The βE-Domain of Wheat Ec-1 Metallothionein: A Metal-Binding Domain with a Distinctive Structure

A strong 13C chemical shift signature provides the coordination mode of histidines in zinc-binding proteins

Zinc is the second most abundant metal ion incorporated in proteins, and is in many cases a crucial component of protein three-dimensional structures. Zinc ions are frequently coordinated by cysteine and histidine residues. Whereas cysteines bind to zinc via their unique S(γ) atom, histidines can coordinate zinc with two different coordination modes, either N(δ1) or N(ε2) is coordinating the zinc ion. The determination of this coordination mode is crucial for the accurate structure determination of a histidine-containing zinc-binding site by NMR. NMR chemical shifts contain a vast amount of information on local electronic and structural environments and surprisingly their utilization for the determination of the coordination mode of zinc-ligated histidines has been limited so far to (15)N nuclei. In the present report, we observed that the (13)C chemical shifts of aromatic carbons in zinc-ligated histidines represent a reliable signature of their coordination mode. Using a statistical analysis of (13)C chemical shifts, we show that (13)C(δ2) chemical shift is sensitive to the histidine coordination mode and that the chemical shift difference δ{(13)C(ε1)} - δ{(13)C(δ2)} provides a reference-independent marker of this coordination mode. The present approach allows the direct determination of the coordination mode of zinc-ligated histidines even with non-isotopically enriched protein samples and without any prior structural information.

Mining genomes of marine cyanobacteria for elements of zinc homeostasis

Zinc is a recognized essential element for the majority of organisms, and is indispensable for the correct function of hundreds of enzymes and thousands of regulatory proteins. In aquatic photoautotrophs including cyanobacteria, zinc is thought to be required for carbonic anhydrase and alkaline phosphatase, although there is evidence that at least some carbonic anhydrases can be cambialistic, i.e., are able to acquire in vivo and function with different metal cofactors such as Co²⁺ and Cd²⁺. Given the global importance of marine phytoplankton, zinc availability in the oceans is likely to have an impact on both carbon and phosphorus cycles. Zinc concentrations in seawater vary over several orders of magnitude, and in the open oceans adopt a nutrient-like profile. Most studies on zinc handling by cyanobacteria have focused on freshwater strains and zinc toxicity; much less information is available on marine strains and zinc limitation. Several systems for zinc homeostasis have been characterized in the freshwater species Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803, but little is known about zinc requirements or zinc handling by marine species. Comparative metallo-genomics has begun to explore not only the putative zinc proteome, but also specific protein families predicted to have an involvement in zinc homeostasis, including sensors for excess and limitation (SmtB and its homologs as well as Zur), uptake systems (ZnuABC), putative intracellular zinc chaperones (COG0523) and metallothioneins (BmtA), and efflux pumps (ZiaA and its homologs).

Minimal functional sites allow a classification of zinc sites in proteins

Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design.

High cadmium-binding ability of a novel Colocasia esculenta metallothionein increases cadmium tolerance in Escherichia coli and tobacco

Experimental evidence in vivo as to the functional roles and binding properties to cadmium (Cd) of type-2 plants metallothionein (MT) has been limited thus far. We investigated the biological role of metallothionein from Colocasia esculenta (CeMT2b) in Escherichia coli and tobacco, and developed a new model for the relationship between Cd tolerance and Cd-binding ability. Heterologous expression of CeMT2b in Escherichia coli greatly enhanced Cd tolerance and accumulated Cd content as compared to control cells. The molecular weight of CeMT2b increased with Cd, and CeMT2b bound up to 5.96±1 molar ratio (Cd/protein). Under Cd stress, transgenic tobacco plants displayed much better seedling growth and high Cd accumulation than the wild type. The presence of an extra CXC motif in CeMT2b contributed to the enhanced Cd-tolerance. The present study provides the first insight into the ability of type-2 plant MT to bind physiological Cd.

