7dbw - Revision history

OCA at 16:30, 29 November 2023

OCA — Wed, 29 Nov 2023 16:30:26 GMT

←Older revision		Revision as of 16:30, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7dbw' size='340' side='right'caption='[[7dbw]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='7dbw' size='340' side='right'caption='[[7dbw]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7dbw]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Rhodococcus_imtechensis_jcm_13270~~ Rhodococcus imtechensis ~~jcm~~ 13270]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dbw]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_imtechensis_RKJ300_=_JCM_13270 Rhodococcus imtechensis RKJ300 = JCM 13270]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBW FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~W59_00989 (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=1165867 Rhodococcus imtechensis JCM 13270])~~</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]] 2.5Å</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=7dbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbw OCA], [https://pdbe.org/7dbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbw RCSB], [https://www.ebi.ac.uk/pdbsum/7dbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbw 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=7dbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbw OCA], [https://pdbe.org/7dbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbw RCSB], [https://www.ebi.ac.uk/pdbsum/7dbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I0WZP1_RHOOP I0WZP1_RHOOP]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rhodococcus imtechensis ~~jcm~~ 13270]]	+	[[Category: Rhodococcus imtechensis RKJ300 = JCM 13270]]
-	[[Category: Guo, Y]]	+	[[Category: Guo Y]]
-	[[Category: Zheng~~, J T~~]]	+	[[Category: Zheng JT]]
-	[[Category: Zhou~~, N Y]]~~	+	[[Category: Zhou NY]]
-	~~[[Category: Biodegradation]]~~	+
-	~~[[Category: Flavin-dependent two-component monooyxgenase]]~~	+
-	~~[[Category: Hydroxylase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Para-nitrophenol~~]]	+

OCA at 14:11, 17 November 2021

OCA — Wed, 17 Nov 2021 14:11:02 GMT

←Older revision		Revision as of 14:11, 17 November 2021
Line 1:		Line 1:

	==PnpA1, the oxygenase component of a two-component para-nitrophenol hydroxylase from Rhodococcus imtechensis RKJ300==		==PnpA1, the oxygenase component of a two-component para-nitrophenol hydroxylase from Rhodococcus imtechensis RKJ300==
-	<StructureSection load='7dbw' size='340' side='right'caption='[[7dbw]]' scene=''>	+	<StructureSection load='7dbw' size='340' side='right'caption='[[7dbw]], [[Resolution\|resolution]] 2.50Å' 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=7DBW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7DBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dbw]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_imtechensis_jcm_13270 Rhodococcus imtechensis jcm 13270]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DBW 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=7dbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbw OCA], [~~http~~://pdbe.org/7dbw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7dbw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7dbw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbw ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">W59_00989 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1165867 Rhodococcus imtechensis JCM 13270])</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=7dbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbw OCA], [https://pdbe.org/7dbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dbw RCSB], [https://www.ebi.ac.uk/pdbsum/7dbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbw ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	para-Nitrophenol (PNP) is a hydrolytic product of organophosphate insecticides, such as parathion and methylparathion, in soil. Aerobic microbial degradation of PNP has been classically shown to proceed via the "hydroquinone (HQ) pathway" in Gram-negative degraders, whereas it proceeds via the "benzenetriol (BT) pathway" in Gram-positive ones. The "HQ pathway" is initiated by a single-component PNP 4-monooxygenase and the "BT pathway" by a two-component PNP 2-monooxygenase. Their regioselectivity intrigued us enough to investigate their catalytic difference through structural study. PnpA1 is the oxygenase component of the two-component PNP 2-monooxygenase from Gram-positive Rhodococcus imtechensis strain RKJ300. It also catalyzes the hydroxylation of 4-nitrocatechol (4NC) and 2-chloro-4-nitrophenol (2C4NP). However, the mechanisms are unknown. Here, PnpA1 was structurally determined to be a member of the group D flavin-dependent monooxygenases with an acyl coenzyme A (acyl-CoA) dehydrogenase fold. The crystal structure and site-directed mutagenesis underlined the direct involvement of Arg100 and His293 in catalysis. The bulky side chain of Val292 was proposed to push the substrate toward flavin adenine dinucleotide (FAD), hence positioning the substrate properly. An N450A variant was found with improved activity for 4NC and 2C4NP-probably because of the reduced steric hindrance. PnpA1 shows an obvious difference in substrate selectivity with its close homologues TcpA and TftD, which may be caused by the unique Thr296 and a different conformation in the loop from positions 449 to 454 (loop 449-454). Above all, our study allows structural comparison between the two types of PNP monooxygenases. An explanation that accounts for their regioselectivity was proposed: the different PNP binding manners determine their choice of ortho- or para-hydroxylation on PNP. IMPORTANCE Single-component PNP monoxygenases hydroxylate PNP at the 4 position, while two-component ones do so at the 2 position. However, their catalytic and structural differences remain elusive. The structure of single-component PNP 4-monooxygenase has previously been determined. In this study, to illustrate their catalytic difference, we resolved the crystal structure of PnpA1, a typical two-component PNP 2-monooxygenase. The roles of several key amino acid residues in substrate binding and catalysis were revealed, and a variant with improved activities toward 4NC and 2C4NP was obtained. Moreover, through comparison of the two types of PNP monooxygenases, a hypothesis was proposed to account for their catalytic difference, which gives us a better understanding of these two similar reactions at the molecular level. In addition, these results will also be of further aid in rational design of enzymes in bioremediation and biosynthesis.
		+
		+	Single-Component and Two-Component para-Nitrophenol Monooxygenases: Structural Basis for Their Catalytic Difference.,Guo Y, Li DF, Zheng J, Xu Y, Zhou NY Appl Environ Microbiol. 2021 Oct 28;87(22):e0117121. doi: 10.1128/AEM.01171-21., Epub 2021 Sep 1. PMID:34469195<ref>PMID:34469195</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dbw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Guo Y]]	+	[[Category: Rhodococcus imtechensis jcm 13270]]
-	[[Category: Zheng JT]]	+	[[Category: Guo, Y]]
-	[[Category: Zhou NY]]	+	[[Category: Zheng, J T]]
		+	[[Category: Zhou, N Y]]
		+	[[Category: Biodegradation]]
		+	[[Category: Flavin-dependent two-component monooyxgenase]]
		+	[[Category: Hydroxylase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Para-nitrophenol]]

