Nickel-responsive transcriptional regulators

Metallomics ◽  
2015 ◽  
Vol 7 (9) ◽  
pp. 1305-1318 ◽  
Author(s):  
Francesco Musiani ◽  
Barbara Zambelli ◽  
Micaela Bazzani ◽  
Luca Mazzei ◽  
Stefano Ciurli
Keyword(s):  
Metal Binding ◽  
Transcriptional Regulators ◽  
Structural Features ◽  
Metal Coordination ◽  
Coordination Modes ◽  
Binding Thermodynamics

The structural features, metal coordination modes and metal binding thermodynamics of known Ni(ii)-dependent transcriptional regulators are highlighted and discussed.

Zwitterionic structures of selenocysteine-containing dipeptides and their interactions with Cu(II) ions

2015 ◽  
Vol 69 (4) ◽  
Author(s):  
Gunajyoti Das ◽  
Shilpi Mandal
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Copper Ions ◽  
Structural Features ◽  
Molecular Structures ◽  
Metal Coordination ◽  
Basis Sets ◽  
Metal Ion Binding ◽  
Carboxylate Groups ◽  
Td Dft

AbstractThe molecular structures of a series of selenocysteine-containing dipeptides in their zwitterionic forms were studied using the B3LYP/6-311++G(d,p) level in the aqueous phase. The B3LYP and BHandHLYP functionals in combination with 6-311++G(d,p) and LANL2DZ basis sets were used to investigate the effects of metal coordination on the structural and molecular properties of the dipeptides by complexing them with bivalent copper ions. The results from this DFT study provide valuable insights into the interaction enthalpies (metal ion-binding affinities) and free energies, the influence of the C-terminal moiety on the backbone structural features, the existence of various types of intramolecular H-bond interactions, harmonic vibrational frequencies, along with various other electronic properties pertaining to the zwitterions of the dipeptide molecules as well as their metallic complexes. Metal coordination via the carboxylate groups tends to enhance the planarity of the amide planes. The participations of the N- and C-terminal side-chain moieties in metal-binding markedly enhance the thermodynamic stability of the metalated dipeptides. The theoretical λmax values, calculated using the TD/DFT level for all the systems, well represent the occurrence of d-d transitions in the Cu-dipeptide complexes

scholarly journals The structural chemistry of zinc(ii) and nickel(ii) dithiocarbamate complexes

2021 ◽  
Vol 19 (1) ◽  
pp. 974-986
Author(s):  
Tanzimjahan A. Saiyed ◽  
Jerry O. Adeyemi ◽  
Damian C. Onwudiwe
Keyword(s):  
Complex Formation ◽  
Metal Ions ◽  
Structural Properties ◽  
Binding Sites ◽  
Biological Systems ◽  
Structural Chemistry ◽  
Metal Coordination ◽  
Nickel Ions ◽  
Coordination Modes ◽  
Biomedical Fields

Abstract Dithiocarbamate complexes are of immense interest due to their diverse structural properties and extensive application in various areas. They possess two sulfur atoms that often act as the binding sites for metal coordination in a monodentate, bidentate, or anisodentate fashion. These different coordination modes enhance the possibility for complex formation and make them useful in different areas especially in biomedical fields. A synergy exists in the metal ions and dithiocarbamate moieties, which tends to exert better properties than the respective individual components of the complex. These improved properties have also been attributed to the presence of the C–S bonds. Zinc and nickel ions have been majorly found to bind to the dithiocarbamate in bidentate modes, and consequently different geometries have resulted from this interaction. The aim of this review is to present some studies on the synthesis, structural chemistry, and the relevance of zinc and nickel dithiocarbamates complexes especially in biological systems.

Peptide Bond Modification for Metal Coordination: 2. Metal-Binding Properties of Peptide-Derived Pentaaza-Macrocyclic Templates

2001 ◽  
pp. 593-594 ◽  
Author(s):  
Yunpeng Ye ◽  
Garland R. Marshall ◽  
Ron Smith ◽  
Craig Durmstorff ◽  
Urszula Slomczynska
Keyword(s):  
Metal Binding ◽  
Peptide Bond ◽  
Metal Coordination ◽  
Binding Properties

scholarly journals A trapped human PPM1A–phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity

2018 ◽  
Vol 293 (21) ◽  
pp. 7993-8008 ◽  
Author(s):  
Subrata Debnath ◽  
Dalibor Kosek ◽  
Harichandra D. Tagad ◽  
Stewart R. Durell ◽  
Daniel H. Appella ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Metal Ions ◽  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Catalytic Domain ◽  
Protein Phosphatases ◽  
Random Order ◽  
Structural Features

Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg2+ or Mn2+ ions for activity in vitro. The crystal structure of human PPM1A (also known as PP2Cα), the first PPM structure determined, displays two tightly bound Mn2+ ions in the active site and a small subdomain, termed the Flap, located adjacent to the active site. Some recent crystal structures of bacterial or plant PPM phosphatases have disclosed two tightly bound metal ions and an additional third metal ion in the active site. Here, the crystal structure of the catalytic domain of human PPM1A, PPM1Acat, complexed with a cyclic phosphopeptide, c(MpSIpYVA), a cyclized variant of the activation loop of p38 MAPK (a physiological substrate of PPM1A), revealed three metal ions in the active site. The PPM1Acat D146E–c(MpSIpYVA) complex confirmed the presence of the anticipated third metal ion in the active site of metazoan PPM phosphatases. Biophysical and computational methods suggested that complex formation results in a slightly more compact solution conformation through reduced conformational flexibility of the Flap subdomain. We also observed that the position of the substrate in the active site allows solvent access to the labile third metal-binding site. Enzyme kinetics of PPM1Acat toward a phosphopeptide substrate supported a random-order, bi-substrate mechanism, with substantial interaction between the bound substrate and the labile metal ion. This work illuminates the structural and thermodynamic basis of an innate mechanism regulating the activity of PPM phosphatases.