Structural features specific to plant metallothioneins

The metallothionein (MT) superfamily combines a large variety of small cysteine-rich proteins from nearly all phyla of life that have the ability to coordinate various transition metal ions, including Zn(II), Cd(II), and Cu(I). The members of the plant MT family are characterized by great sequence diversity, requiring further subdivision into four subfamilies. Very peculiar and not well understood is the presence of rather long cysteine-free amino acid linkers between the cysteine-rich regions. In light of the distinct differences in sequence to MTs from other families, it seems obvious to assume that these differences will also be manifested on the structural level. This was already impressively demonstrated with the elucidation of the three-dimensional structure of the wheat E(c)-1 MT, which revealed two metal cluster arrangements previously unprecedented for any MT. However, as this structure is so far the only one available for the plant MT family, other sources of information are in high demand. In this review the focus is thus set on any structural features known, deduced, or assumed for the plant MT proteins. This includes the determination of secondary structural elements by circular dichroism, IR, and Raman spectroscopy, the analysis of the influence of the long linker regions, and the evaluation of the spatial arrangement of the sequence separated cysteine-rich regions with the aid of, e.g., limited proteolytic digestion. In addition, special attention is paid to the contents of divalent metal ions as the metal ion to cysteine ratios are important for predicting and understanding possible metal-thiolate cluster structures.

Protein and metal cluster structure of the wheat metallothionein domain γ-E(c)-1: the second part of the puzzle

Metallothioneins (MTs) are small cysteine-rich proteins coordinating various transition metal ions, including Zn(II), Cd(II), and Cu(I). MTs are ubiquitously present in all phyla, indicating a successful molecular concept for metal ion binding in all organisms. The plant MT E(c)-1 from Triticum aestivum, common bread wheat, is a Zn(II)-binding protein that comprises two domains and binds up to six metal ions. The structure of the C-terminal four metal ion binding β(E) domain was recently described. Here we present the structure of the N-terminal second domain, γ-E(c)-1, determined by NMR spectroscopy. The γ-E(c)-1 domain enfolds an M (2) (II) Cys(6) cluster and was characterized as part of the full-length Zn(6)E(c)-1 protein as well as in the form of the separately expressed domain, both in the Zn(II)-containing isoform and the Cd(II)-containing isoform. Extended X-ray absorption fine structure analysis of Zn(2)γ-E(c)-1 clearly shows the presence of a ZnS(4) coordination sphere with average Zn-S distances of 2.33 Å. (113)Cd NMR experiments were used to identify the M(II)-Cys connectivity pattern, and revealed two putative metal cluster conformations. In addition, the general metal ion coordination abilities of γ-E(c)-1 were probed with Cd(II) binding experiments as well as by pH titrations of the Zn(II) and Cd(II) forms, the latter suggesting an interaction of the γ domain and the β(E) domain within the full-length protein.

The "magic numbers" of metallothionein

Metallothioneins (MT) are a family of small cysteine rich proteins, which since their discovery in 1957, have been implicated in a range of roles including toxic metal detoxification, protection against oxidative stress, and as a metallochaperone involved in the homeostasis of both zinc and copper. The most well studied member of the family is the mammalian metallothionein, which consists of two domains: a β-domain with 9 cysteine residues, which sequesters 3 Cd(2+) or Zn(2+) or 6 Cu(+) ions, and an α-domain with 11 cysteine residues and, which sequesters 4 Cd(2+) or Zn(2+) or 6 Cu(+) ions. Despite over half a century of research, the exact functions of MT are still unknown. Much of current research aims to elucidate the mechanism of metal binding, as well as to isolate intermediates in metal exchange reactions; reactions necessary to maintain homeostatic equilibrium. These studies further our understanding of the role(s) of this remarkable and ubiquitous protein. Recently, supermetallated forms of the protein, where supermetallation describes metallation in excess of traditional levels, have been reported. These species may potentially be the metal exchange intermediates necessary to maintain homeostatic equilibrium. This review focuses on recent advances in the understanding of the mechanistic properties of metal binding, the implications for the metal induced protein folding reactions proposed for metallothionein metallation, the value of "magic numbers", which we informally define as the commonly determined metal-to-protein stoichiometric ratios and the significance of the new supermetallated states of the protein and the possible interpretation of the structural properties of this new metallation status. Together we provide a commentary on current experimental and theoretical advances and frame our consideration in terms of the possible functions of MT.

Plant metallothioneins--metal chelators with ROS scavenging activity?

