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Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites.

ABSTRACT: The metalloregulatory protein NikR from Helicobacter pylori (HpNikR) is a master regulator of gene expression which both activates and represses specific genes in response to nickel availability. Here, we report the first crystal structure (at 2.37 Å resolution) of Ni(II)HpNikR prepared directly from the holo protein. The protein contains four nickel ions located in two distinct coordination environments. Two nickel ions are bound to sites in a four-coordinate square-planar geometry as predicted on the basis of the structures of NikR from Escherichia coli and Pyrococcus horikoshii . The remaining two nickel ions are bound to sites with unexpected 5- or 6-coordination geometries which were previously thought to be involved in nickel incorporation into the protein. The nickel with 5-/6-coordination geometry utilizes three histidines from two separate monomeric HpNikR units along with two or three water molecules as ligands. The spatial location of the nickel in the 5-/6-coordinate site is within approximately 5 Å of the expected site if a 4-coordinate square-planar geometry occurred. Two of the histidines that participate as ligands in the 5-/6-coordinate site would also participate as ligands if the 4-coordinate site was occupied, making it impossible for both sites to be occupied simultaneously. DFT calculations show that the 5-/6-coordinate geometries are energetically favorable when the local protein environment is included in the calculations. The presence of two distinct coordination environments in HpNikR is suggested to be related to the specificity and binding affinity of this transcription factor for DNA.

SUBMITTER: West AL

PROVIDER: S-EPMC2958704 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

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Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites.

West Abby L AL St John Franz F Lopes Pedro E M PE MacKerell Alexander D AD Pozharski Edwin E Michel Sarah L J SL

Journal of the American Chemical Society 20101001 41

The metalloregulatory protein NikR from Helicobacter pylori (HpNikR) is a master regulator of gene expression which both activates and represses specific genes in response to nickel availability. Here, we report the first crystal structure (at 2.37 Å resolution) of Ni(II)HpNikR prepared directly from the holo protein. The protein contains four nickel ions located in two distinct coordination environments. Two nickel ions are bound to sites in a four-coordinate square-planar geometry as predicted ...[more]

PMID: 20863122

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Project description:New Co(II), Ni(II), and Cu(II) complexes were synthesized with the Schiff base ligand obtained by the condensation of sulfathiazole with salicylaldehyde. Their characterization was performed by elemental analysis, molar conductance, spectroscopic techniques (IR, diffuse reflectance and UV-Vis-NIR), magnetic moments, thermal analysis, and calorimetry (thermogravimetry/derivative thermogravimetry/differential scanning calorimetry), while their morphological and crystal systems were explained on the basis of powder X-ray diffraction results. The IR data indicated that the Schiff base ligand is tridentate coordinated to the metallic ion with two N atoms from azomethine group and thiazole ring and one O atom from phenolic group. The composition of the complexes was found to be of the [ML2]∙nH2O (M = Co, n = 1.5 (1); M = Ni, n = 1 (2); M = Cu, n = 4.5 (3)) type, having an octahedral geometry for the Co(II) and Ni(II) complexes and a tetragonally distorted octahedral geometry for the Cu(II) complex. The presence of lattice water molecules was confirmed by thermal analysis. XRD analysis evidenced the polycrystalline nature of the powders, with a monoclinic structure. The unit cell volume of the complexes was found to increase in the order of (2) < (1) < (3). SEM evidenced hard agglomerates with micrometric-range sizes for all the investigated samples (ligand and complexes). EDS analysis showed that the N:S and N:M atomic ratios were close to the theoretical ones (1.5 and 6.0, respectively). The geometric and electronic structures of the Schiff base ligand 4-((2-hydroxybenzylidene) amino)-N-(thiazol-2-yl) benzenesulfonamide (HL) was computationally investigated by the density functional theory (DFT) method. The predictive molecular properties of the chemical reactivity of the HL and Cu(II) complex were determined by a DFT calculation. The Schiff base and its metal complexes were tested against some bacterial strains (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis). The results indicated that the antibacterial activity of all metal complexes is better than that of the Schiff base.

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Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites.

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Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites.

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