6jhm - Revision history

OCA at 10:09, 22 November 2023

OCA — Wed, 22 Nov 2023 10:09:37 GMT

←Older revision		Revision as of 10:09, 22 November 2023
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	<StructureSection load='6jhm' size='340' side='right'caption='[[6jhm]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6jhm' size='340' side='right'caption='[[6jhm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jhm]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ralstonia_pickettii_dtp0602~~ Ralstonia pickettii ~~dtp0602~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jhm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ralstonia_pickettii_DTP0602 Ralstonia pickettii DTP0602]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JHM FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>hadA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=1366050 Ralstonia pickettii DTP0602])</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]] 2.3Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4~~-~~hydroxyphenylacetate_3-monooxygenase 4-hydroxyphenylacetate 3-monooxygenase]~~, ~~with EC number~~ [~~http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.9 1.14.14.9] </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=6jhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhm OCA], [https://pdbe.org/6jhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jhm RCSB], [https://www.ebi.ac.uk/pdbsum/6jhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhm 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=6jhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhm OCA], [~~http~~://pdbe.org/6jhm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jhm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jhm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q53008_RALPI Q53008_RALPI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6jhm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jhm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 4-hydroxyphenylacetate 3-monooxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ralstonia pickettii ~~dtp0602~~]]	+	[[Category: Ralstonia pickettii DTP0602]]
-	[[Category: Chaiyen, P]]	+	[[Category: Chaiyen P]]
-	[[Category: Chitnumsub, P]]	+	[[Category: Chitnumsub P]]
-	[[Category: Jaruwat, A]]	+	[[Category: Jaruwat A]]
-	[[Category: Pimviriyakul, P]]	+	[[Category: Pimviriyakul P]]
-	~~[[Category: Chlorophenol 4-monooxygenase]]~~	+
-	~~[[Category: Flavin monooxygenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:17, 1 January 2020

OCA — Wed, 01 Jan 2020 11:17:49 GMT

←Older revision		Revision as of 11:17, 1 January 2020
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	<StructureSection load='6jhm' size='340' side='right'caption='[[6jhm]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6jhm' size='340' side='right'caption='[[6jhm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jhm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jhm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ralstonia_pickettii_dtp0602 Ralstonia pickettii dtp0602]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JHM FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylacetate_3-monooxygenase 4-hydroxyphenylacetate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.9 1.14.14.9] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hadA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1366050 Ralstonia pickettii DTP0602])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylacetate_3-monooxygenase 4-hydroxyphenylacetate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.9 1.14.14.9] </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=6jhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhm OCA], [http://pdbe.org/6jhm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhm RCSB], [http://www.ebi.ac.uk/pdbsum/6jhm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhm 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=6jhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhm OCA], [http://pdbe.org/6jhm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhm RCSB], [http://www.ebi.ac.uk/pdbsum/6jhm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhm ProSAT]</span></td></tr>
	</table>		</table>
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	[[Category: 4-hydroxyphenylacetate 3-monooxygenase]]		[[Category: 4-hydroxyphenylacetate 3-monooxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Ralstonia pickettii dtp0602]]
	[[Category: Chaiyen, P]]		[[Category: Chaiyen, P]]
	[[Category: Chitnumsub, P]]		[[Category: Chitnumsub, P]]

