Visualizing the metal-binding versatility of copper trafficking sites

Important Structural Features of Thiolate-Rich Four-Helix Bundles for Cu(I) Uptake and Removal

A family of bacterial copper storage proteins (the Csps) possess thiolate-lined four-helix bundles whose cores can be filled with Cu(I) ions. The majority of Csps are cytosolic (Csp3s), and in vitro studies carried out to date indicate that the Csp3s from Methylosinus trichosporium OB3b (MtCsp3), Bacillus subtilis (BsCsp3), and Streptomyces lividans (SlCsp3) are alike. Bioinformatics have highlighted homologues with potentially different Cu(I)-binding properties from these characterized "classical" Csp3s. Determination herein of the crystal structure of the protein (RkCsp3) from the methanotroph Methylocystis sp. strain Rockwell with Cu(I) bound identifies this as the first studied example of a new subgroup of Csp3s. The most significant structural difference from classical Csp3s is the presence of only two Cu(I) sites at the mouth of the bundle via which Cu(I) ions enter and leave. This is due to the absence of three Cys residues and a His-containing motif, which allow classical Csp3s to bind five to six Cu(I) ions in this region. Regardless, RkCsp3 exhibits rapid Cu(I) binding and the fastest measured Cu(I) removal rate for a Csp3 when using high-affinity ligands as surrogate partners. New experiments on classical Csp3s demonstrate that their His-containing motif is not essential for fast Cu(I) uptake and removal. Other structural features that could be important for these functionally relevant in vitro properties are discussed.

Disrupting Cu trafficking as a potential therapy for cancer

Copper ions play a crucial role in various cellular biological processes. However, these copper ions can also lead to toxicity when their concentration is not controlled by a sophisticated copper-trafficking system. Copper dys-homeostasis has been linked to a variety of diseases, including neurodegeneration and cancer. Therefore, manipulating Cu-trafficking to trigger selective cancer cell death may be a viable strategy with therapeutic benefit. By exploiting combined in silico and experimental strategies, we identified small peptides able to bind Atox1 and metal-binding domains 3-4 of ATP7B proteins. We found that these peptides reduced the proliferation of cancer cells owing to increased cellular copper ions concentration. These outcomes support the idea of harming copper trafficking as an opportunity for devising novel anti-cancer therapies.

Quantifying and comparing radiation damage in the Protein Data Bank

Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.

Characterization of a Bacillus megaterium strain with metal bioremediation potential and in silico discovery of novel cadmium binding motifs in the regulator, CadC

Bioremediation of toxic metal ions using bacterial strains is a promising tool. Metal binding motifs in microbial proteins are involved in the regulation and transport of such toxic metals for metal detoxification. A bacterial strain designated TWSL_4 with metal (Cu, Cd, and Pb) resistance and removal ability was isolated and identified as a Bacillus megaterium strain using 16S rRNA gene analysis. An operon with 2 open reading frames (ORFs) was identified, cloned, and sequenced. ORF1 and ORF2 were identical to the cadmium efflux system accessory protein (CadC) and cadmium-translocating P-type ATPases (CadA) of B. megaterium strain YC4-R4 respectively. A protein homology search using Swiss model retrieved no crystal structures for CadC and CadA of Bacillus sp.. CadC of TWSL_4 had a sequence identity of 53% to the CadC (121aa) protein and 51.69% to the CadC crystal structure (1U2W.1.B; GMQE=0.75) of Staphylococcus sp. pI258. Molecular dynamic simulation studies revealed the presence of three metal binding regions in CadC of TWSL_4, [ASP7-TYR9], [ASP100-HIS102], and [LYS113-ASP116]. This is the first report showing evidence for the presence of Cd²⁺ and Zn²⁺ metal binding motifs in the CadC regulator of the Bacillus megaterium cad operon. The bacterial strain TWSL_4 was also found to contain two different P type ATPases encoding genes, cadA and zosA involved in metal resistance. Furthermore, the metal bioremediation potential of strain TWSL_4 was confirmed using an industrial effluent. KEY POINTS: • Isolation of a metal-resistant bacterial strain with potential for industrial bioremediation. • Discovery of novel Cd binding sites in CadC of the cad operon from B. megaterium. • Involvement of aspartic acid in the coordination of metal ions (Cd²⁺).

