6UXU

X-ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation

Summary for 6UXU

• Entry DOI: 10.2210/pdb6uxu/pdb
• Descriptor: Chlorothalonil hydrolytic dehalogenase, ZINC ION (3 entities in total)
• Functional Keywords: hydrolase, dehalogenase, dechlorination, zn-dependent, metal binding protein
• Biological source: Ochrobactrum sp. CTN-11
• Total number of polymer chains: 2
• Total formula weight: 65665.27

Authors

Catlin, D.S.,Liu, D. (deposition date: 2019-11-08, release date: 2020-05-13, Last modification date: 2024-03-06)

Primary citation

Catlin, D.S.,Yang, X.,Bennett, B.,Holz, R.C.,Liu, D.
Structural basis for the hydrolytic dehalogenation of the fungicide chlorothalonil.
J.Biol.Chem., 295:8668-8677, 2020

PubMed 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 sp. CTN-3, with 15 of its N-terminal residues truncated (Chd), 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. Chd 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 His, His, Asp, Asn, and a water/hydroxide as ligands. A conserved His residue, His, 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 Trp On the basis of these results, along with previously reported kinetics data, we propose a refined catalytic mechanism for Chd-mediated TPN dehalogenation.

PubMed: 32358058
DOI: 10.1074/jbc.RA120.013150

Experimental method

X-RAY DIFFRACTION (1.962 Å)