Zinc Ion Binding Site Research Articles

The zinc ions stabilize the three-dimensional structure and are required for the binding of staphylococcal enterotoxin-like protein P (SEIP) with MHC-II receptors

Staphylococcus aureus is a common human and animal pathogen. These bacteria have various pathogenicity factors, including enterotoxin-like proteins. SElP (staphylococcal enterotoxin-like protein P) has potential zinc ion-binding sites and is able to interact with major histocompatibility complex class II (MHCII) and T-cell receptor (TCR). A method for the expression and isolation of the enterotoxin-like protein of Staphylococcus aureus (SElP) was developed. The expression was carried out in E. coli cells, and the protein was isolated by affinity chromatography on a NiNTA column. The endotoxins were separated by affinity chromatography on Affi-Prep® polymyxin. It was shown by gel filtration that the resulting protein had a monomeric form. The protein in zinc-bound and zinc-free forms was characterized by protein melting using fluorescence method and it was shown that zinc stabilizes the spatial structure of SElP. The functional activity of SElP was investigated by the ability to interact with the histocompatibility antigen class II receptor (MHC-II) exposed on the B cell line Raji by flow cytofluorometry. The zinc-bound and zinc-free forms were shown to differ in their interaction with MHC-II. The localization of the zinc-binding site was confirmed by the introduction of the H225 and D227 mutations. The mutant protein was characterized by melting, and its propensity to form aggregates was shown.

Unravelling the inhibitory zinc ion binding site and the metal exchange mechanism in human DPP III.

Dipeptidyl peptidase III (DPP III), a zinc-dependent exopeptidase, is widely distributed in organisms and present in almost all human tissues. In addition to its involvement in protein catabolism, it plays a role in oxidative stress and blood pressure regulation, and there is evidence of its involvement in pain modulation. Excess zinc ions have been found to inhibit its hydrolytic activity, but the binding affinity, binding site geometry, and mechanism of inhibitory activity have been unknown. Using several different computational approaches, we determined the inhibitory zinc ion binding site, its coordination and relative binding affinity. During some simulations the translocation of the zinc ion from the inhibitory to the catalytic binding site was observed, accompanied by movement of the catalytic zinc ion toward the exit of the substrate binding site. The traced behavior suggests an associative type of metal ion exchange, in which the formation of the ternary complex between enzyme and two metal ions precedes the exit of the catalytic metal ion. Differently from our previous findings that binding of a peptide induces partial opening of hDPP III, the globularity of the protein did not change in MD simulations of the hermorphin-like peptide bound to hDPP III with two zinc ions. However, the entrance to the interdomain cleft widens during Zn diffusion into the protein and was found to be the highest energy barrier in the process of metal translocation from the solvent to the active site. Finally, we discuss why excess zinc reduces enzyme activity.

Crystal structure of the C-terminal domain of DENR

The density regulated protein (DENR) forms a stable heterodimer with malignant T-cell-amplified sequence 1 (MCT-1). DENR-MCT-1 heterodimer then participates in regulation of non-canonical translation initiation and ribosomal recycling. The N-terminal domain of DENR interacts with MCT-1 and carries a classical tetrahedral zinc ion-binding site, which is crucial for the dimerization. DENR-MCT-1 binds the small (40S) ribosomal subunit through interactions between MCT-1 and helix h24 of the 18S rRNA, and through interactions between the C-terminal domain of DENR and helix h44 of the 18S rRNA. This later interaction occurs in the vicinity of the P site that is also the binding site for canonical translation initiation factor eIF1, which plays the key role in initiation codon selection and scanning. Sequence homology modeling and a low-resolution crystal structure of the DENR-MCT-1 complex with the human 40S subunit suggests that the C-terminal domain of DENR and eIF1 adopt a similar fold. Here we present the crystal structure of the C-terminal domain of DENR determined at 1.74 Å resolution, which confirms its resemblance to eIF1 and advances our understanding of the mechanism by which DENR-MCT-1 regulates non-canonical translation initiation and ribosomal recycling.

Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation

The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR's MCT-1-binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.