An EPR Study on the Interaction between the Cu(I) Metal Binding Domains of ATP7B and the Atox1 Metallochaperone

Copper’s essentiality and toxicity mean it requires a sophisticated regulation system for its acquisition, cellular distribution and excretion, which until now has remained elusive. Herein, we applied continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) spectroscopy in solution to resolve the copper trafficking mechanism in humans, by considering the route travelled by Cu(I) from the metallochaperone Atox1 to the metal binding domains of ATP7B. Our study revealed that Cu(I) is most likely mediated by the binding of the Atox1 monomer to metal binding domain 1 (MBD1) and MBD4 of ATP7B in the final part of its extraction pathway, while the other MBDs mediate this interaction and participate in copper transfer between the various MBDs to the ATP7B membrane domain. This research also proposes that MBD1-3 and MBD4-6 act as two independent units.

Cytosolic Copper Binding by a Bacterial Storage Protein and Interplay with Copper Efflux

Escherichia coli has a well-characterized copper (Cu) transporting ATPase (CopA) that removes this potentially toxic metal ion from the cytosol. Growth of the strain lacking CopA (ΔcopA) is inhibited above 0.5 mM Cu, whilst a similar effect does not occur in wild type (WT) E. coli until over 2.5 mM Cu. Limited expression of CopA can restore growth to WT levels in ΔcopAE. coli in the presence of Cu. To study the influence of a bacterial cytosolic Cu storage protein (Csp3) on how E. coli handles Cu, the protein from Bacillus subtilis (BsCsp3) has been overexpressed in the WT and ΔcopA strains. BsCsp3 can protect both strains from Cu toxicity, promoting growth at up to ~1.5 and ~3.5 mM Cu, respectively. Higher levels of Csp3 expression are needed to provide resistance to Cu toxicity in ΔcopAE. coli. At 1.5 mM Cu, BsCsp3 purified from ΔcopAE. coli binds up to approximately four equivalents of Cu(I) per monomer. A similar number of Cu(I) equivalents can be bound by BsCsp3 purified from WT E. coli also grown at 1.5 mM Cu, a concentration that does not cause toxicity in this strain. Much lower amounts of BsCsp3 are produced in WT E. coli grown in the presence of 3.4 mM Cu, but the protein still counteracts toxicity and is almost half loaded with Cu(I). Csp3s can protect E. coli from Cu toxicity by sequestering cuprous ions in the cytosol. This appears to include an ability to acquire and withhold Cu(I) from the main efflux system in a heterologous host.

The pivotal role of MBD4–ATP7B in the human Cu(i) excretion path as revealed by EPR experiments and all-atom simulations

Atox1–MBD4 interaction mediates the in-cell Cu(i) concentration.

The Coordination Chemistry of Copper Uptake and Storage for Methane Oxidation

Methanotrophs are remarkable bacteria that utilise large quantities of copper (Cu) to oxidize the potent greenhouse gas methane. To assist in providing the Cu they require for this process some methanotrophs can secrete the Cu-sequestering modified peptide methanobactin. These small molecules bind Cu^I with very high affinity and crystal structures have given insight into why this is the case, and also how the metal ion may be released within the cell. A much greater proportion of methanotrophs, genomes of which have been sequenced, possess a member of a newly discovered bacterial family of copper storage proteins (the Csps). These are tetramers of four-helix bundles whose cores are lined with Cys residues enabling the binding of large numbers of Cu^I ions. In methanotrophs, a Csp exported from the cytosol stores Cu^I for the active site of the ubiquitous enzyme that catalyses the oxidation of methane. The presence of cytosolic Csps, not only in methanotrophs but in a wide range of bacteria, challenges the dogma that these organisms have no requirement for Cu in this location. The properties of the Csps, with an emphasis on Cu^I binding and the structures of the sites formed, are the primary focus of this review.

Visualizing Biological Copper Storage: The Importance of Thiolate-Coordinated Tetranuclear Clusters

Bacteria possess cytosolic proteins (Csp3s) capable of binding large quantities of copper and preventing toxicity. Crystal structures of a Csp3 plus increasing amounts of Cu^I provide atomic-level information about how a storage protein loads with metal ions. Many more sites are occupied than Cu^I equiv added, with binding by twelve central sites dominating. These can form [Cu₄ (S-Cys)₄ ] intermediates leading to [Cu₄ (S-Cys)₅ ]^- , [Cu₄ (S-Cys)₆ ]^2- , and [Cu₄ (S-Cys)₅ (O-Asn)]^- clusters. Construction of the five Cu^I sites at the opening of the bundle lags behind the main core, and the two least accessible sites at the opposite end of the bundle are occupied last. Facile Cu^I cluster formation, reminiscent of that for inorganic complexes with organothiolate ligands, is largely avoided in biology but is used by proteins that store copper in the cytosol of prokaryotes and eukaryotes, where this reactivity is also key to toxicity.

