scholarly journals Mechanistic and In silico Characterization of Metal ion Requirements of Escherichia coli Zinc Phosphodiesterase Activity

2020 ◽  
Vol 5 (1) ◽  
pp. 56-65
Author(s):  
Adedoyin Igunnu ◽  
Micheal F. Dada ◽  
Tamonokorite AbelJack-Soala ◽  
Ireoluwa Y. Joel ◽  
Oluwafunmibi O. Lanre-Ogun ◽  
...  

AbstractZinc phosphodiesterase (ZiPD) participates in the maturation of tRNA precursors. The roles of metal ions in promoting phosphoryl transfer reaction on zinc phosphodiesterase (ZiPD) activity have not been fully characterized. Therefore, this study investigated the effects of some metal ions on phosphodiesterase activity of Escherichia coli ZiPD as well as the binding site and binding affinity of the metal ions. ZiPD activity was measured by monitoring the rate of hydrolysis of bis-para-nitrophenyl phosphate (bis-pNPP) in the presence of some selected divalent metal ions (Mn2+, Co2+, Mg2+ and Zn2+). The results obtained revealed that Mn2+ at 1 mM activated ZiPD activity by 4-fold with binding affinity score of 1.795. Co2+ at 0.5 mM activated ZiPD activity by 2-fold with binding affinity score of 1.773. Mg2+ at 0.5 mM enhanced the binding affinity of ZiPD for bis-pNPP but did not increase the turnover rate of ZiPD. Zn2+ at 1.5 mM activated ZiPD activity by 2-fold via increased affinity of ZiPD for bis-pNPP. In conclusion, the findings from this study showed that Mn2+ and Zn2+ are the most effective stimulatory ions of ZiPD for bis-pNPP while Zn2+ exerted the highest binding affinity of ZiPD for bis-pNPP.

1999 ◽  
Vol 23 (2) ◽  
pp. 106-107
Author(s):  
Shin-ichi Kondo ◽  
Kitaro Yoshida ◽  
Yumihiko Yano

The intramolecular transesterification reaction of 2-hydroxypropyl 4-nitrophenyl phosphate is greatly accelerated (105–106 fold) by the addition of divalent metal ions such as Zn2+ and Cu2+ in MeCN without a base; the metal ion effect is quite sensitive to the content of H2O in MeCN.


2001 ◽  
Vol 204 (6) ◽  
pp. 1053-1061 ◽  
Author(s):  
A. Sacher ◽  
A. Cohen ◽  
N. Nelson

Transition metals are essential for many metabolic processes, and their homeostasis is crucial for life. Metal-ion transporters play a major role in maintaining the correct concentrations of the various metal ions in living cells. Little is known about the transport mechanism of metal ions by eukaryotic cells. Some insight has been gained from studies of the mammalian transporter DCT1 and the yeast transporter Smf1p by following the uptake of various metal ions and from electrophysiological experiments using Xenopus laevis oocytes injected with RNA copies (c-RNA) of the genes for these transporters. Both transporters catalyze the proton-dependent uptake of divalent cations accompanied by a ‘slippage’ phenomenon of different monovalent cations unique to each transporter. Here, we further characterize the transport activity of DCT1 and Smf1p, their substrate specificity and their transport properties. We observed that Zn(2+) is not transported through the membrane of Xenopus laevis oocytes by either transporter, even though it inhibits the transport of the other metal ions and enables protons to ‘slip’ through the DCT1 transporter. A special construct (Smf1p-s) was made to enhance Smf1p activity in oocytes to enable electrophysiological studies of Smf1p-s-expressing cells. 54Mn(2+) uptake by Smf1p-s was measured at various holding potentials. In the absence of Na(+) and at pH 5.5, metal-ion uptake was not affected by changes in negative holding potentials. Elevating the pH of the medium to 6.5 caused metal-ion uptake to be influenced by the holding potential: ion uptake increased when the potential was lowered. Na(+) inhibited metal-ion uptake in accordance with the elevation of the holding potential. A novel clutch mechanism of ion slippage that operates via continuously variable stoichiometry between the driving-force pathway (H(+)) and the transport pathway (divalent metal ions) is proposed. The possible physiological advantages of proton slippage through DCT1 and of Na(+) slippage through Smf1p are discussed.


