Mutagenic analysis of the conserved residues in dehalogenase IVa of<i>Burkholderia cepacia</i>MBA4

Pang, Benjamin C. M.; Tsang, Jwh

doi:10.1111/j.1574-6968.2001.tb10876.x

Cited by 21 publications

(13 citation statements)

References 18 publications

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“…The fully conserved lysine and aspartic acid in case of haloacid dehalogenase superfamily have been obtained previously and it is proposed that they might be involved in the catalytic site of these enzymes which involves the dehalogenation of xenobiotics [ 30 ]. Further study about the site directed mutagenesis experiment reported previously also confirmed the importance of these two residues [ 31 , 32 ]. Functional similarities with some common motifs that are unique for the group were observed.…”

Section: Discussionsupporting

confidence: 58%

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

Satpathy

Konkimalla

Ratha

2016

Advances in Bioinformatics

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2-Haloalkanoic acid dehalogenase enzymes have broad range of applications, starting from bioremediation to chemical synthesis of useful compounds that are widely distributed in fungi and bacteria. In the present study, a total of 81 full-length protein sequences of 2-haloalkanoic acid dehalogenase from bacteria and fungi were retrieved from NCBI database. Sequence analysis such as multiple sequence alignment (MSA), conserved motif identification, computation of amino acid composition, and phylogenetic tree construction were performed on these primary sequences. From MSA analysis, it was observed that the sequences share conserved lysine (K) and aspartate (D) residues in them. Also, phylogenetic tree indicated a subcluster comprised of both fungal and bacterial species. Due to nonavailability of experimental 3D structure for fungal 2-haloalkanoic acid dehalogenase in the PDB, molecular modelling study was performed for both fungal and bacterial sources of enzymes present in the subcluster. Further structural analysis revealed a common evolutionary topology shared between both fungal and bacterial enzymes. Studies on the buried amino acids showed highly conserved Leu and Ser in the core, despite variation in their amino acid percentage. Additionally, a surface exposed tryptophan was conserved in all of these selected models.

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Section: Discussionsupporting

confidence: 58%

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

Satpathy

Konkimalla

Ratha

2016

Advances in Bioinformatics

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“…A unique characteristic among epoxide hydrolases is that although they commonly have low sequential similarities, their catalytic residues remain conserved. Based on previous studies, the catalytically important residues of L-2-haloacid dehalogenase [23] and DehIVa [22,25] were indicated by asterisk (*) in supplementary Figure S2; almost all of these residues were conserved in CESH[L]. The existence of conserved catalytically important residues in CESH[L] (Asp18, Thr22, Arg55, Thr133, Lys164, Tyr170 and Asp193), which may consist a catalytic pocket at the interface of two functional domains (Fig.…”

Section: Characterization Of the Recombinant Enzymesmentioning

confidence: 99%

High Yield Recombinant Expression, Characterization and Homology Modeling of Two Types of Cis-epoxysuccinic Acid Hydrolases

Cui

Wang

et al. 2012

Protein J

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The cis-epoxysuccinate hydrolases (CESHs), members of epoxide hydrolase, catalyze cis-epoxysuccinic acid hydrolysis to form D: (-)-tartaric acid or L: (+)-tartaric acid which are important chemicals with broad scientific and industrial applications. Two types of CESHs (CESH[D: ] and CESH[L: ], producing D: (-)- and L: (+)-tartaric acids, respectively) have been reported with low yield and complicated purification procedure in previous studies. In this paper, the two CESHs were overexpressed in Escherichia coli using codon-optimized genes. High protein yields by one-step purifications were obtained for both recombinant enzymes. The optimal pH and temperature were measured for both recombinant CESHs, and the properties of recombinant enzymes were similar to native enzymes. Kinetics parameters measured by Lineweaver-Burk plot indicates both enzymes exhibited similar affinity to cis-epoxysuccinic acid, but CESH[L: ] showed much higher catalytic efficiency than CESH[D: ], suggesting that the two CESHs have different catalytic mechanisms. The structures of both CESHs constructed by homology modeling indicated that CESH[L: ] and CESH[D: ] have different structural folds and potential active site residues. CESH[L: ] adopted a typical α/β-hydrolase fold with a cap domain and a core domain, whereas CESH[D: ] possessed a unique TIM barrel fold composed of 8 α-helices and 8 β-strands, and 2 extra short α-helices exist on the top and bottom of the barrel, respectively. A divalent metal ion, preferred to be zinc, was found in CESH[D: ], and the ion was proved to be crucial to the enzymatic activity. These results provide structural insight into the different catalytic mechanisms of the two CESHs.

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“…There are two groups of unique haloacid dehalogenases which have been better characterized as Group I and II α-Haloacid dehalogenase based on their different substrate intermediate catalytic mechanisms. While hydrolytic water performs a direct nucleophilic attack on the substrate α-carbon, displacing the bound halogen in Group I, the reaction proceeds through an esterified intermediate hydrolysis in Group II [ 23 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 ]. Biochemically characterized yeast phosphatases from the haloacid dehalogenase superfamily active against various phosphorylated metabolites and peptides and implicated in detoxification of phosphorylated compounds and pseudouridine have been reviewed [ 59 ].…”

Section: Introductionmentioning

confidence: 99%

Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications

et al. 2018

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The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.

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Mutagenic analysis of the conserved residues in dehalogenase IVa ofBurkholderia cepaciaMBA4

Cited by 21 publications

References 18 publications

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

High Yield Recombinant Expression, Characterization and Homology Modeling of Two Types of Cis-epoxysuccinic Acid Hydrolases

Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications

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