OCA at 07:26, 4 November 2020

OCA — Wed, 04 Nov 2020 07:26:32 GMT

←Older revision		Revision as of 07:26, 4 November 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7dbw is ON HOLD~~	+	==PnpA1, the oxygenase component of a two-component para-nitrophenol hydroxylase from Rhodococcus imtechensis RKJ300==
-		+	<StructureSection load='7dbw' size='340' side='right'caption='[[7dbw]]' scene=''>
-	~~Authors: Guo, Y., Zheng, J.T., Zhou, N.Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DBW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7DBW FirstGlance]. <br>
-	~~Description:~~ PnpA1, the oxygenase component of a two-component para-nitrophenol hydroxylase from Rhodococcus imtechensis RKJ300	+	</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=7dbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dbw OCA], [http://pdbe.org/7dbw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7dbw RCSB], [http://www.ebi.ac.uk/pdbsum/7dbw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7dbw ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Zhou, N.~~Y]]	+	__TOC__
-	[[Category: Zheng~~, J.T~~]]	+	</StructureSection>
-	[[Category: ~~Guo, Y~~]]	+	[[Category: Large Structures]]
		+	[[Category: Guo Y]]
		+	[[Category: Zheng JT]]
		+	[[Category: Zhou NY]]

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

OCA — Wed, 28 Oct 2020 19:04:44 GMT

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

←Older revision

Revision as of 19:04, 28 October 2020

OCA: New page: '''Unreleased structure''' The entry 7dbw is ON HOLD Authors: Guo, Y., Zheng, J.T., Zhou, N.Y. Description: PnpA1, the oxygenase component of a two-component para-nitrophenol hydroxyla...

OCA — Wed, 28 Oct 2020 19:04:43 GMT

New page: '''Unreleased structure''' The entry 7dbw is ON HOLD Authors: Guo, Y., Zheng, J.T., Zhou, N.Y. Description: PnpA1, the oxygenase component of a two-component para-nitrophenol hydroxyla...

New page

'''Unreleased structure'''

The entry 7dbw is ON HOLD

Authors: Guo, Y., Zheng, J.T., Zhou, N.Y.

Description: PnpA1, the oxygenase component of a two-component para-nitrophenol hydroxylase from Rhodococcus imtechensis RKJ300
[[Category: Unreleased Structures]]
[[Category: Zhou, N.Y]]
[[Category: Zheng, J.T]]
[[Category: Guo, Y]]