7awv - Revision history

OCA at 07:46, 1 May 2024

2024-05-01T07:46:13Z

←Older revision		Revision as of 07:46, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='7awv' size='340' side='right'caption='[[7awv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='7awv' size='340' side='right'caption='[[7awv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7awv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AWV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7awv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_opacus Rhodococcus opacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AWV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.2Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/FMN-dependent_NADH-azoreductase FMN-dependent NADH-azoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.17 1.7.1.17] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=7awv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7awv OCA], [https://pdbe.org/7awv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7awv RCSB], [https://www.ebi.ac.uk/pdbsum/7awv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7awv 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=7awv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7awv OCA], [https://pdbe.org/7awv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7awv RCSB], [https://www.ebi.ac.uk/pdbsum/7awv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7awv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A1B1KJ01_RHOOP A0A1B1KJ01_RHOOP]] Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines.[HAMAP-Rule:MF_01216] Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones.[HAMAP-Rule:MF_01216]	+	[https://www.uniprot.org/uniprot/A0A1B1KJ01_RHOOP A0A1B1KJ01_RHOOP] Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines.[HAMAP-Rule:MF_01216] Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones.[HAMAP-Rule:MF_01216]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Azo dyes are important to various industries such as textile industries. However, these dyes are known to comprise toxic, mutagenic, and carcinogenic representatives. Several approaches have already been employed to mitigate the problem such as the use of enzymes. Azoreductases have been well-studied in its capability to reduce azo dyes. AzoRo from Rhodococcus opacus 1CP has been found to be accepting only methyl red as a substrate, surmising that the enzyme may have a narrow active site. To determine the active site configuration of AzoRo at atomic level and identify the key residues involved in substrate binding and enzyme specificity, we have determined the crystal structure of holo-AzoRo and employed a rational design approach to generate AzoRo variants. The results reported here show that AzoRo has a different configuration of the active site when compared with other bacterial NAD(P)H azoreductases, having other key residues playing a role in the substrate binding and restricting the enzyme activity towards different azo dyes. Moreover, it was observed that AzoRo has only about 50% coupling yield to methyl red and p-benzoquinone - giving rise to the possibility that NADH oxidation still occurs even during catalysis. Results also showed that AzoRo is more active and more efficient towards quinones (about four times higher than methyl red).	+
-		+
-	Identification of molecular basis that underlie enzymatic specificity of AzoRo from Rhodococcus opacus 1CP: A potential NADH:quinone oxidoreductase.,Ngo ACR, Qi J, Juric C, Bento I, Tischler D Arch Biochem Biophys. 2022 Jan 19;717:109123. doi: 10.1016/j.abb.2022.109123. PMID:35051387<ref>PMID:35051387</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7awv" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: FMN-dependent NADH-azoreductase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bento, I]]	+	[[Category: Rhodococcus opacus]]
-	[[Category: Juric, C]]	+	[[Category: Bento I]]
-	[[Category: Ngo, A]]	+	[[Category: Juric C]]
-	[[Category: Qi, J]]	+	[[Category: Ngo A]]
-	[[Category: Tischler, D]]	+	[[Category: Qi J]]
-	~~[[Category: Actinobacterium]]~~	+	[[Category: Tischler D]]
-	~~[[Category: Azoreductase]]~~	+
-	~~[[Category: Dye degradation]]~~	+
-	~~[[Category: Nadh-quinone oxido-reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:30, 9 February 2022

2022-02-09T07:30:51Z

←Older revision		Revision as of 07:30, 9 February 2022
Line 1:		Line 1:

	==Azoreductase (AzoRo) from Rhodococcus opacus 1CP==		==Azoreductase (AzoRo) from Rhodococcus opacus 1CP==
-	<StructureSection load='7awv' size='340' side='right'caption='[[7awv]]' scene=''>	+	<StructureSection load='7awv' size='340' side='right'caption='[[7awv]], [[Resolution\|resolution]] 2.20Å' 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=7AWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AWV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7awv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AWV FirstGlance]. <br>
-	</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=7awv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7awv OCA], [https://pdbe.org/7awv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7awv RCSB], [https://www.ebi.ac.uk/pdbsum/7awv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7awv 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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/FMN-dependent_NADH-azoreductase FMN-dependent NADH-azoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.17 1.7.1.17] </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=7awv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7awv OCA], [https://pdbe.org/7awv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7awv RCSB], [https://www.ebi.ac.uk/pdbsum/7awv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7awv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A1B1KJ01_RHOOP A0A1B1KJ01_RHOOP]] Also exhibits azoreductase activity. Catalyzes the reductive cleavage of the azo bond in aromatic azo compounds to the corresponding amines.[HAMAP-Rule:MF_01216] Quinone reductase that provides resistance to thiol-specific stress caused by electrophilic quinones.[HAMAP-Rule:MF_01216]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Azo dyes are important to various industries such as textile industries. However, these dyes are known to comprise toxic, mutagenic, and carcinogenic representatives. Several approaches have already been employed to mitigate the problem such as the use of enzymes. Azoreductases have been well-studied in its capability to reduce azo dyes. AzoRo from Rhodococcus opacus 1CP has been found to be accepting only methyl red as a substrate, surmising that the enzyme may have a narrow active site. To determine the active site configuration of AzoRo at atomic level and identify the key residues involved in substrate binding and enzyme specificity, we have determined the crystal structure of holo-AzoRo and employed a rational design approach to generate AzoRo variants. The results reported here show that AzoRo has a different configuration of the active site when compared with other bacterial NAD(P)H azoreductases, having other key residues playing a role in the substrate binding and restricting the enzyme activity towards different azo dyes. Moreover, it was observed that AzoRo has only about 50% coupling yield to methyl red and p-benzoquinone - giving rise to the possibility that NADH oxidation still occurs even during catalysis. Results also showed that AzoRo is more active and more efficient towards quinones (about four times higher than methyl red).
		+
		+	Identification of molecular basis that underlie enzymatic specificity of AzoRo from Rhodococcus opacus 1CP: A potential NADH:quinone oxidoreductase.,Ngo ACR, Qi J, Juric C, Bento I, Tischler D Arch Biochem Biophys. 2022 Jan 19;717:109123. doi: 10.1016/j.abb.2022.109123. PMID:35051387<ref>PMID:35051387</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7awv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: FMN-dependent NADH-azoreductase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bento I]]	+	[[Category: Bento, I]]
-	[[Category: Juric C]]	+	[[Category: Juric, C]]
-	[[Category: Ngo A]]	+	[[Category: Ngo, A]]
-	[[Category: Qi J]]	+	[[Category: Qi, J]]
-	[[Category: Tischler D]]	+	[[Category: Tischler, D]]
		+	[[Category: Actinobacterium]]
		+	[[Category: Azoreductase]]
		+	[[Category: Dye degradation]]
		+	[[Category: Nadh-quinone oxido-reductase]]
		+	[[Category: Oxidoreductase]]

