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Structural basis for the hydrolytic dehalogenation of the fungicide chlorothalonil. J Biol Chem 2020 Jun 26;295(26):8668-8677

Date

05/03/2020

Pubmed ID

32358058

Pubmed Central ID

PMC7324493

DOI

10.1074/jbc.RA120.013150

Scopus ID

2-s2.0-85087253833 (requires institutional sign-in at Scopus site)   4 Citations

Abstract

Cleavage of aromatic carbon-chlorine bonds is critical for the degradation of toxic industrial compounds. Here, we solved the X-ray crystal structure of chlorothalonil dehalogenase (Chd) from Pseudomonas sp. CTN-3, with 15 of its N-terminal residues truncated (ChdT), using single-wavelength anomalous dispersion refined to 1.96 Å resolution. Chd has low sequence identity (<15%) compared with all other proteins whose structures are currently available, and to the best of our knowledge, we present the first structure of a Zn(II)-dependent aromatic dehalogenase that does not require a coenzyme. ChdT forms a "head-to-tail" homodimer, formed between two α-helices from each monomer, with three Zn(II)-binding sites, two of which occupy the active sites, whereas the third anchors a structural site at the homodimer interface. The catalytic Zn(II) ions are solvent-accessible via a large hydrophobic (8.5 × 17.8 Å) opening to bulk solvent and two hydrophilic branched channels. Each active-site Zn(II) ion resides in a distorted trigonal bipyramid geometry with His117, His257, Asp116, Asn216, and a water/hydroxide as ligands. A conserved His residue, His114, is hydrogen-bonded to the Zn(II)-bound water/hydroxide and likely functions as the general acid-base. We examined substrate binding by docking chlorothalonil (2,4,5,6-tetrachloroisophtalonitrile, TPN) into the hydrophobic channel and observed that the most energetically favorable pose includes a TPN orientation that coordinates to the active-site Zn(II) ions via a CN and that maximizes a π-π interaction with Trp227 On the basis of these results, along with previously reported kinetics data, we propose a refined catalytic mechanism for Chd-mediated TPN dehalogenation.

Author List

Catlin DS, Yang X, Bennett B, Holz RC, Liu D

Author

Brian Bennett D.Phil. Professor and Chair in the Physics department at Marquette University




MESH terms used to index this publication - Major topics in bold

Bacterial Proteins
Biodegradation, Environmental
Catalytic Domain
Crystallography, X-Ray
Fungicides, Industrial
Halogenation
Hydrolases
Hydrolysis
Molecular Docking Simulation
Nitriles
Protein Conformation
Pseudomonas
Substrate Specificity