Bacterial cytosolic proteins with a high capacity for Cu(I) that protect against copper toxicity

Bacteria are thought to avoid using the essential metal ion copper in their cytosol due to its toxicity. Herein we characterize Csp3, the cytosolic member of a new family of bacterial copper storage proteins from Methylosinus trichosporium OB3b and Bacillus subtilis. These tetrameric proteins possess a large number of Cys residues that point into the cores of their four-helix bundle monomers. The Csp3 tetramers can bind a maximum of approximately 80 Cu(I) ions, mainly via thiolate groups, with average affinities in the (1–2) × 10¹⁷ M⁻¹ range. Cu(I) removal from these Csp3s by higher affinity potential physiological partners and small-molecule ligands is very slow, which is unexpected for a metal-storage protein. In vivo data demonstrate that Csp3s prevent toxicity caused by the presence of excess copper. Furthermore, bacteria expressing Csp3 accumulate copper and are able to safely maintain large quantities of this metal ion in their cytosol. This suggests a requirement for storing copper in this compartment of Csp3-producing bacteria.

A four-helix bundle stores copper for methane oxidation

Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase. Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper. Methane monooxygenases are nature's primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock. Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location.

Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones

Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.

Investigating the role of zinc and copper binding motifs of trafficking sites in the cyanobacterium Synechocystis PCC 6803

Although zinc and copper are required by proteins with very different functions, these metals can be delivered to cellular locations by homologous metal transporters within the same organism, as demonstrated by the cyanobacterial ( Synechocystis PCC 6803) zinc exporter ZiaA and thylakoidal copper importer PacS. The N-terminal metal-binding domains of these transporters (ZiaAN and PacSN, respectively) have related ferredoxin folds also found in the metallochaperone Atx1, which delivers copper to PacS, but differ in the residues found in their M/IXCXXC metal-binding motifs. To investigate the role of the nonconserved residues in this region on metal binding, the sequence from ZiaAN has been introduced into Atx1 and PacSN, and the motifs of Atx1 and PacSN swapped. The motif sequence can tune Cu(I) affinity only approximately 3-fold. However, the introduction of the ZiaAN motif (MDCTSC) dramatically increases the Zn(II) affinity of both Atx1 and PacSN by up to 2 orders of magnitude. The Atx1 mutant with the ZiaAN motif crystallizes as a side-to-side homodimer very similar to that found for [Cu(I)2-Atx1]2 ( Badarau et al. Biochemistry 2010 , 49 , 7798 ). In a crystal structure of the PacSN mutant possessing the ZiaAN motif (PacSN(ZiaAN)), the Asp residue from the metal-binding motif coordinates Zn(II). This demonstrates that the increased Zn(II) affinity of this variant and the high Zn(II) affinity of ZiaAN are due to the ability of the carboxylate to ligate this metal ion. Comparison of the Zn(II) sites in PacSN(ZiaAN) structures provides additional insight into Zn(II) trafficking in cyanobacteria.

Crosstalk between Cu(I) and Zn(II) homeostasis via Atx1 and cognate domains

The copper metallochaperone Atx1 and the N-terminal metal-binding domain of a copper-transporting ATP-ase can form tight Zn(II)-mediated hetero-complexes in both cyanobacteria and humans. Copper and zinc homeostasis could be linked by metal binding to these CXXC-containing proteins.

