6l3w - Revision history

OCA at 10:51, 22 November 2023

OCA — Wed, 22 Nov 2023 10:51:04 GMT

←Older revision		Revision as of 10:51, 22 November 2023
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	<StructureSection load='6l3w' size='340' side='right'caption='[[6l3w]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6l3w' size='340' side='right'caption='[[6l3w]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6l3w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Environmental_sequence Environmental sequence~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L3W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6L3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6l3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Metagenome Metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L3W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FE:FE+(III)+ION'>FE</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]] 2.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~2,3-dihydroxybiphenyl 1,2-dioxygenase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=256318 environmental sequence]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6l3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l3w OCA], [~~http~~://pdbe.org/6l3w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6l3w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6l3w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6l3w 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=6l3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l3w OCA], [https://pdbe.org/6l3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l3w RCSB], [https://www.ebi.ac.uk/pdbsum/6l3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l3w ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 6l3w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6l3w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Environmental sequence]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Solanki, V~~]]	+	[[Category: Metagenome]]
-	[[Category: ~~Thakur, K G~~]]	+	[[Category: Solanki V]]
-	[[Category: ~~Catechol]]~~	+	[[Category: Thakur KG]]
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Halotolerant]]~~	+
-	~~[[Category: Metalloprotein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 18:36, 11 December 2019

OCA — Wed, 11 Dec 2019 18:36:16 GMT

←Older revision		Revision as of 18:36, 11 December 2019
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	<StructureSection load='6l3w' size='340' side='right'caption='[[6l3w]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6l3w' size='340' side='right'caption='[[6l3w]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6l3w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6l3w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Environmental_sequence Environmental sequence]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L3W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2,3-dihydroxybiphenyl 1,2-dioxygenase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=256318 environmental sequence])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6l3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l3w OCA], [http://pdbe.org/6l3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l3w RCSB], [http://www.ebi.ac.uk/pdbsum/6l3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l3w ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6l3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l3w OCA], [http://pdbe.org/6l3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l3w RCSB], [http://www.ebi.ac.uk/pdbsum/6l3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l3w ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The release of synthetic chemical pollutants in the environment is posing serious health risks. Enzymes, including oxygenases, play a crucial role in xenobiotic degradation. In the present study, we employed a functional metagenomics approach to overcome the limitation of cultivability of microbes under standard laboratory conditions in order to isolate novel dioxygenases capable of degrading recalcitrant pollutants. Fosmid clones possessing dioxygenase activity were further sequenced, and their genes were identified using bioinformatics tools. Two positive fosmid clones, SD3 and RW1, suggested the presence of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC-SD3) and catechol 2,3-dioxygenase (C23O-RW1), respectively. Recombinant versions of these enzymes were purified to examine their pollutant-degrading abilities. The crystal structure of BphC-SD3 was determined at 2.6-A resolution, revealing a two-domain architecture, i.e., N-terminal and C-terminal domains, with the sequential arrangement of betaalphabetabetabeta in each domain, characteristic of Fe-dependent class II type I extradiol dioxygenases. The structure also reveals the presence of conserved amino acids lining the catalytic pocket and Fe(3+) metal ion in the large funnel-shaped active site in the C-terminal domain. Further studies suggest that Fe(3+) bound in the BphC-SD3 active site probably imparts aerobic stability. We further demonstrate the potential application of BphC-SD3 in biosensing of catecholic compounds. The halotolerant and oxygen-resistant properties of these enzymes reported in this study make them potential candidates for bioremediation and biosensing applications.IMPORTANCE The disposal and degradation of xenobiotic compounds have been serious issues due to their recalcitrant properties. Microbial oxygenases are the fundamental enzymes involved in biodegradation that oxidize the substrate by transferring oxygen from molecular oxygen. Among oxygenases, catechol dioxygenases are more versatile in biodegradation and are well studied among the bacterial world. The use of catechol dioxygenases in the field is currently not practical due to their aerobically unstable nature. The significance of our research lies in the discovery of aerobically stable and halotolerant catechol dioxygenases that are efficient in degrading the targeted environmental pollutants and, hence, could be used as cost-effective alternatives for the treatment of hypersaline industrial effluents. Moreover, the structural determination of novel catechol dioxygenases would greatly enhance our knowledge of the function of these enzymes and facilitate directed evolution to further enhance or engineer desired properties.
		+
		+	Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach.,Sidhu C, Solanki V, Pinnaka AK, Thakur KG mSystems. 2019 Nov 26;4(6). pii: 4/6/e00316-19. doi: 10.1128/mSystems.00316-19. PMID:31771973<ref>PMID:31771973</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6l3w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Environmental sequence]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Solanki, V]]		[[Category: Solanki, V]]

OCA at 11:02, 13 November 2019

OCA — Wed, 13 Nov 2019 11:02:34 GMT

←Older revision		Revision as of 11:02, 13 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6l3w is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of BphC, a halotolerant catechol dioxygenase==
-		+	<StructureSection load='6l3w' size='340' side='right'caption='[[6l3w]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~Authors~~: ~~Thakur~~, K.G., ~~Solanki~~, V.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6l3w]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L3W FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of BphC~~, ~~a halotolerant catechol dioxygenase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6l3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l3w OCA], [http://pdbe.org/6l3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l3w RCSB], [http://www.ebi.ac.uk/pdbsum/6l3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l3w ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Solanki, V]]		[[Category: Solanki, V]]
-	[[Category: Thakur, K.G]]	+	[[Category: Thakur, K G]]
		+	[[Category: Catechol]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Halotolerant]]
		+	[[Category: Metalloprotein]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "6l3w" [edit=sysop:move=sysop]

OCA — Wed, 23 Oct 2019 04:50:57 GMT

Protected "6l3w" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:50, 23 October 2019

OCA: New page: '''Unreleased structure''' The entry 6l3w is ON HOLD until Paper Publication Authors: Thakur, K.G., Solanki, V. Description: Crystal structure of BphC, a halotolerant catechol dioxygen...

OCA — Wed, 23 Oct 2019 04:50:54 GMT

New page: '''Unreleased structure''' The entry 6l3w is ON HOLD until Paper Publication Authors: Thakur, K.G., Solanki, V. Description: Crystal structure of BphC, a halotolerant catechol dioxygen...

New page

'''Unreleased structure'''

The entry 6l3w is ON HOLD until Paper Publication

Authors: Thakur, K.G., Solanki, V.

Description: Crystal structure of BphC, a halotolerant catechol dioxygenase
[[Category: Unreleased Structures]]
[[Category: Solanki, V]]
[[Category: Thakur, K.G]]