Cloning, sequence, and expression analyses of the Chrysanthemum morifolium flowering-related gene CmCOL (CONSTANS-like)

We cloned the CmCOL gene (GenBank accession: KC589293) from Chrysanthemum morifolium ‘Jinba’. The complete cDNA sequence is 1439 bp in length; the open reading frame is 1161 bp and encodes a polypeptide of 387 amino acids. Analysis of the amino acid sequence shows homology to the protein encoded by the plant flowering gene CO (CONSTANS). CmCOL contains a typical, functional CO domain at the N-terminus, two B box-type zinc finger domains, eight predicted zinc ion binding sites, one CCT(CO, CO-Like, TOC1) domain near the C-terminus and a specific six amino acid consensus sequence (G-I/V-V-P-S/T-F) at the C-terminus, and belongs to CONSTANS family Group I. A protein phylogenetic tree revealed 99% identity between CmCOL and Chrysanthemum seticuspe f. boreale CONSTANS-like1. We predict that CmCOL localizes to the nucleus, is not secreted and lacks a signal peptide. Relative fluorescence quantitative analysis showed that CmCOL mRNA is most highly expressed in the leaves and follows a diurnal expression pattern, with a maximum at 04:00, its lowest point at 16:00 and maintaining this low expression until 20:00. Short-day conditions elevated CmCOL mRNA expression in the leaves but did not significantly affect expression in the buds. The CmCOL mRNA level in the leaves varied significantly based on the flower bud differentiation stage. Further detailed study of this gene will help to elucidate the molecular mechanisms by which the photoperiod pathway regulates chrysanthemum flower formation. Further, this gene may represent a potential, future target for molecular breeding.

Structural Characterization of the SMRT Corepressor Interacting with Histone Deacetylase 7

The 2525 amino acid SMRT corepressor is an intrinsically disordered hub protein responsible for binding and coordinating the activities of multiple transcription factors and chromatin modifying enzymes. Here we have studied its interaction with HDAC7, a class IIa deacetylase that interacts with the corepressor complex together with the highly active class I deacetylase HDAC3. The binding site of class IIa deacetylases was previously mapped to an approximate 500 amino acid region of SMRT, with recent implication of short glycine-serine-isoleucine (GSI) containing motifs. In order to characterize the interaction in detail, we applied a random library screening approach within this region and obtained a range of stable, soluble SMRT fragments. In agreement with an absence of predicted structural domains, these were characterized as intrinsically disordered by NMR spectroscopy. We identified one of them, comprising residues 1255–1452, as interacting with HDAC7 with micromolar affinity. The binding site was mapped in detail by NMR and confirmed by truncation and alanine mutagenesis. Complementing this with mutational analysis of HDAC7, we show that HDAC7, via its surface zinc ion binding site, binds to a 28 residue stretch in SMRT comprising a GSI motif followed by an alpha helix.

Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket.

Neuropilin‐2 is a transmembrane receptor involved in lymphangiogenesis and neuronal development. In adults, neuropilin‐2 and its homologous protein neuropilin‐1 have been implicated in cancers and infection. Molecular determinants of the ligand selectivity of neuropilins are poorly understood. We have identified and structurally characterized a zinc ion binding site on human neuropilin‐2. The neuropilin‐2‐specific zinc ion binding site is located near the interface between domains b1 and b2 in the ectopic region of the protein, remote from the neuropilin binding site for its physiological ligand, i.e. vascular endothelial growth factor. We also present an X‐ray crystal structure of the neuropilin‐2 b1 domain in a complex with the C‐terminal sub‐domain of VEGF‐A. Zn2+ binding to neuropilin‐2 destabilizes the protein structure but this effect was counteracted by heparin, suggesting that modifications by glycans and zinc in the extracellular matrix may affect functional neuropilin‐2 ligand binding and signalling activity.

