Deciphering the catalytic amino acid residues of l -2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1: An in silico analysis

Adamu, Aliyu; Wahab, Roswanira Abdul; Shamsir, Mohd Shahir; Aliyu, Firdausi; Huyop, Fahrul

doi:10.1016/j.compbiolchem.2017.08.007

Cited by 11 publications

(4 citation statements)

References 38 publications

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“…Other kinds of dehalogenases, termed haloacetate dehalogenase (EC 3.8.1.3) that acts specifically on halogenated acetates to yield glycolate, are also in group II [13]. To understand how these dehalogenases function, in silico studies on enzyme-substrate binding need to be carried out provided that full dehalogenase sequence can be obtained in gene isolation by PCR [14][15].…”

Section: ■ Introductionmentioning

confidence: 99%

Further Analysis of <i>Burkholderia pseudomallei</i> MF2 and Identification of Putative Dehalogenase Gene by PCR

Edbeib¹,

Wahab

Huyop

et al. 2020

Indones. J. Chem.

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Halogenated organic compounds are extensively and widely used as pesticides, herbicides, and antibiotics that contribute to the pollution. This research was aimed to further analyze and characterize a bacterium that has the ability to utilize 2,2dichloropropionic acid (2,2-DCP) as a model to study dehalogenase enzyme production. Microscopic observation, biochemical tests and PCR technique were carried out in order to characterize the isolated bacterium. Strain MF2 showed its ability to grow on 10 mM 2,2-DCP liquid minimal medium with doubling time of 13 h with maximum chloride ion released of 19.8 molCl -/mL. The 16S rDNA analysis suggested that strain MF2 belongs to the genus Burkholderia. This was supported by the microscopic observation and biochemical tests. Dehalogenase gene was observed when using only primers dehIfor1 and dehIrev2 derived from group I deh PCR primer sequences, whereas no amplification using dhlB-314-forward and dhlB-637-reverse (group II dehalogenase) and haloacetate dehalogenase (H2-1157-forward and H2-1662-reverse) PCR primer sequences. The results suggested that, possibly, dehalogenase from MF2 was related to group I deh. In conclusion, strain MF2 showed the ability to utilize 2,2-DCP as sole source of carbon and energy. Further analysis revealed the MF2 strain consisted of dehalogenase gene that could be used for degradation of man-made halogenated compounds present in the environment. Using existing dehalogenase PCR primers, it was possible to amplify the dehalogenase genes sequence.

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Section: ■ Introductionmentioning

confidence: 99%

Further Analysis of <i>Burkholderia pseudomallei</i> MF2 and Identification of Putative Dehalogenase Gene by PCR

Edbeib¹,

Wahab

Huyop

et al. 2020

Indones. J. Chem.

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“…The cut-off distance for Van der Waal's interactions (calculated using the particle mesh Ewald method [44]) was 10 Å. Hydrogen covalent bonds were constrained using SHAKE [45]. This length of simulation is consistent with recent studies on engineered proteins (for example, [46][47][48][49]).…”

Section: Molecular Dynamicsmentioning

confidence: 65%

Modulation of the mobility of a key region in human galactokinase: Impacts on catalysis and stability

McAuley

Huang

Timson

2018

Bioorganic Chemistry

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Galactokinase catalyses the phosphorylation of α-d-galactose and some structurally related monosaccharides. The enzyme is of interest due to its potential as a biocatalyst for the production of sugar 1-phosphates and due to its involvement in the inherited metabolic disease type II galactosemia. It has been previously shown that a region (residues 231-245) in human galactokinase often has altered mobility when active site residues are varied. We hypothesised that the reverse may be true and that designing changes to this region might affect the functioning of the active site of the enzyme. Focussing on four residues (Leu-231, Gln-242, Glu-244 and Glu-245) we conducted molecular dynamics simulations to explore the effects of changing these residues to glycine or serine. In most cases the variations resulted in local changes to the 231-245 region and global changes to the root mean squared fluctuation (RMSF) of the protein. The four serine variants were expressed as recombinant proteins. All had altered steady state enzyme kinetic parameters with α-d-galactose as a substrate. However, these changes were generally less than ten-fold in magnitude. Changes were also observed with 2-deoxy-α-d-galactose, α-d-galactosamine and α-d-talose as substrates, including (in some cases) loss of detectable activity, suggesting that these variations can tune the specificity of the enzyme. This study demonstrates that activity and specificity of human galactokinase can be modulated by variations designed to affect active site flexibility. It is likely that this principle can be generalised to other enzymes.

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“…The details of this analysis are presented in ESI †. 50 The most stable conformations obtained by molecular docking simulations of title compounds were subjected further to the analysis of physicochemical and pharmacokinetic properties of the title compounds employing a free online web server SwissADME. For this purpose, the SMILES notations of structures were applied for calculation.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Several coumarin derivatives and their Pd(ii) complexes as potential inhibitors of the main protease of SARS-CoV-2, anin silicoapproach

et al. 2020

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Deciphering the catalytic amino acid residues of l -2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1: An in silico analysis

Cited by 11 publications

References 38 publications

Further Analysis of <i>Burkholderia pseudomallei</i> MF2 and Identification of Putative Dehalogenase Gene by PCR

Further Analysis of <i>Burkholderia pseudomallei</i> MF2 and Identification of Putative Dehalogenase Gene by PCR

Modulation of the mobility of a key region in human galactokinase: Impacts on catalysis and stability

Several coumarin derivatives and their Pd(ii) complexes as potential inhibitors of the main protease of SARS-CoV-2, anin silicoapproach

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