Nickel-binding Protein Research Articles

Metal Binding Activity of the Escherichia coli Hydrogenase Maturation Factor HypB

The formation of the [NiFe] metallocenter of Escherichia coli hydrogenase 3 requires the participation of proteins encoded by the hydrogenase pleiotropy operon hypABCDEF. The insertion of Ni(II) into the precursor enzyme follows the incorporation of the iron center and is the function of HypA, a Zn(II)-binding protein, and HypB, a GTPase. The Ni(II) donor and the mechanism of transfer of Ni(II) into the hydrogenase precursor protein are not known. In this study, we demonstrate that HypB is a nickel-binding protein capable of binding 1 equiv of Ni(II) with a K(d) in the sub-picomolar range. In addition, HypB has a weaker metal-binding site that is not specific for Ni(II) over Zn(II). Examination of the isolated C-terminal GTPase domain revealed that the high-affinity metal binding capability was severely abrogated but the low-affinity site was intact. By mutating conserved cysteine and histidine residues in E. coli HypB, we have localized the high-affinity Ni(II)-binding site to an N-terminal CXXCGC motif and the low-affinity metal-binding site to the GTPase domain. A model for the function of HypB during the Ni(II) loading of hydrogenase is proposed.

Backbone 1H, 13C, and 15 E. coli nickel binding protein NikA

Backbone 1H, 13C, and 15 E. coli nickel binding protein NikA

Nickel-Binding Properties of the C-Terminal Tail Peptide of Bacillus pasteurii UreE

Urease activation, which is critical to the virulence of many human and animal pathogens, is mediated by several accessory proteins. UreE, the only nickel-binding protein among the urease accessory proteins, catalyzes the activation of urease by transporting nickel ions into the urease active sites. The nickel-binding properties of UreE are still not clear, particularly for the protein from Bacillus pasteurii (Bp). Since the flexible C-terminal tail of BpUreE possesses two conserved histidines, the nickel-binding properties of the tail peptide were examined by circular dichroism spectroscopy, size-exclusion chromatography, and nuclear magnetic resonance spectroscopy. Specific nickel binding leading to alteration of the peptide backbone geometry was clearly observed. Side-chains of the two conserved histidines were identified as the main ligands for nickel coordination. The peptide became dimerized upon nickel binding and the binding stoichiometry was estimated as 1 equivalent of nickel per peptide dimer. Altogether, it is postulated that the C-terminal tail of BpUreE contributes to the nickel binding of the protein in different ways between the dimeric and tetrameric protein folds.

Structural Characterization of the Nickel-binding Properties of Bacillus pasteurii Urease Accessory Protein (Ure)E in Solution

Urease activation is critical to the virulence of many human and animal pathogens. Urease possesses multiple, nickel-containing active sites, and UreE, the only nickel-binding protein among the urease accessory proteins, activates urease by transporting nickel ions. We performed NMR experiments to investigate the solution structure and the nickel-binding properties of Bacillus pasteurii (Bp) UreE. The secondary structures and global folds of BpUreE were determined for its metal-free and nickel-bound forms. The results indicated that no major structural change of BpUreE arises from the nickel binding. In addition to the previously identified nickel-binding site (Gly(97)-Cys(103)), the C-terminal tail region (Lys(141)-His(147)) was confirmed for the first time to be involved in the nickel binding. The C-terminally conserved sequence ((144)GHQH(147)) was confirmed to have an inherent nickel-binding ability. Nickel addition to 1.6 mm subunit, a concentration where BpUreE predominantly forms a tetramer upon the nickel binding, induced a biphasic spectral change consistent with binding of up to at least three nickel ions per tetrameric unit. In contrast, nickel addition to 0.1 mm subunit, a concentration at which the protein is primarily a dimer, caused a monophasic spectral change consistent with more than 1 equivalent per dimeric unit. Combined with the equilibrium dialysis results, which indicated 2.5 nickel equivalents binding per dimer at a micromolar protein concentration, the nickel-binding stoichiometry of BpUreE at a physiological concentration could be three nickel ions per dimer. Altogether, the present results provide the first detailed structural data concerning the nickel-binding properties of intact, wild-type BpUreE in solution.