Biochemical Insights into the Role of Matrix Metalloproteinases in Regeneration: Challenges and Recent Developments

Matrix metalloproteinases (MMPs) are a group of proteases that belong to the metazincin family. These proteins consist of similar structures featuring a signaling peptide, a propeptide domain, a catalytic domain where the notable zinc ion binding site is found and a hinge region that binds to the C-terminal hemoplexin domain. MMPs can be produced by numerous cell types through secretion or localization to the cell membrane. While certain chemical compounds have been known to generally inhibit MMPs, naturally occurring proteins known as tissue inhibitors of metalloproteinases (TIMPs) effectively interact with MMPs to modify their biological roles. MMPs are very important enzymes that actively participate in remodeling the extracellular matrix by degrading certain constituents, along with promoting cell proliferation, migration, differentiation, apoptosis and angiogenesis. In normal adult tissue, they are almost undetectable; however, when perturbed through injury, disease or pregnancy, they have elevated expression. The goal of this review is to identify new experimental findings that have provided further insight into the role of MMPs in skeletal muscle, nerve and dermal tissue, as well as in the liver, heart and kidneys. Increased expression of MMPs can improve the regeneration potential of wounds; however, an imbalance between MMP and TIMP expression can prove to be destructive for afflicted tissues.

RING Domains Functioning as E3 Ligases Reveal Distinct Structural Features: A Molecular Dynamics Simulation Study

RING domain, a cysteine-rich motif that chelates two zinc ions, has been shown to regulate many biological processes such as mediating a crucial step in the ubiquitinylation pathway In order to investigate the distinct structural features for the RING domains functioning as E3 ligases, several molecular dynamics simulations involving the c-Cbl, CNOT4 (with E3 ligase function), and p44 (no E3 ligase function) RING domains were conducted in this study. Our results reveal that the structural stability of the recognition site is a basic requirement for the RING domains functioning as E3 ligases. The structural stability of the recognition site is maintained by the hydrophobic core and hydrogen bonding network. Another important structural feature of the RING domains functioning as E3 ligases is the stable distances between the recognition site and the zinc ion binding sites S1 and S2. Moreover, the RING domains functioning as E3 ligases seem to exhibit lower β stability due to the higher proportion of proline residues in their sequences. However, no significant difference of the other secondary (α and turn) and the tertiary structural stabilities can be observed among these three RING domains.

Molecular Dynamics Simulations to Investigate the Effects of Zinc Ions on the Structural Stability of the c-Cbl RING Domain

In eukaryotic cells, ubiquitylation of proteins plays a critical role in regulating diverse cell processes by the ubiquitin activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin protein ligase (E3). E3 is the key component that confers specificity to ubiquitylation and directs the conjugation of ubiquitin to a specific target protein. RING domains are small structured protein domains that require the coordination of zinc ions for a stable tertiary fold and some of them are involved in the E3 family. In this study, we reported the detailed relationships between the two zinc ions and the structural stability of the c-Cbl RING domain by molecular dynamics simulations. Our results show that these two zinc ions play an important role in maintaining both the secondary and tertiary structural stabilities of the c-Cbl RING domain. Our results also reveal that the secondary structural stability of the c-Cbl RING domain is mainly determined by the hydrogen-bonding networks in or near the two zinc ion binding sites. Our results further demonstrate that zinc ion binding site 2 is more structurally stable than site 1.

Crystal structure of a novel zinc-binding ATP sulfurylase from Thermus thermophilus HB8.

ATP sulfurylase (ATPS) is a ubiquitous enzyme that catalyzes the transfer of the adenylyl group from ATP to inorganic sulfate, producing adenosine 5'-phosphosulfate (APS) and pyrophosphate. The crystal structure of ATPS from Thermus thermophilus HB8 (TtATPS, 347 amino acid residues) in complex with APS was determined at 2.5 A resolution. TtATPS is composed of three domains [domain I (residues 1-134), domain II (residues 135-290), and domain III (residues 291-347)], like the Riftia pachyptila symbiont ATPS, but lacks a fourth domain present in ATPSs from the yeast Saccharomyces cerevisiae and from the fungus Penicillium chrysogenum. TtATPS forms a dimer in the crystal, and the manner of subunit association is different from that observed in dimeric R. pachyptila symbiont ATPS and in the hexameric S. cerevisiae and P. chrysogenum ATPSs. APS is located in the active site of TtATPS, which contains several motifs (QXRN, HXXH, and GRD) conserved in ATPSs. Unexpectedly, TtATPS binds one metal ion per subunit in domain III. XAFS measurement of the crystal and the Bijvoet difference Fourier map unambiguously characterized the metal ion as a zinc ion. The zinc ion is tetrahedrally coordinated by Cys294, Cys297, Cys306, and His310, and could not be removed from the protein by treatment with EDTA. The zinc ion binding site is far from the active site. Because all four residues coordinated to the zinc ion are conserved in the ATPSs from thermophilic bacteria such as Archaeoglobus fulgidus, Pyrococcus abyssi, and Sulfolobus solfataricus, zinc ion chelation may contribute to the thermal stability of these ATPSs.