1994 ◽  
Vol 300 (2) ◽  
pp. 373-381 ◽  
Author(s):  
P Spencer ◽  
P M Jordan

Two distinct metal-binding sites, termed alpha and beta, have been characterized in 5-aminolaevulinic acid dehydratase from Escherichia coli. The alpha-site binds a Zn2+ ion that is essential for catalytic activity. This site can also utilize other metal ions able to function as a Lewis acid in the reaction mechanism, such as Mg2+ or Co2+. The beta-site is exclusively a transition-metal-ion-binding site thought to be involved in protein conformation, although a metal bound at this site only appears to be essential for activity if Mg2+ is to be bound at the alpha-site. The alpha- and beta-sites may be distinguished from one another by their different abilities to bind divalent-metal ions at different pH values. The occupancy of the beta-site with Zn2+ results in a decrease of protein fluorescence at pH 6. Occupancy of the alpha- and beta-sites with Co2+ results in u.v.-visible spectral changes. Spectroscopic studies with Co2+ have tentatively identified three cysteine residues at the beta-site and one at the alpha-site. Reaction with N-ethyl[14C]maleimide preferentially labels cysteine-130 at the alpha-site when Co2+ occupies the beta-site.


2003 ◽  
Vol 81 (1) ◽  
pp. 53-63 ◽  
Author(s):  
Erwin Buncel ◽  
Ruby Nagelkerke ◽  
Gregory RJ Thatcher

In continuation of our studies of alkali metal ion catalysis and inhibition at carbon, phosphorus, and sulfur centers, the role of alkali metal ions in nucleophilic displacement reactions of p-nitrophenyl phenylphosphonate (PNPP) has been examined. All alkali metal ions studied acted as catalysts. Alkali metal ions added as inert salts increased the rate while decreased rate resulted on M+ complexation with 18-crown-6 ether. Kinetic analysis indicated the interaction of possibly three potassium ions, four sodium ions, and five lithium ions in the transition state of the reactions of ethoxide with PNPP. Pre-association of the anionic substrate with two metals ions in the ground state gave the best fit to the experimental data of the sodium system. Thus, the study gives evidence of the role of several metal ions in nucleophilic displacement reactions of ethoxide with anionic PNPP, both in the ground state and in the transition state. Molecular modeling of the anionic transition state implies that the size of the monovalent cation and the steric requirement of the pentacoordinate transition state are the primary limitations on the number of cations that can be brought to bear to stabilize the transition state and catalyze nucleophilic substitution at phosphorus. The bearing of the present work on metal ion catalysis in enzyme systems is discussed, in particular enzymes that catalyze phosphoryl transfer, which often employ multiple metal ions. Our results, both kinetic and modeling, reveal the importance of electrostatic stabilization of the transition state for phosphoryl transfer that may be effected by multiple cations, either monovalent metal ions or amino acid residues. The more such cations can be brought into contact with the anionic transition state, the greater the catalysis observed.Key words: alkali metal ion catalysis, nucleophilic displacement at phosphorus, multiple metal ion catalysis, phosphoryl transfer.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1096-1096
Author(s):  
Maria Cristina Bravo ◽  
Catherine G McGuinness ◽  
Matthew Gissel ◽  
Thomas Orfeo ◽  
Kenneth G. Mann

