approximately 8 Å toward the extracellular side against the static TMs which mediate dimerization. These findings allow us to conclude that BbZIP is an elevator-type transporter.

The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS

The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.

Manganese transport in mammals by zinc transporter family proteins, ZNT and ZIP

Manganese (Mn) is an essential trace element required for various biological processes. However, excess Mn causes serious side effects in humans, including parkinsonism. Thus, elucidation of Mn homeostasis at the systemic, cellular, and molecular levels is important. Many metal transporters and channels can be involved in the transport and homeostasis of Mn, and an increasing body of evidence shows that several zinc (Zn) transporters belonging to the ZIP and ZNT families, specifically, ZNT10, ZIP8, and ZIP14, play pivotal roles in Mn metabolism. Mutations in the genes encoding these transporter proteins are associated with congenital disorders related to dysregulated Mn homeostasis in humans. Moreover, single nucleotide polymorphisms of ZIP8 are associated with multiple clinical phenotypes. In this review, we discuss the recent literature on the structural and biochemical features of ZNT10, ZIP8, and ZIP14, including transport mechanisms, regulation of expression, and pathophysiological functions. Because a disturbance in Mn homeostasis is closely associated with a variety of phenotypes and risk of human diseases, these transporters constitute a significant target for drug development. An understanding of the roles of these key transporters in Mn metabolism should provide new insights into pharmacological applications of their inhibitors and enhancers in human diseases.

Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter

Zinc homeostasis in mammals is constantly and precisely maintained by sophisticated regulatory proteins. Among them, the Zrt/Irt-like protein (ZIP) regulates the influx of zinc into the cytoplasm. In this work, we have employed all-atom molecular dynamics simulations to investigate the Zn²⁺ transport mechanism in prokaryotic ZIP obtained from Bordetella bronchiseptica (BbZIP) in a membrane bilayer. Additionally, the structural and dynamical transformations of BbZIP during this process have been analyzed. This study allowed us to develop a hypothesis for the zinc influx mechanism and formation of the metal-binding site. We have created a model for the outward-facing form of BbZIP (experimentally only the inward-facing form has been characterized) that has allowed us, for the first time, to observe the Zn²⁺ ion entering the channel and binding to the negatively charged M2 site. It is thought that the M2 site is less favored than the M1 site, which then leads to metal ion egress; however, we have not observed the M1 site being occupied in our simulations. Furthermore, removing both Zn²⁺ ions from this complex resulted in the collapse of the metal-binding site, illustrating the "structural role" of metal ions in maintaining the binding site and holding the proteins together. Finally, due to the long Cd²⁺-residue bond distances observed in the X-ray structures, we have proposed the existence of an H₃O⁺ ion at the M2 site that plays an important role in protein stability in the absence of the metal ion.

Expression, Purification and Characterization of a ZIP Family Transporter from Desulfovibrio vulgaris

The ZIP family transport zinc ions from the extracellular medium across the plasma membrane or from the intracellular compartments across endomembranes, which play fundamental roles in metal homeostasis and are broadly involved in physiological and pathological processes. Desulfovibrio is the predominant sulphate-reducing bacteria in human colonic microbiota, but also a potential choice for metal bioremediation. while, there are no published studies describing the zinc transporters from Desulfovibrio up to now. In this study, we obtained for the first time a heterologously expressed ZIP homolog from Desulfovibrio vulgaris, termed dvZip. The purified dvZip was reconstituted into proteoliposomes, and confirmed its zinc transport ability in vitro. By combining topology prediction, homology modeling and phylogenetic approaches, we also noticed that dvZip belongs to the GufA and probably have 8 transmembrane α-helical segments (TM 1-8) in which both termini are located on the extracellular, with TM2, 4, 5 and 7 create an inner bundle. We believe that purification and characterization of zinc (probably also cadmium) transporters from Desulfovibrio vulgaris such as dvZip could shed light on understanding of metal homeostasis of Desulfovibrio and provided protein products for future detailed function and structural studies.

Zinc transporters and their functional integration in mammalian cells

Zinc is a ubiquitous biological metal in all living organisms. The spatiotemporal zinc dynamics in cells provide crucial cellular signaling opportunities, but also challenges for intracellular zinc homeostasis with broad disease implications. Zinc transporters play a central role in regulating cellular zinc balance and subcellular zinc distributions. The discoveries of two complementary families of mammalian zinc transporters (ZnTs and ZIPs) in the mid-1990s spurred much speculation on their metal selectivity and cellular functions. After two decades of research, we have arrived at a biochemical description of zinc transport. However, in vitro functions are fundamentally different from those in living cells, where mammalian zinc transporters are directed to specific subcellular locations, engaged in dedicated macromolecular machineries, and connected with diverse cellular processes. Hence, the molecular functions of individual zinc transporters are reshaped and deeply integrated in cells to promote the utilization of zinc chemistry to perform enzymatic reactions, tune cellular responsiveness to pathophysiologic signals, and safeguard cellular homeostasis. At present, the underlying mechanisms driving the functional integration of mammalian zinc transporters are largely unknown. This knowledge gap has motivated a shift of the research focus from in vitro studies of purified zinc transporters to in cell studies of mammalian zinc transporters in the context of their subcellular locations and protein interactions. In this review, we will outline how knowledge of zinc transporters has been accumulated from in-test-tube to in-cell studies, highlighting new insights and paradigm shifts in our understanding of the molecular and cellular basis of mammalian zinc transporter functions.

Toward unzipping the ZIP metal transporters: structure, evolution, and implications on drug discovery against cancer

The Zrt-/Irt-like protein (ZIP) family consists of divalent metal transporters, ubiquitous in all kingdoms of life. Since the discovery of the first ZIPs in the 1990s, the ZIP family has been expanding to contain tens of thousands of members playing key roles in uptake and homeostasis of life-essential trace elements, primarily zinc, iron and manganese. Some family members are also responsible for toxic metal (particularly cadmium) absorption and distribution. Their central roles in trace element biology, and implications in many human diseases, including cancers, have elicited interest across multiple disciplines for potential applications in biomedicine, agriculture and environmental protection. In this review and perspective, selected areas under rapid progress in the last several years, including structural biology, evolution, and drug discovery against cancers, are summarised and commented. Future research to address the most prominent issues associated with transport and regulation mechanisms are also discussed.

Transcription factors and transporters in zinc homeostasis: lessons learned from fungi

Zinc is an essential nutrient for all organisms because this metal serves as a critical structural or catalytic cofactor for many proteins. These zinc-dependent proteins are abundant in the cytosol as well as within organelles of eukaryotic cells such as the nucleus, mitochondria, endoplasmic reticulum, Golgi, and storage compartments such as the fungal vacuole. Therefore, cells need zinc transporters so that they can efficiently take up the metal and move it around within cells. In addition, because zinc levels in the environment can vary drastically, the activity of many of these transporters and other components of zinc homeostasis is regulated at the level of transcription by zinc-responsive transcription factors. Mechanisms of post-transcriptional control are also important for zinc homeostasis. In this review, the focus will be on our current knowledge of zinc transporters and their regulation by zinc-responsive transcription factors and other mechanisms in fungi because these organisms have served as useful paradigms of zinc homeostasis in all organisms. With this foundation, extension to other organisms will be made where warranted.