6uxu - Revision history

OCA at 14:34, 6 March 2024

OCA — Wed, 06 Mar 2024 14:34:35 GMT

←Older revision		Revision as of 14:34, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6uxu' size='340' side='right'caption='[[6uxu]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='6uxu' size='340' side='right'caption='[[6uxu]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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>	+	<table><tr><td colspan='2'>[[6uxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ochrobactrum_sp._CTN-11 Ochrobactrum sp. CTN-11]. 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 [https://proteopedia.org/fgij/fg.htm?mol=6UXU FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.962Å</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='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='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>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6uxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxu OCA], [https://pdbe.org/6uxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uxu RCSB], [https://www.ebi.ac.uk/pdbsum/6uxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxu ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/E2JB04_9HYPH E2JB04_9HYPH]
-	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: Ochrobactrum sp. ~~ctn~~-1]]	+	[[Category: Ochrobactrum sp. CTN-11]]
-	[[Category: Catlin~~, D S~~]]	+	[[Category: Catlin DS]]
-	[[Category: Liu, D]]	+	[[Category: Liu D]]
-	~~[[Category: Dechlorination]]~~	+
-	~~[[Category: Dehalogenase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Zn-dependent~~]]	+

OCA at 14:38, 8 July 2020

OCA — Wed, 08 Jul 2020 14:38:25 GMT

←Older revision		Revision as of 14:38, 8 July 2020
Line 1:		Line 1:

	==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 DS]]	+	[[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]]

OCA at 05:34, 13 May 2020

OCA — Wed, 13 May 2020 05:34:07 GMT

←Older revision		Revision as of 05:34, 13 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6uxu ~~is ON HOLD until Paper Publication~~	+	==X-ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation==
-		+	<StructureSection load='6uxu' size='340' side='right'caption='[[6uxu]]' scene=''>
-	~~Authors~~:	+	== 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>
-	~~Description~~:	+	</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>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Catlin DS]]
		+	[[Category: Liu D]]

OCA at 05:59, 18 December 2019

OCA — Wed, 18 Dec 2019 05:59:18 GMT

←Older revision		Revision as of 05:59, 18 December 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6uxu is ON HOLD	+	The entry 6uxu is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6uxu" [edit=sysop:move=sysop]

OCA — Wed, 20 Nov 2019 13:55:01 GMT

Protected "6uxu" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:55, 20 November 2019

OCA: New page: '''Unreleased structure''' The entry 6uxu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Nov 2019 13:54:59 GMT

New page: '''Unreleased structure''' The entry 6uxu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6uxu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]