Crystal Structures of the Liganded and Unliganded Nickel-binding Protein NikA from Escherichia coli

Bacteria have evolved a number of tightly controlled import and export systems to maintain intracellular levels of the essential but potentially toxic metal nickel. Nickel homeostasis systems include the dedicated nickel uptake system nik found in Escherichia coli, a member of the ABC family of transporters, that involves a periplasmic nickel-binding protein, NikA. This is the initial nickel receptor and mediator of the chemotactic response away from nickel. We have solved the crystal structure of NikA protein in the presence and absence of nickel, showing that it behaves as a "classical" periplasmic binding protein. In contrast to other binding proteins, however, the ligand remains accessible to the solvent and is not completely enclosed. No direct bonds are formed between the metal cation and the protein. The nickel binding site is apolar, quite unlike any previously characterized protein nickel binding site. Despite relatively weak binding, NikA is specific for nickel. Using isothermal titration calorimetry, the dissociation constant for nickel was found to be approximately 10 microm and that for cobalt was approximately 20 times higher.

A fluorescence-based sensing system for the environmental monitoring of nickel using the nickel binding protein from Escherichia coli.

A sensing system for nickel based on the nickel binding protein (NBP) from Escherichia coli is shown to be feasible. The versatility of NBP was demonstrated by its use in three different assay formats. When the NBP binds nickel, it undergoes a conformational change that can be used as the basis for an optical sensing system for nickel. The NBP gene was overexpressed in E. coli and the protein purified in a single step using perfusion anion-exchange chromatography. A unique cysteine residue at position 15 in the NBP was labeled with the fluorophore, N-[2-(1-maleimidyl)ethyl]-7-(diethylamino)coumarin-3-carboxamide (MDCC). In a spectrofluorimetric assay, there was a maximum of 65% quenching of the fluorescence signal produced by NBP-MDCC in the presence of nickel. A response curve for nickel using NBP-MDCC revealed a detection limit of 8 x 10(-8) mol L(-1). NBP-MDCC was also used to develop assays in microtiter plate and fiber optic bundle formats. Detection limits for nickel using these formats were also in the submicromolar range. Selectivity studies conducted with other divalent metals, including copper, cobalt, iron, cadmium, and manganese, showed that fluorescence quenching for cobalt was similar in magnitude but with a detection limit more than 10-fold higher than for nickel. The quenching responses were lower for the other metals, with detection limits at least 10 to 100 times higher than for nickel. These results suggest that fluorescently labeled NBP is potentially useful in the development of a sensing system for nickel.

The Identification, Purification, and Characterization of CooJ: A NICKEL-BINDING PROTEIN THAT IS CO-REGULATED WITH THE Ni-CONTAINING CO DEHYDROGENASE FROM RHODOSPIRILLUM RUBRUM

CooJ, a nickel-binding protein from the CO dehydrogenase system of Rhodospirillum rubrum, was purified by immobilized metal affinity chromatography. CooJ is a CO-induced protein predicted to contain a nickel binding motif composed of 16 histidine residues in the final 34 amino acids of the 12.5-kDa protein. When cells grown in the presence of CO were fractionated on an immobilized metal affinity chromatography column and analyzed by SDS-polyacrylamide gel electrophoresis, the major protein observed in the effluent migrated at an apparent molecular mass of 19 kDa. The 19-kDa protein was absent in extracts of cells grown in the absence of CO and the mutant strain, UR294, which lacks a functional cooJ gene. N-terminal sequence analysis confirmed that the 19-kDa protein is the product of the cooJ gene. Purified CooJ was shown to bind four nickel atoms per CooJ monomer with a Kd of 4.3 microM. Other divalent metals competed with the following order of affinity and corresponding Ki: Zn2+ (5 microM) > Cd2+ (19 microM) > Co2+ (23 microM) > Cu2+ (122 microM). CooJ chromatographed on a calibrated Superose 12 gel filtration column eluted at 39 kDa, a position consistent with a multimeric native molecular mass for CooJ.

Nickel binding protein isolated from Helicobacter pylori; useful in diagnosis and treatment of H. pylori infection, eg. in gastric disorders, and for non-clinical nickel detoxification : New England Med. Cent. Hosp; Tufts-Coll. World 9533 767; 14 December 1995

Nickel binding protein isolated from Helicobacter pylori; useful in diagnosis and treatment of H. pylori infection, eg. in gastric disorders, and for non-clinical nickel detoxification : New England Med. Cent. Hosp; Tufts-Coll. World 9533 767; 14 December 1995

Purification and characterization of the periplasmic nickel-binding protein NikA of Escherichia coli K12.

