Haloalkane dehalogenases (EC 3.8.1.5) are microbial enzymes that catalyse the hydrolytic conversion of halogenated compounds, resulting in a halide ion, a proton and an alcohol. These enzymes are used in industrial biocatalysis, bioremediation and biosensing of environmental pollutants or for molecular tagging in cell biology. The novel haloalkane dehalogenase DpaA described here was isolated from the psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2, which was found in marine sediment collected from the East Sea near Korea. Gel-filtration experiments and size-exclusion chromatography provided information about the dimeric composition of the enzyme in solution. The DpaA enzyme was crystallized using the sitting-drop vapour-diffusion method, yielding rod-like crystals that diffracted X-rays to 2.0 Å resolution. Diffraction data analysis revealed a case of merohedral twinning, and subsequent structure modelling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to haloalkane dehalogenase subfamily I.

Download full-text PDF

Source
http://dx.doi.org/10.1107/S2059798321000486DOI Listing

Publication Analysis

Top Keywords

haloalkane dehalogenase
12
novel haloalkane
8
dehalogenase dpaa
8
paraglaciecola agarilytica
8
agarilytica no2
8
tetrameric structure
4
structure novel
4
haloalkane
4
dpaa
4
dpaa paraglaciecola
4

Similar Publications

Generative artificial intelligence (AI) models trained on natural protein sequences have been used to design functional enzymes. However, their ability to predict individual reaction steps in enzyme catalysis remains unclear, limiting the potential use of sequence information for enzyme engineering. In this study, we demonstrated that sequence information can predict the rate of the S2 step of a haloalkane dehalogenase using a generative maximum-entropy (MaxEnt) model.

View Article and Find Full Text PDF

Bacteria of the genus are the most studied microorganisms that biodegrade persistent perfluoroorganic pollutants, and the research of their application for the remediation of environmental sites using biotechnological approaches remains relevant. The aim of this study was to investigate the ability of a known destructor of perfluorooctane sulfonic acid from the genus to accelerate and enhance the destruction of long-chain perfluorocarboxylic acids (PFCAs), specifically perfluorooctanoic acid and perfluorononanoic acid, in water and soil in association with the strain . 5(3), which has previously confirmed genetic potential for the degrading of PFCAs.

View Article and Find Full Text PDF

1,2-DCA biodegradation potential of an aquifer assessed in situ and in aerobic and anaerobic microcosms.

Environ Microbiome

December 2024

Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STeBiCeF), University of Palermo, Palermo, Italy.

Background: 1,2-dichloroethane (1,2-DCA) biodegradation can occur through aerobic or anaerobic pathways that can be exploited in bioremediation strategies. Bioremediation interventions are site specific and generally based on anaerobic pathways, nevertheless expanding knowledge on proper conditions favoring the biodegradation and especially on 1,2-DCA degrading microorganisms is crucial. In this work the intrinsic biodegradation potential of an aquifer impacted by Chlorinated Aliphatic Hydrocarbons (mainly 1,2-DCA) was evaluated by characterizing the aquifer microbiome across space and time and by setting up biostimulation treatments in microcosms under different aerobic and anaerobic conditions, in parallel.

View Article and Find Full Text PDF

Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.

J Chem Inf Model

January 2025

Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland.

The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries.

View Article and Find Full Text PDF

A Haloalkane Dehalogenase DhaA Nanoparticle Based on Pullulan Conjugation and Polyethyleneimine Adsorption.

Appl Biochem Biotechnol

November 2024

State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, China.

Haloalkane dehalogenase DhaA is a member of the α/β-hydrolase superfamily and can degrade the halogenated compounds. However, the enzyme could not tolerate harsh and extreme environmental conditions, such as high temperature, extreme pH, and hypersaline, which limits its practical applications. Pullulan is a hydrophilic polysaccharide and acts as an additive to improve the enzyme stability.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!