NMR Solution Structure of Mob1, a Mitotic Exit Network Protein and its Interaction with an NDR Kinase Peptide

Proteins of the Mob1/phocein family are found in all eukaryotic cells. In yeast, they are activating subunits of Dbf2-related protein kinases involved in cell cycle control. Despite the wide occurrence of these proteins, their biological functions remain poorly understood. Here we report the solution structure of the Mob1 protein from Xenopus laevis solved by heteronuclear multidimensional NMR. The structure reveals a fold constituted by a central left-handed four-helix bundle, one connecting helix, two flanking helices and a long flexible loop. The clustering of two Cys and two His residues, and zinc measurement by atomic absorption spectroscopy support the existence of a zinc ion binding site. Our NMR structure is in good agreement with the recently described X-ray structure of human Mob1-A. Chemical shift perturbations observed upon addition of a peptide encompassing the basic region of the N-terminal regulatory domain of NDR kinase were used to identify and map a specific interaction between Mob1 and this kinase. The chemical shift changes indicate that the main interaction occurs on the acidic and conserved surface of Mob1. This surface was previously hypothesized to be the interaction surface according to the X-ray structure and was identified as functionally important in yeast. Our data suggest that the NDR kinase is a functional Dbf2 homologue in animal cells and contributes to the understanding of the molecular function of Mob1 proteins.

Chelating agents stabilize the monomeric state of the zinc binding human papillomavirus 16 E6 oncoprotein.

The E6 protein of human papillomavirus 16 is known to be difficult and, when overexpressed, insoluble and agglomerated. It has two putative zinc ion binding sites crucial for its function. No metallochaperone has yet been found to deliver zinc ions to the E6 protein. Here, we report that a specific chelating agent, which we think functionally mimics a metallochaperone, stabilized the soluble monomeric form of E6 and inhibited multimerization in vitro. This effect seemed to depend on the chelating strength of the agent. While strong chelating agents precipitated the E6 protein and weak chelating agents did not favor the monomeric form of E6, chelating agents of intermediate strength [L-penicillamine and ethylene glycol bis(beta-aminoethyl)-N,N,N',N'-tetraacetic acid (EGTA)] effectively support the formation of a monomer. We did not observe formation of a dimer or defined oligomers. Degradation assays imply that the monomer is the biologically active form of the protein. Since EGTA favors the formation of monomeric over agglomerated E6 protein, we propose that chelating agents of appropriate strength could assist zinc delivery to recombinant metalloproteins in vitro and may even destabilize existing agglomerates.

Characterization of aminopeptidase N from the brush border membrane of the larvae midgut of silkworm, Bombyx mori as a zinc enzyme

Three GPI-anchored proteins, aminopeptidase N, alkaline phosphatase and alkaline phosphodiesterase I were released from the midgut brush border membrane of Bombyx mori by phosphatidylinositol-specific phopholipase C and the aminopeptidase N was purified to a homogeneous state. N-terminus and 6 internal sequences, one of which possessed part of zinc-binding motif, showed homology with those from other species. The zinc content in purified aminopeptidase N was estimated as approximately 0.72 mol/mol of the protein and 1,10-phenanthroline completely inhibited the enzyme activity, suggesting zinc requirement for the activity. The aminopeptidase N activity was inhibited not only by probestin and actinonin, but also strongly depressed by amastatin, while leuhistin and bestatin were less inhibitory. These suggest that the active site of aminopeptidase N might be structurally different from those of mammals. Calcium and magnesium ions stimulated the aminopeptidase N activity, but copper ion was rather inhibitory. Zinc ion showed bi-modal effect on the activity, i.e., stimulatory at low concentration, but inhibitory at higher than 100 μM. This inhibition was completely restored by EDTA. These results suggest that the aminopeptidase N possesses two zinc ion-binding sites with high and low affinity as essential and inhibitory one, as well as some regulatory metal-binding sites.