Construction of crystal structures of metal(II)–benzoates (M=Mn, Ni, Co, Cu, Zn, and Cd) and 1,2-bis(4-pyridyl)ethane: Effects of metal coordination modes and their catalytic activities

2009 ◽  
Vol 362 (11) ◽  
pp. 4119-4126 ◽  
Author(s):  
Soo Hyun Kim ◽  
Byeong Kwon Park ◽  
Young Joo Song ◽  
Seung Man Yu ◽  
Hyo Geun Koo ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Metal Coordination ◽  
Coordination Modes ◽  
Catalytic Activities

scholarly journals Analysis of Genes That Encode DtxR-Like Transcriptional Regulators in Pathogenic and Saprophytic Corynebacterial Species

2004 ◽  
Vol 72 (4) ◽  
pp. 1885-1895 ◽  
Author(s):  
Diana Marra Oram ◽  
Ana Avdalovic ◽  
Randall K. Holmes
Keyword(s):  
Gene Expression ◽  
Metal Binding ◽  
Regulatory Protein ◽  
Transcriptional Regulators ◽  
Chromosomal Dna ◽  
Regulate Gene Expression ◽  
Protein Levels ◽  
Diphtheria Toxin Repressor ◽  
Conserved Region ◽  
High Level

ABSTRACT Metal-dependent transcriptional regulators of the diphtheria toxin repressor (DtxR) family have been identified in a wide variety of bacterial genera, where they control gene expression in response to one of two metal ions, Fe2+ or Mn2+. DtxR of Corynebacterium diphtheriae is the best characterized of these important metal-dependent regulators. The genus Corynebacterium includes many phenotypically diverse species, and the prevalence of DtxR-like regulators within the genus is unknown. We assayed chromosomal DNA from 42 different corynebacterial isolates, representing 33 different species, for the presence of a highly conserved region of the dtxR gene that encodes the DNA-binding helix-turn-helix motif and metal-binding site 1 within domains 1 and 2 of DtxR. The chromosome of all of the isolates contained this conserved region of dtxR, and DNA sequencing revealed a high level of nucleotide sequence conservation within this region in all of the corynebacterial species (ranging from 62 to 100% identity and averaging 70% identity with the dtxR prototype). The level of identity was even greater for the predicted protein sequences encoded by the dtxR-like genes, ranging from 81 to 100% identity and averaging 91% identity with DtxR. Using a DtxR-specific antiserum we confirmed the presence of a DtxR-like protein in extracts of most of the corynebacterial isolates and determined the precise amount of DtxR per cell in C. diphtheriae. The high level of identity at both DNA and protein levels suggests that all of the isolates tested encode a functional DtxR-like Fe2+-activated regulatory protein that can bind homologs of the DtxR operator and regulate gene expression in response to iron.

scholarly journals A novel computational approach for genome-wide prediction of small RNAs in bacteria

2014 ◽  
Author(s):  
Lei Li ◽  
Hoi Shan Kwan
Keyword(s):  
Small Rnas ◽  
Computational Prediction ◽  
Transcriptional Regulators ◽  
Structural Features ◽  
Extensive Study ◽  
Bacterial Physiology ◽  
Genome Wide ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Window Approach

Small regulatory RNAs (sRNAs) are the most abundant post-transcriptional regulators in bacteria. They serve ubiquitous roles that control nearly every aspects of bacterial physiology. Identification of important features from sRNAs sequences will guide the computational prediction of new sRNA sequences for a better understanding of the pervasive sRNA-mediated regulation in bacteria. In this study, we have performed systematic analyses of many sequence and structural features that are possibly related to sRNA properties and identified a subset of significant features that effectively discriminate sRNAs sequences from random sequences. we then used a neural network model that integrated these subfeatures on unlabeled testing datasets, and it had achieved a 92.2% recall and 89.8% specificity. Finally, we applied this prediction model for genome-wide identification of sRNAs-encoded genes using a sliding-window approach. We recovered multiple known sRNAs and hundreds of predicted new sRNAs. These candidate novel sRNAs deserve extensive study to better understand the sRNA-mediated regulatory network in bacteria.

Structural Features of the Metal Binding Sites in Transferrins by EXAFS and Other Spectroscopic Techniques

1987 ◽  
pp. 176-184 ◽  
Author(s):  
I. Bertini ◽  
S. Mangani ◽  
L. Messoria ◽  
S. Mobilio ◽  
P. L. Orioli
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Structural Features ◽  
Spectroscopic Techniques ◽  
Metal Binding Sites
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