OCA at 06:39, 6 November 2019

OCA — Wed, 06 Nov 2019 06:39:50 GMT

←Older revision		Revision as of 06:39, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jhm is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Flavin-dependent Monooxygenase HadA==
		+	<StructureSection load='6jhm' size='340' side='right'caption='[[6jhm]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jhm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JHM FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylacetate_3-monooxygenase 4-hydroxyphenylacetate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.14.9 1.14.14.9] </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=6jhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jhm OCA], [http://pdbe.org/6jhm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jhm RCSB], [http://www.ebi.ac.uk/pdbsum/6jhm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jhm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	HadA is a flavin-dependent monooxygenase that can catalyze the denitration and dehalogenation of a wide variety of toxicants such as pesticides. Although these enzymatic reactions are useful for bioremediation or biocatalysis, the application of HadA for these purposes is not yet possible because of its low thermostability. In this work we have engineered HadA to be more thermostable through the use of structural, in silico, and rational approaches. The X-ray structure of HadA was solved to obtain a reliable three-dimensional protein model for further prediction of thermostable variants. In silico analysis by using two bioinformatic tools-FireProt and Disulfide by Design-suggested 102 variants that we then further refined by applying rational criteria including the location of a particular residue and its nearby interactions, as well as other biophysical parameters to narrow down the list to six candidates. The G513Y variant was found to be an optimal engineered candidate because it has significantly improved stability relative to the wild-type enzyme and equivalent activity. G513Y has an activity half-life 72 (50 degrees C) and 160 times (45 degrees C) longer than that of the wild-type enzyme. Coupled together with thermostable reactions of reduced flavin and NADH-regenerating systems, the G513Y variant can be used to catalyze denitration of 4nitrophenol at 45 degrees C. Structure/sequence alignments of HadA and its homologues indicate that several flavin-dependent monooxygenases also contain amino acid residues homologous to the G513 of HadA, hence opening up the possibility of applying this engineering approach to improving their thermostabilities as well. Molecular dynamics (MD) simulations confirmed that the improved thermostability of the G513Y variant was due to aromatic hydrocarbon interactions between Y513 and N359, L347, G348, and F349.

-	~~Authors: Jaruwat, A~~., ~~Pimviriyakul~~, P., ~~Chitnumsub~~, P., Chaiyen, P.	+	Identification of a Hotspot Residue for Improving the Thermostability of a Flavin-Dependent Monooxygenase.,Pongpamorn P, Watthaisong P, Pimviriyakul P, Jaruwat A, Lawan N, Chitnumsub P, Chaiyen P Chembiochem. 2019 Jun 23. doi: 10.1002/cbic.201900413. PMID:31231908<ref>PMID:31231908</ref>

-	~~Description: Crystal structure~~ of ~~Flavin~~-~~dependent Monooxygenase HadA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Jaruwat, A~~]]	+	<div class="pdbe-citations 6jhm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 4-hydroxyphenylacetate 3-monooxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Chaiyen, P]]		[[Category: Chaiyen, P]]
	[[Category: Chitnumsub, P]]		[[Category: Chitnumsub, P]]
		+	[[Category: Jaruwat, A]]
	[[Category: Pimviriyakul, P]]		[[Category: Pimviriyakul, P]]
		+	[[Category: Chlorophenol 4-monooxygenase]]
		+	[[Category: Flavin monooxygenase]]
		+	[[Category: Oxidoreductase]]

OCA at 05:26, 6 March 2019

OCA — Wed, 06 Mar 2019 05:26:20 GMT

←Older revision		Revision as of 05:26, 6 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Jaruwat, A., Pimviriyakul, P., Chitnumsub, P., Chaiyen, P.		Authors: Jaruwat, A., Pimviriyakul, P., Chitnumsub, P., Chaiyen, P.

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

OCA — Wed, 27 Feb 2019 13:36:49 GMT

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

←Older revision

Revision as of 13:36, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6jhm is ON HOLD Authors: Jaruwat, A., Pimviriyakul, P., Chitnumsub, P., Chaiyen, P. Description: Crystal structure of Flavin-dependent Monooxygenas...

OCA — Wed, 27 Feb 2019 13:36:47 GMT

New page: '''Unreleased structure''' The entry 6jhm is ON HOLD Authors: Jaruwat, A., Pimviriyakul, P., Chitnumsub, P., Chaiyen, P. Description: Crystal structure of Flavin-dependent Monooxygenas...

New page

'''Unreleased structure'''

The entry 6jhm is ON HOLD

Authors: Jaruwat, A., Pimviriyakul, P., Chitnumsub, P., Chaiyen, P.

Description: Crystal structure of Flavin-dependent Monooxygenase HadA
[[Category: Unreleased Structures]]
[[Category: Jaruwat, A]]
[[Category: Chaiyen, P]]
[[Category: Chitnumsub, P]]
[[Category: Pimviriyakul, P]]