A structural model for the prostate disease marker, human prostate‐specific antigen

Prostate-specific antigen (PSA) provides an excellent serum marker for prostate cancer, the most frequent form of cancer in American males. PSA is a 237-residue protease based on sequence homology to kallikrein-like enzymes. To predict the 3-dimensional structure of PSA, homology modeling studies were performed based on sequence and structural alignments with tonin, pancreatic kallikrein, chymotrypsin, and trypsin. The structurally conserved regions of the 4 reference X-ray proteins provided the core structure of PSA, whereas the loop structures were modeled on the loops of tonin and kallikrein. The unique "kallikrein loop" insert, between Ser 95b and Pro 95k of kallikrein, was constructed using molecular mechanics, dynamics, and electrostatics calculations. In the resulting PSA structure, the catalytic triad, involving residues His 57, Asp 102, and Ser 195, and hydrophobic and electrostatic interactions typical of serine proteases were extremely well conserved. Similarly, the 5-disulfide bonds of kallikrein were also conserved in PSA. These results, together with the fact that no major steric clashes arose during the modeling process, provide strong evidence for the validity of the PSA model. Calculation of the electrostatic potential contours of kallikrein and PSA was carried out using the finite difference Poisson-Boltzmann method. The calculations revealed matching areas of negative potential near the catalytic triad, but differences in the positive potential surrounding the active site. The PSA glycosylation site, Asn 61, is fully accessible to the solvent and is enclosed in a positive region of the isopotential map. The bottom of the substrate specificity pocket, residue S1, is a serine (Ser 189) as in chymotrypsin, rather than aspartate (Asp 189) as in tonin, kallikrein, and trypsin. This fact, plus other features of the S1 binding-pocket region, suggest that PSA would prefer substrates with hydrophobic residues at the P1 position. The location of a potential zinc ion binding site involving the side chain of histidines 91, 101, and 233 is also suggested. This PSA model should facilitate the understanding and prediction of structural and functional properties of this important cancer marker.

Cadmium-113 Magnetic Resonance Spectroscopy

Cadmium-113 nuclear magnetic resonance spectroscopy has been used in studies of the structure and dynamics of inorganic and bioinorganic molecules. Chemical dynamics play an important role in the analysis of relaxation and chemical shift data. Naïve interpretations of relaxation data can be checked by performing these experiments at a variety of temperatures and magnetic field strengths. A combination of solid- and liquid-state nuclear magnetic resonance measurements can provide the user with unambiguous data on chemical shielding. These data can be used to characterize zinc and calcium ion binding sites in metalloproteins.

Cadmium-113 nuclear magnetic resonance studies of bovine insulin: two-zinc insulin hexamer specifically binds calcium.

By use of cadmium-113 nuclear magnetic resonance spectroscopy, a specific calcium ion binding site has been identified in the bovine two-zinc insulin hexamer. This site is composed of six glutamyl carboxylate groups clustered in the center of the hexamer, and is distinct from the normal zinc ion binding sites.

Copper and zinc ion binding by bovine, dog, and rat serum albumins

An ultrafiltration technique was used to study stripping by glycine of the first copper and zinc ion equivalents bound by bovine, dog, and rat serum albumins at pH 7.5. Affinity of dog serum albumin for copper was poorer than for the other albumins, consistent with the absence in the former albumin of the copper binding site present at the amino terminus of the latter albumins. Affinities of all three proteins for zinc were similar, suggesting that the albumin amino terminus is not the primary zinc ion binding site.