The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system specific for nickel. In this report, we describe the overproduction of the periplasmic nickel-binding protein NikA by cloning the nikA gene into an overexpression vector, pRE1. NikA was purified free of nickel to near homogeneity from the periplasm by hydrophobic and ion-exchange chromatography. N-terminal amino acid sequencing confirmed that the leader peptide of NikA had been removed. The nickel-binding properties of the protein has been studied by monitoring the quenching of intrinsic protein fluorescence. NikA binds one atom of nickel/molecule of protein with a dissociation constant (Kd) of less than 0.1 microM. Other metals (cobalt, copper, iron) are bound at least 10-fold less tightly. The high specificity for Ni2+ is also demonstrated by high-performance immobilized-metal-ion affinity chromatography. Biosynthesis of NikA occurred only under anaerobic conditions and was dependent on the general anaerobic regulator FNR. It was repressed by the presence of 250 microM Ni2+ in the growth medium and was not affected by either 30 mM formate or 100 mM nitrate. Anaerobically grown wild-type strain MC4100 contains about 23,000 molecules of NikA/cell. In addition to the effect on nickel transport, nikA mutation affects also the nickel sensing in Tar-dependent repellent chemotaxis.

Crystallization and Preliminary X-ray Diffraction Study of the Nickel-binding Protein NikA of Escherichia coli

NikA, a periplasmic nickel-binding protein involved in nickel-repellent chemotaxis has been crystallized. The crystals are hexagonal with space group P6 2 (or its enantiomorph) with a = 160.3 Å and c = 138.4 Å and they diffract to at least 3.0 Å resolution in the laboratory. NikA presents sequence homology with several periplasmic solute-binding proteins from Gram-negative bacteria.

The product of the hypB gene, which is required for nickel incorporation into hydrogenases, is a novel guanine nucleotide-binding protein

The products of the hyp operon genes are essential for the formation of catalytically active hydrogenases in Escherichia coli. At least one of these auxiliary proteins, HYPB, appears to be involved in nickel liganding to the hydrogenase apoprotein, since mutations in hypB can be phenotypically suppressed by high nickel concentrations in the medium (R. Waugh and D. H. Boxer, Biochimie 68:157-166, 1986). To approach the identification of the specific function of HYPB, we overexpressed the hypB gene and purified and characterized the gene product. HYPB is a homodimer of 31.6-kDa subunits, and it binds guanine nucleotides, with a Kd for GDP of 1.2 microM. The protein displays a low level of GTPase activity, with a kcat of 0.17 min-1. The apparent Km for GTP, as measured in the GTP hydrolysis reaction, was determined to be 4 microM. A chromatography system was established to measure nickel insertion into hydrogenase 3 from E. coli and to determine the effects of lesions in hypB. Nickel appears to be associated only with the processed large subunit of hydrogenase 3 in the wild type, and hypB mutants accumulate the precursor form of this subunit, which is devoid of nickel. The results are discussed in terms of a model in which HYPB is involved in nickel donation to the hydrogenase apoprotein and in which GTP hydrolysis is thought to reverse the interaction between either HYPB or another nickel-binding protein and the hydrogenase apoprotein after the nickel has been released.

Kinetics of nickel binding in hepatic and renal cytosol of63NiCl2-treated rats

Elution profiles of nickel-binding protein were investigated in hepatic and renal cytosol of rats at various time intervals (6, 16, 24, and 48 h) after intraperitoneal administration of(63)Ni (1 mg Ni/kg. B. Wt. = 400 µCi as(63)NiCl2). The nickel-binding proteins were characterized in terms of absorbance at 254 nm, sulfhydryl content, and(63)Ni counts. The results demonstrated that in liver it was bound to both high as well as low mol wt sulfhydryl proteins and glutathione-like moiety with a maximum incorporation at 16 h, after which it declined and by 48 h, very little(63)Ni was associated with the bioligands. In kidney the incorporation of(63)Ni was approximately 400-fold higher than liver and most of(63)Ni was associated with the low mol. wt. sulfhydryl moiety. Kidney also exhibited maximum incorporation of(63)Ni at 16 h that was metabolized by 48 h.