Abstract Introduction The rapid coagulation response to vascular injury is mediated by the formation of three enzyme cofactor complexes (extrinsic tenase, intrinsic tenase and prothrombinase) on membrane surfaces. A common structural feature of these proteases is their GLA domains, each of which requires the binding of divalent metal ions at multiple sites to achieve the conformation necessary for optimal membrane and cofactor binding. Both Ca2+ and Mg2+ ions have been reported to bind to GLA domain sites. However almost all studies kinetically characterizing these complexes have been done in the presence of Ca2+ (2-5 mM) as the sole metal ion, despite the relatively equivalent availability in plasma of both free Ca2+ (∼1.1 mM) and Mg2+ (∼0.6 mM) (Ca2+/Mg2+). A recent study has systematically examined the effects of various Ca2+ concentrations with and without Mg2+ on the membrane binding of activated protein C (APC) and FVIIa and enzymatic activity of APC and the extrinsic tenase complex which were enhanced in Ca2+/Mg2+ relative to Ca2+ alone (Vadivel, K., et al, 2013 JMB). In the current study we compare the effects of plasma levels of Ca2+ and Mg2+ versus Ca2+alone on the catalytic performances of the extrinsic tenase, intrinsic tenase and prothrombinase complexes individually and collectively. Methods All experiments were conducted in Hepes buffered saline pH 7.4 containing 0.1% PEG and either 2 mM Ca2+ or 1.1 mM Ca2+/0.6 mM Mg2+ (Ca2+/Mg2+). In closed system experiments, enzyme-cofactor complexes were assembled on phospholipid vesicles composed of a 3:1 ratio of synthetic phosphatidylcholine and phosphatidylserine (PCPS), and zymogen activation monitored via sampling into assay mixtures containing the appropriate chromogenic substrate. In open system experiments complexes were preassembled on PCPS coated capillaries, the zymogen delivered in the flowing phase and the extent of zymogen activation monitored in the effluent as described previously (Haynes, LM., et al, 2011 Biophys J). The combined interaction of the procoagulant enzyme cofactor complexes under both metal ion conditions was studied in a synthetic coagulation proteome monitoring thrombin (IIa) generation as previously described (van’t Veer, C., and Mann, KG, 1997 JBC). Results Extrinsic tenase The extrinsic tenase complex had an approximately two-fold higher rate of FXa generation in the presence of Ca2+/Mg2+ (1.78 ±0.05 pM/s) versus Ca2+ alone (0.88 ± 0.02 pM/s) (N=3, p<0.001). Experiments were also conducted in the absence or presence of tissue factor pathway inhibitor (TFPI); in the presence of TFPI and Ca2+/Mg2+ ions the extrinsic tenase complex was three times as catalytically active compared to TFPI and Ca2+ only (N=3, p<0.05). Direct FXa inhibition by TFPI was not significantly different between the Ca2+ and Ca2+/Mg2+ containing buffers. Intrinsic tenase In closed system experiments the intrinsic tenase complex showed impaired FXa generation in the presence of Ca2+/Mg2+ (29.3 ± 3.4 pM/s) compared to Ca2+ alone (51.7 ± 3.0 pM/s) (N=3, p<0.001). Thrombin activation of FVIII was not statistically different between both buffers, however the presence of Ca2+/Mg2+ resulted in a more rapid loss of cofactor activity over Ca2+ alone. Prothrombinase Under flow, IIa generation measured from prothrombinase was not statistically different between both buffers when measured at five different shear rates (100-1000s-1, N≥2). Plasma proteome In the synthetic coagulation proteome (N=4) the presence of Ca2+/Mg2+ led to an average 31% increase in maximum IIa levels compared to Ca2+alone and an average decrease of 1 minute to reach maximum levels. Conclusions In summary, the presence of plasma levels of Ca2+ and Mg2+, compared to Ca2+ alone, enhances the initiation phase of the extrinsic pathway of coagulation by enhancing the rate of FXa generation from the extrinsic tenase complex while also impairing the TFPI inhibition of the extrinsic tenase complex. These procoagulant effects are potentially abrogated by the suppressive effects of Ca2+/Mg2+ on the intrinsic tenase complex, potentially caused by the increased rate of spontaneous inactivation of FVIIIa. These results highlight the importance of complementing the assessments of individual enzyme complex systems with studies of the larger complex systems in which they function to identify the net physiologic impact of metal ions that target various components in the coagulation cascade. Disclosures: Mann: Haematologic Technologies, Inc: Equity Ownership, Membership on an entity’s Board of Directors or advisory committees.


Biochemistry ◽  
1977 ◽  
Vol 16 (25) ◽  
pp. 5449-5454 ◽  
Author(s):  
Cheng-Wen Wu ◽  
Felicia Y. H. Wu ◽  
David C. Speckhard

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Sarita Singh ◽  
Jyoti Singh ◽  
Sunita Gulia ◽  
Rita Kakkar

Density functional calculations have been performed on four-coordinate kojate complexes of selected divalent metal ions in order to determine the affinity of the metal ions for the kojate ion. The complexation reactions are characterized by high energies, showing that they are highly exothermic. It is found that Ni(II) exhibits the highest affinity for the kojate ion, and this is attributed to the largest amount of charge transfer from the ligand to the metal ion. The Ni(II) complex has distorted square planar structure. The HOMOs and LUMOs of the complexes are also discussed. All complexes display a strong band at ~1500 cm−1 corresponding to the stretching frequency of the weakened carbonyl bond. Comparison of the complexation energies for the two steps shows that most of the complexation energy is realized in the first step. The energy released in the second step is about one-third that of the first step.


2021 ◽  
Vol 8 ◽  
Author(s):  
Jongseo Park ◽  
Hyung-Seop Youn ◽  
Jun Yop An ◽  
Youngjin Lee ◽  
Soo Hyun Eom ◽  
...  

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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