Copper-substituted forms of the wild type and C42A variant of rubredoxin

In order to gain insights into the interplay between Cu(I) and Cu(II) in sulfur-rich protein environments, the first preparation and characterization of copper-substituted forms of the wild-type rubredoxin (Rd) from Desulfovibrio vulgaris Hildenborough are reported, as well as those of its variant C42A-Rd. The initial products appear to be tetrahedral Cu(I)(S-Cys)n species for the wild type (n=4) and the variant C42A (n=3, with an additional unidentified ligand). These species are unstable to aerial oxidation to products, whose properties are consistent with square planar Cu(II)(S-Cys)n species. These Cu(II) intermediates are susceptible to auto-reduction by ligand S-Cys to produce stable Cu(I) final products. The original Cu(I) center in the wild-type system can be regenerated by reduction, suggesting that the active site can accommodate Cu(I)(S-Cys)2 and Cys-S-S-Cys fragments in the final product. The absence of one S-Cys ligand prevents similar regeneration in the C42A-Rd system. These results emphasize the redox instability of Cu(II)-(S-Cys)n centers.

The influence of protein folding on the copper affinities of trafficking and target sites

The relative influence of protein unfolding on the Cu(I) affinity of trafficking and target sites for copper has been determined. For the copper metallochaperone Atx1 from Synechocystis PCC 6803 (a cyanobacterium), Saccharomyces cerevisiae and humans unfolding in urea results in a decrease in the Cu(I) affinity from (4-5) × 10(17) M(-1) to (1-3) × 10(16) M(-1) at pH 7. The affinities of the unfolded Atx1s are similar to those for CXXC-containing peptides. Partial unfolding, due to the loop 5 His61Lys mutation in Synechocystis Atx1, gives rise to a more limited decrease in Cu(I) affinity. For the copper target protein plastocyanin from Synechocystis, chemical unfolding results in the Cu(I) affinity decreasing by 5-orders of magnitude. This differential influence of protein unfolding on Cu(I) affinity is due to a more complex copper site structure in the target protein, including numerous interactions of non-coordinating residues with ligating amino acids. This second-coordination sphere is much simpler in the Atx1s with the main interaction provided by the loop 5 residue that tunes the Cu(I) affinity by altering the pK(a) of the C-terminal Cys ligand of the CXXC motif. This interaction and others are absent in the unfolded Atx1s and the two Cys ligands have pK(a) values reminiscent of free thiols (>8) resulting in lowered Cu(I) affinities at pH 7. Residues close to the active site of the thiol-disulfide oxidoreductase thioredoxin appear to lower the Cu(I) affinity of its CXXC motif to 3.1 × 10(15) M(-1) at pH 7, presumably to prevent copper binding in vivo. The structure of a copper site, including the number and relative position of ligands in the primary structure and the complexity of the second-coordination sphere, results in dramatically different effects of unfolding on Cu(I) affinity that has important implications for copper homeostasis.

Dynamic multibody protein interactions suggest versatile pathways for copper trafficking

As part of intracellular copper trafficking pathways, the human copper chaperone Hah1 delivers Cu(+) to the Wilson's Disease Protein (WDP) via weak and dynamic protein-protein interactions. WDP contains six homologous metal binding domains (MBDs) connected by flexible linkers, and these MBDs all can receive Cu(+) from Hah1. The functional roles of the MBD multiplicity in Cu(+) trafficking are not well understood. Building on our previous study of the dynamic interactions between Hah1 and the isolated fourth MBD of WDP, here we study how Hah1 interacts with MBD34, a double-domain WDP construct, using single-molecule fluorescence resonance energy transfer (smFRET) combined with vesicle trapping. By alternating the positions of the smFRET donor and acceptor, we systematically probed Hah1-MBD3, Hah1-MBD4, and MBD3-MBD4 interaction dynamics within the multidomain system. We found that the two interconverting interaction geometries were conserved in both intermolecular Hah1-MBD and intramolecular MBD-MBD interactions. The Hah1-MBD interactions within MBD34 are stabilized by an order of magnitude relative to the isolated single-MBDs, and thermodynamic and kinetic evidence suggest that Hah1 can interact with both MBDs simultaneously. The enhanced interaction stability of Hah1 with the multi-MBD system, the dynamic intramolecular MBD-MBD interactions, and the ability of Hah1 to interact with multiple MBDs simultaneously suggest an efficient and versatile mechanism for the Hah1-to-WDP pathway to transport Cu(+).

