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6uxu
From Proteopedia
(Difference between revisions)
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==X-ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation== | ==X-ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation== | ||
| - | <StructureSection load='6uxu' size='340' side='right'caption='[[6uxu]]' scene=''> | + | <StructureSection load='6uxu' size='340' side='right'caption='[[6uxu]], [[Resolution|resolution]] 1.96Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UXU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UXU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6uxu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ochrobactrum_sp._ctn-1 Ochrobactrum sp. ctn-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UXU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UXU FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6uxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxu OCA], [http://pdbe.org/6uxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uxu RCSB], [http://www.ebi.ac.uk/pdbsum/6uxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxu ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">chd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=589024 Ochrobactrum sp. CTN-1])</td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6uxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxu OCA], [http://pdbe.org/6uxu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uxu RCSB], [http://www.ebi.ac.uk/pdbsum/6uxu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxu ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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 A 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 alpha-helices from each monomer, with three Zn(II)-binding sites, two of which occupy the active sites, while the third anchors a structural site at the homodimer interface. The catalytic Zn(II) ions are solvent-accessible via a large hydrophobic (8.5 x 17.8 A) opening to bulk solvent and two hydrophilic branched channels. Each active-site Zn(II) ion resides in a distorted trigonal bipyramid geometry with His-117, His-257, Asp-116, Asn-216, and a water/hydroxide as ligands. A conserved His residue, His-114, 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 (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 pi-pi interaction with Trp-227. On the basis of these results, along with previously reported kinetics data, we propose a refined catalytic mechanism for Chd-mediated TPN dehalogenation. | ||
| + | |||
| + | Structural basis for the hydrolytic dehalogenation of the fungicide chlorothalonil.,Catlin DS, Yang X, Bennett B, Holz RC, Liu D J Biol Chem. 2020 Apr 30. pii: RA120.013150. doi: 10.1074/jbc.RA120.013150. PMID:32358058<ref>PMID:32358058</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6uxu" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Catlin | + | [[Category: Ochrobactrum sp. ctn-1]] |
| - | [[Category: Liu D]] | + | [[Category: Catlin, D S]] |
| + | [[Category: Liu, D]] | ||
| + | [[Category: Dechlorination]] | ||
| + | [[Category: Dehalogenase]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Metal binding protein]] | ||
| + | [[Category: Zn-dependent]] | ||
Revision as of 14:38, 8 July 2020
X-ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation
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