OCA at 06:57, 2 February 2022

2022-02-02T06:57:45Z

←Older revision		Revision as of 06:57, 2 February 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7awv ~~is ON HOLD until Paper Publication~~	+	==Azoreductase (AzoRo) from Rhodococcus opacus 1CP==
-		+	<StructureSection load='7awv' size='340' side='right'caption='[[7awv]]' scene=''>
-	~~Authors~~: ~~Bento, I~~., ~~Ngo~~, A., ~~Qi, J~~., ~~Juric, C~~., ~~Tischler, D~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AWV FirstGlance]. <br>
-	~~Description: Azoreductase (AzoRo) from Rhodococcus opacus 1CP~~	+	</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=7awv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7awv OCA], [https://pdbe.org/7awv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7awv RCSB], [https://www.ebi.ac.uk/pdbsum/7awv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7awv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Bento, I]]	+	__TOC__
-	[[Category: ~~Tischler, D~~]]	+	</StructureSection>
-	[[Category: Ngo, A]]	+	[[Category: Large Structures]]
-	[[Category: ~~Juric, C~~]]	+	[[Category: Bento I]]
-	[[Category: ~~Qi, J~~]]	+	[[Category: Juric C]]
		+	[[Category: Ngo A]]
		+	[[Category: Qi J]]
		+	[[Category: Tischler D]]

OCA at 04:55, 11 August 2021

2021-08-11T04:55:53Z

←Older revision		Revision as of 04:55, 11 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7awv is ON HOLD	+	The entry 7awv is ON HOLD until Paper Publication

	Authors: Bento, I., Ngo, A., Qi, J., Juric, C., Tischler, D.		Authors: Bento, I., Ngo, A., Qi, J., Juric, C., Tischler, D.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Bento, I]]		[[Category: Bento, I]]
-	[[Category: Ngo, A]]
	[[Category: Tischler, D]]		[[Category: Tischler, D]]
		+	[[Category: Ngo, A]]
	[[Category: Juric, C]]		[[Category: Juric, C]]
	[[Category: Qi, J]]		[[Category: Qi, J]]

OCA at 08:01, 12 May 2021

2021-05-12T08:01:24Z

←Older revision		Revision as of 08:01, 12 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7awv is ON HOLD ~~until sometime in the future~~	+	The entry 7awv is ON HOLD

	Authors: Bento, I., Ngo, A., Qi, J., Juric, C., Tischler, D.		Authors: Bento, I., Ngo, A., Qi, J., Juric, C., Tischler, D.
Line 7:		Line 7:
	Description: Azoreductase (AzoRo) from Rhodococcus opacus 1CP		Description: Azoreductase (AzoRo) from Rhodococcus opacus 1CP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Tischler, D]]
-	[[Category: Qi, J]]
	[[Category: Bento, I]]		[[Category: Bento, I]]
	[[Category: Ngo, A]]		[[Category: Ngo, A]]
		+	[[Category: Tischler, D]]
	[[Category: Juric, C]]		[[Category: Juric, C]]
		+	[[Category: Qi, J]]

OCA: Protected "7awv" [edit=sysop:move=sysop]

2020-11-18T07:54:30Z

Protected "7awv" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:54, 18 November 2020

OCA: New page: '''Unreleased structure''' The entry 7awv is ON HOLD until sometime in the future Authors: Bento, I., Ngo, A., Qi, J., Juric, C., Tischler, D. Description: Azoreductase (AzoRo) from Rh...

2020-11-18T07:54:29Z

New page: '''Unreleased structure''' The entry 7awv is ON HOLD until sometime in the future Authors: Bento, I., Ngo, A., Qi, J., Juric, C., Tischler, D. Description: Azoreductase (AzoRo) from Rh...

New page

'''Unreleased structure'''

The entry 7awv is ON HOLD until sometime in the future

Authors: Bento, I., Ngo, A., Qi, J., Juric, C., Tischler, D.

Description: Azoreductase (AzoRo) from Rhodococcus opacus 1CP
[[Category: Unreleased Structures]]
[[Category: Tischler, D]]
[[Category: Qi, J]]
[[Category: Bento, I]]
[[Category: Ngo, A]]
[[Category: Juric, C]]