Metal ion effects in intramolecular reactions. Effects of divalent metal ions on intramolecular acetamido group participation in ester hydrolysis

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

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Modeling of neotame and fructose thermochemistry: Comparison with mono and divalent metal ions by Computational and experimental approach

Scientific Reports ◽

10.1038/s41598-019-54626-9 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Deepali Sharma ◽

Suvardhan Kanchi ◽

Ayyappa Bathinapatla ◽

Inamuddin ◽

Abdullah M. Asiri

Keyword(s):

Metal Ions ◽

Metal Ion ◽

Density Functional ◽

Divalent Metal ◽

Basis Set ◽

Hydroxyl Groups ◽

Specific Cell ◽

Water Medium ◽

Artificial Sweetener ◽

Divalent Metal Ions

AbstractThe metal complexes can demonstrate various interesting biological activities in the human body. However, the role of certain metal ions for specific cell activities is still subject to debate. This study is aimed at comparing the thermochemical properties of neotame (artificial sweetener) and α, β-fructose in gas phase and water medium. The interaction of α and β-fructose, neotame with monovalent and divalent metal ions was studied and comprehended by density functional theory (DFT) using B3LYP functional, 6–311 + G (d, p) and D3 basis set. Metal ion affinities (MIA) values depicted that ionic radius of metal ions played an important role in the interaction of α, β-fructose and neotame. The ∆G parameter was calculated to predict and understand the interaction of metal ions with α and β-fructose, neotame. The results suggested that the presence of hydroxyl groups and oxygen atoms in sugar molecules acted as preferred sites for the binding and interaction of mono and divalent ions. For the first time computational study has been introduced in the present study to review the progress in the application of metal binding with sugar molecules especially with neotame. Moreover, voltammetric behaviour of neotame-Zn2+ was studied using cyclic and differential pulse voltammetry. The obtained results suggest that the peak at −1.13 V is due to the reduction of Zn2+ in 0.1 M phosphate buffer medium at pH 5.5. Whereas, addition of 6-fold higher concentration of neotame to the ZnCl2.2H2O resulted in a new irreversible cathodic peak at −0.83, due to the reduction of neotame-Zn2+ complex. The Fourier transform infrared spectroscopy (FTIR) results indicates that the β-amino group (-NH) and carboxyl carbonyl (-C = O) groups of neotame is participating in the chelation process, which is further supported by DFT studies. The findings of this study identify the efficient chelation factors as major contributors into metal ion affinities, with promising possibilities to determine important biological processes in cell wall and glucose transmembrane transport.

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Divalent metal ion effects on a mutant histidinol phosphate phosphatase from Salmonella typhimurium

Archives of Biochemistry and Biophysics ◽

10.1016/0003-9861(74)90211-2 ◽

1974 ◽

Vol 162 (2) ◽

pp. 513-522 ◽

Cited By ~ 8

Author(s):

L.L. Houston ◽

Margaret E. Graham

Keyword(s):

Salmonella Typhimurium ◽

Metal Ion ◽

Divalent Metal ◽

Divalent Metal Ion ◽

Ion Effects ◽

Metal Ion Effects ◽

Histidinol Phosphate Phosphatase

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Complementary Metal Ion Specificity of the Metal-Citrate Transporters CitM and CitH of Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.182.22.6374-6381.2000 ◽

2000 ◽

Vol 182 (22) ◽

pp. 6374-6381 ◽

Cited By ~ 51

Author(s):

Bastiaan P. Krom ◽

Jessica B. Warner ◽

Wil N. Konings ◽

Juke S. Lolkema

Keyword(s):

Bacillus Subtilis ◽

Metal Ions ◽

Metal Ion ◽

Physiological Function ◽

Divalent Metal ◽

Uptake System ◽

Divalent Metal Ions ◽

Ion Specificity ◽

Citrate Transporter ◽

Wide Range

ABSTRACT Citrate uptake in Bacillus subtilis is stimulated by a wide range of divalent metal ions. The metal ions were separated into two groups based on the expression pattern of the uptake system. The two groups correlated with the metal ion specificity of two homologousB. subtilis secondary citrate transporters, CitM and CitH, upon expression in Escherichia coli. CitM transported citrate in complex with Mg2+, Ni2+, Mn2+, Co2+, and Zn2+ but not in complex with Ca2+, Ba2+, and Sr2+. CitH transported citrate in complex with Ca2+, Ba2+, and Sr2+ but not in complex with Mg2+, Ni2+, Mn2+, Co2+, and Zn2+. Both transporters did not transport free citrate. Nevertheless, free citrate uptake could be demonstrated in B. subtilis, indicating the expression of at least a third citrate transporter, whose identity is not known. For both the CitM and CitH transporters it was demonstrated that the metal ion promoted citrate uptake and, vice versa, that citrate promoted uptake of the metal ion, indicating that the complex is the transported species. The results indicate that CitM and CitH are secondary transporters that transport complexes of divalent metal ions and citrate but with a complementary metal ion specificity. The potential physiological function of the two transporters is discussed.

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