The crystal structure of the phosphotriesterase from M. tuberculosis, another member of phosphotriesterase-like lactonase family

Zhang, Liang; Wang, Huiying; Liu, Xiang; Zhou, Weihong; Rao, Zihe

doi:10.1016/j.bbrc.2019.01.069

Cited by 5 publications

(5 citation statements)

References 31 publications

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“…However, the calculation of partial charges via quantum approaches is time-consuming, especially for proteins formed by thousands of atoms. For this reason, herein, a contact surface of the PTE was first determined through a home-made algorithm and using the crystallographic structure of the enzyme at pH = 7 [14]. The electrostatic charges on large fragments of external amino acids were calculated in the frame of density functional theory (DFT) using the Löwdin method as implemented in NWChem [15].…”

Section: Quantum Calculationsmentioning

confidence: 99%

Enzyme Immobilization on Polymer Membranes: A Quantum and Molecular Mechanics Study

et al. 2019

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Adsorption of the phosphotriesterase on a polysulfone membrane surface was investigated in this paper through a double-scale computational approach. Surface charges of the enzyme, as well as membrane, were calculated at sub and nanoscale while protein adsorption was simulated at larger scale. Adsorption energies were calculated as a function of the enzyme–surface distance, and for each distance, several protein rotations were tested to find the most stable orientations of the macromolecule. The results of this model were useful in obtaining information about the adhesion of the enzyme and to give indications on the orientations of its binding site. Adsorption energies agreed with the literature data. Furthermore, the binding site of the immobilized phosphotriesterase was less accessible with respect to native enzymes due to the steric hindrance of the polymer surface; thus, a reduction of its efficiency is expected. The proposed methodology made use of fundamental quantities, calculated without resorting to adjustable or empirical parameters, providing basic outputs useful for ascertaining enzymatic catalysis rate.

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Section: Quantum Calculationsmentioning

confidence: 99%

Enzyme Immobilization on Polymer Membranes: A Quantum and Molecular Mechanics Study

et al. 2019

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“…However, those enzymes which have been studied well enough [9], have a similar active center as compared with OPH. Perhaps, the most studied and interesting lactonases are SsoPox from archaea Sulfolobus solfataricus [35] and mPHP from bacteria Mycobacterium tuberculosis [36] (Figure 4a,b). The structure of SsoPox dimer (A), mPHP monomer (B), and OPAA dimer (C) according to X-ray diffraction data (PDB 3UF9, 4IF2, and 3L24, respectively).…”

Section: Other Enzymes Of Pll Familymentioning

confidence: 99%

“…This site is located at the junction of two subunits in a homodimer, and therefore the stability of such protein molecule can be further increased. This enzyme also contains His254Arg/His257Val substitutions (according to OPH numbering), and the activity of mPHP containing Zn 2+ ions is reduced by another 2 orders of magnitude towards paraoxon as compared to SsoPox [36].…”

Section: Other Enzymes Of Pll Familymentioning

confidence: 99%

Enzymes, Reacting with Organophosphorus Compounds as Detoxifiers: Diversity and Functions

Lyagin

Ефременко

2021

IJMS

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Organophosphorus compounds (OPCs) are able to interact with various biological targets in living organisms, including enzymes. The binding of OPCs to enzymes does not always lead to negative consequences for the body itself, since there are a lot of natural biocatalysts that can catalyze the chemical transformations of the OPCs via hydrolysis or oxidation/reduction and thereby provide their detoxification. Some of these enzymes, their structural differences and identity, mechanisms, and specificity of catalytic action are discussed in this work, including results of computational modeling. Phylogenetic analysis of these diverse enzymes was specially realized for this review to emphasize a great area for future development(s) and applications.

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“…[14,19] Notably, phosphotriesterase (PTE) is one of the few metallohydrolases capable of efficiently degrading PTs, [20] and is found in various organisms, including bacteria and certain plants. Its unique divalent zinc cation (Zn II Zn II ) cofactor [21] plays a crucial role in the enzyme catalytic activity, facilitating the hydrolysis of PTs, which usually occurs in alkaline pH conditions. [14] Strategies have been developed to mimic these enzymes' behavior synthetically.…”

Section: Introductionmentioning

confidence: 99%

“…[23,26] Moreover, besides providing these electronic interactions, species such as imidazole and its derivatives like benzimidazole (BIMZ) could be suitable candidates for acting as a nucleophile. Those groups have been widely reported in organophosphates (OP) hydrolysis, [7,11,[41][42][43][44][45] and their bioavailability [21,29,46,47] makes them a suitable choice for bioinspired molecules.…”

Section: Introductionmentioning

confidence: 99%

Phosphate Triester Hydrolysis by Mononuclear Iron(III) Complexes: The Role of Benzimidazole in the Second Coordination Sphere

Luiz,

Farias,

Alzamora

et al. 2024

Eur J Inorg Chem

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Over the years, phosphate ester hydrolysis promoted by coordination compounds has attracted extensive research on developing new bioinspired compounds. However, the literature lacks sufficient examples displaying activity toward phosphate triesters specifically, limiting the understanding of efficient strategies for its hydrolysis. Herein, we report the preparation and characterization of three mononuclear iron(III) complexes (1, 2, and 3) and their hydrolase‐like activity. Complexes 2 and 3 contained benzimidazole (BIMZ) moieties and were strategically designed to separate the BIMZ moiety from the first coordination sphere, and complex 1 was used as a reference. Several techniques provided structural information, including spectrophotometry, spectrometry, electrochemistry, elemental analysis, and 57Fe Mossbauer. Density functional theory (DFT) revealed distorted octahedral geometries due to the presence of the BIMZ groups. These groups also directly affected the protonation equilibria and catalytic activity. The phosphate triester diethyl‐2,4‐dinitrophenylphosphate (DEDNPP) hydrolysis was enhanced at least 27 times compared to the uncatalyzed reaction, with complexes 2 and 3, containing the BIMZ moiety showing higher catalytic rates (kcat). Moreover, a longer carbon chain led to a higher hydrolysis rate but less interaction with substrate. These findings provide a foundation for further investigations and developing into efficient catalysts for agrochemical degradation.

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The crystal structure of the phosphotriesterase from M. tuberculosis, another member of phosphotriesterase-like lactonase family

Cited by 5 publications

References 31 publications

Enzyme Immobilization on Polymer Membranes: A Quantum and Molecular Mechanics Study

Enzyme Immobilization on Polymer Membranes: A Quantum and Molecular Mechanics Study

Enzymes, Reacting with Organophosphorus Compounds as Detoxifiers: Diversity and Functions

Phosphate Triester Hydrolysis by Mononuclear Iron(III) Complexes: The Role of Benzimidazole in the Second Coordination Sphere

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