Cu(I) affinities of the domain 1 and 3 sites in the human metallochaperone for Cu,Zn-superoxide dismutase

The delivery of copper by the human metallochaperone CCS is a key step in the activation of Cu,Zn-superoxide dismutase (SOD1). CCS is a three-domain protein with Cu(I)-binding CXXC and CXC motifs in domains 1 and 3, respectively. A detailed analysis of the binding of copper to CCS, including variants in which the Cys residues from domains 1 and 3 have been mutated to Ser, and also using separate domain 1 and 3 constructs, demonstrates that CCS is able to bind 1 equiv of Cu(I) in both of these domains. The Cu(I) affinity of domain 1 is approximately 5 × 10(17) M(-1) at pH 7.5, while that of domain 3 is at least 1 order of magnitude weaker. The CXXC site will therefore be preferentially loaded with Cu(I), suggesting that domain 1 plays a role in the acquisition of the metal. The delivery of copper to the target occurs via domain 3 whose structural flexibility and ability to be transiently metalated during copper delivery appear to be more important than the Cu(I) affinity of its CXC motif. The Cu(I) affinity of domain 1 of CCS is comparable to that of HAH1, another cytosolic copper metallochaperone. CCS and HAH1 readily exchange Cu(I), providing a mechanism whereby cross-talk can occur between copper trafficking pathways.

Metal selectivity of the Escherichia coli nickel metallochaperone, SlyD

SlyD is a Ni(II)-binding protein that contributes to nickel homeostasis in Escherichia coli. The C-terminal domain of SlyD contains a rich variety of metal-binding amino acids, suggesting broader metal binding capabilities, and previous work demonstrated that the protein can coordinate several types of first-row transition metals. However, the binding of SlyD to metals other than Ni(II) has not been previously characterized. To improve our understanding of the in vitro metal-binding activity of SlyD and how it correlates with the in vivo function of this protein, the interactions between SlyD and the series of biologically relevant transition metals [Mn(II), Fe(II), Co(II), Cu(I), and Zn(II)] were examined by using a combination of optical spectroscopy and mass spectrometry. Binding of SlyD to Mn(II) or Fe(II) ions was not detected, but the protein coordinates multiple ions of Co(II), Zn(II), and Cu(I) with appreciable affinity (K(D) values in or below the nanomolar range), highlighting the promiscuous nature of this protein. The order of affinities of SlyD for the metals examined is as follows: Mn(II) and Fe(II) < Co(II) < Ni(II) ~ Zn(II) ≪ Cu(I). Although the purified protein is unable to overcome the large thermodynamic preference for Cu(I) and exclude Zn(II) chelation in the presence of Ni(II), in vivo studies reveal a Ni(II)-specific function for the protein. Furthermore, these latter experiments support a specific role for SlyD as a [NiFe]-hydrogenase enzyme maturation factor. The implications of the divergence between the metal selectivity of SlyD in vitro and the specific activity in vivo are discussed.

Thermodynamics of copper and zinc distribution in the cyanobacterium Synechocystis PCC 6803

Copper is supplied to plastocyanin for photosynthesis and cytochrome c oxidase for respiration in the thylakoids of Synechocystis PCC 6803 by the membrane-bound P-type ATPases CtaA and PacS, and the metallochaperone Atx1. We have determined the Cu(I) affinities of all of the soluble proteins and domains in this pathway. The Cu(I) affinities of the trafficking proteins range from 5 × 10(16) to 5 × 10(17) M(-1) at pH 7.0, consistent with values for homologues. Unusually, Atx1 binds Cu(I) significantly tighter than the metal-binding domains (MBDs) of CtaA and PacS (CtaA(N) and PacS(N)), and equilibrium copper exchange constants of approximately 0.2 are obtained for transfer to the MBDs. Dimerization of Atx1 increases the affinity for Cu(I), but the loop 5 His61 residue has little influence. The MBD of the zinc exporter ZiaA (ZiaA(N)) exhibits an almost identical Cu(I) affinity, and Cu(I) exchange with Atx1, as CtaA(N) and PacS(N), and the relative stabilities of the complexes must enable the metallochaperone to distinguish between the MBDs. The binding of potentially competing zinc to the trafficking proteins has been studied. ZiaA(N) has the highest Zn(II) affinity and thermodynamics could be important for zinc removal from the cell. Plastocyanin has a Cu(I) affinity of 2.6 × 10(17) M(-1), 15-fold tighter than that of the Cu(A) site of cytochrome c oxidase, highlighting the need for specific mechanisms to ensure copper delivery to both of these targets. The narrow range of Cu(I) affinities for the cytoplasmic copper proteins in Synechocystis will facilitate relocation when copper is limiting.