Metallothioneins (MTs) are ubiquitous cysteine-rich proteins present in plants, animals, fungi and cyanobacteria. In plants, MTs are suggested to be involved in metal tolerance or homeostasis, as they are able to bind metal ions through the thiol groups of their cysteine residues. Recent reports show that MTs are also involved in the scavenging of reactive oxygen species (ROS). The interplay between these roles is not entirely clear. Plants have many MT isoforms with overlapping expression patterns, and no specific role for any of them has been assigned. This review is focused on recent findings on plant MTs.

The isolated Cys2His2 site in EC metallothionein mediates metal-specific protein folding

The selectivity of proteins involved in metal ion homeostasis is an important part of the puzzle to understand how cells allocate the correct metal ions to the correct proteins. Due to their similar ligand-binding properties, and their frequent co-existence in soils, essential zinc and toxic cadmium are a particularly challenging couple. Thus, minimisation of competition of Cd(2+) for Zn(2+) sites is of crucial importance for organisms that are in direct contact with soil. Amongst these, plants have an especially critical role, due to their importance for nutrition and energy. We have studied an embryo-specific, zinc-binding metallothionein (E(C)) from wheat by nuclear magnetic resonance, electrospray mass spectrometry, site-directed mutagenesis, and molecular modelling. Wheat E(C) exploits differences in affinities of Cys(4) and Cys(2)His(2) sites for Cd(2+) and Zn(2+) to achieve metal-selective protein folding. We propose that this may constitute a novel mechanism to discriminate between essential Zn(2+) and toxic Cd(2+).

Metallothioneins: unparalleled diversity in structures and functions for metal ion homeostasis and more

Metallothioneins have been the subject of intense study for five decades, and have greatly inspired the development of bio-analytical methodologies including multi-dimensional and multi-nuclear NMR.With further advancements in molecular biology, protein science, and instrumental techniques, recent years have seen a renaissance of research into metallothioneins. The current report focuses on in vitro studies of so-called class II metallothioneins from a variety of phyla, highlighting the diversity of metallothioneins in terms of structure, biological functions, and molecular functions such as metal ion specificity, thermodynamic stabilities, and kinetic reactivity. We are still far from being able to predict any of these properties, and further efforts will be required to generate the knowledge that will enable a better understanding of what governs the biological and chemical properties of these unusual and intriguing small proteins.

Caenorhabditis elegans metallothionein isoform specificity--metal binding abilities and the role of histidine in CeMT1 and CeMT2

Two metallothionein (MT) isoforms have been identified in the model nematode Caenorhabditis elegans: CeMT1 and CeMT2, comprising two polypeptides that are 75 and 63 residues in length, respectively. Both isoforms encompass a conserved cysteine pattern (19 in CeMT1 and 18 in CeMT2) and, most significantly, as a result of their coordinative potential, CeMT1 includes four histidines, whereas CeMT2 has only one. In the present study, we present a comprehensive and comparative analysis of the metal [Zn(II), Cd(II) and Cu(I)] binding abilities of CeMT1 and CeMT2, performed through spectroscopic and spectrometric characterization of the recombinant metal-MT complexes synthesized for wild-type isoforms (CeMT1 and CeMT2), their separate N- and C-terminal moieties (NtCeMT1, CtCeMT1, NtCeMT2 and CtCeMT2) and a DeltaHisCeMT2 mutant. The corresponding in vitro Zn/Cd- and Zn/Cu-replacement and acidification/renaturalization processes have also been studied, as well as protein modification strategies that make it possible to identify and quantify the contribution of the histidine residues to metal coordination. Overall, the data obtained in the present study are consistent with a scenario where both isoforms exhibit a clear preference for divalent metal ion binding, rather than for Cu coordination, although this preference is more pronounced towards cadmium for CeMT2, whereas it is markedly clearer towards Zn for CeMT1. The presence of histidines in these MTs is revealed to be decisive for their coordination performance. In CeMT1, they contribute to the binding of a seventh Zn(II) ion in relation to the M(II)(6)-CeMT2 complexes, both when synthesized in the presence of supplemented Zn(II) or Cd(II). In CeMT2, the unique C-terminal histidine abolishes the Cu-thionein character that this isoform would otherwise exhibit.