7dp2 - Revision history

OCA at 16:37, 29 November 2023

OCA — Wed, 29 Nov 2023 16:37:25 GMT

←Older revision		Revision as of 16:37, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dp2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingopyxis_sp. Sphingopyxis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DP2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dp2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingopyxis_sp. Sphingopyxis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DP2 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></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]] 2.4000874Å</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></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=7dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dp2 OCA], [https://pdbe.org/7dp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dp2 RCSB], [https://www.ebi.ac.uk/pdbsum/7dp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dp2 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=7dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dp2 OCA], [https://pdbe.org/7dp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dp2 RCSB], [https://www.ebi.ac.uk/pdbsum/7dp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dp2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2L0VUJ4_9SPHN A0A2L0VUJ4_9SPHN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Nitroreductase\|Nitroreductase]]	+	*[[Nitroreductase 3D structures\|Nitroreductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Sphingopyxis sp]]		[[Category: Sphingopyxis sp]]
-	[[Category: Kim~~, S H~~]]	+	[[Category: Kim SH]]
-	[[Category: Park, S]]	+	[[Category: Park S]]
-	[[Category: Rhee, S]]	+	[[Category: Rhee S]]
-	~~[[Category: Dinitroaniline herbicides reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:51, 16 February 2022

OCA — Wed, 16 Feb 2022 10:51:13 GMT

←Older revision		Revision as of 10:51, 16 February 2022
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	==Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH==		==Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH==
-	<StructureSection load='7dp2' size='340' side='right'caption='[[7dp2]]' scene=''>	+	<StructureSection load='7dp2' size='340' side='right'caption='[[7dp2]], [[Resolution\|resolution]] 2.40Å' 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=7DP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DP2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dp2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingopyxis_sp. Sphingopyxis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DP2 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=7dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dp2 OCA], [https://pdbe.org/7dp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dp2 RCSB], [https://www.ebi.ac.uk/pdbsum/7dp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dp2 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></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=7dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dp2 OCA], [https://pdbe.org/7dp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dp2 RCSB], [https://www.ebi.ac.uk/pdbsum/7dp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dp2 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nitroreductases are emerging as attractive bioremediation enzymes, with substrate promiscuity toward both natural and synthetic compounds. Recently, the nitroreductase NfnB from Sphingopyxis sp. strain HMH exhibited metabolic activity for dinitroaniline herbicides including butralin and pendimethalin, triggering the initial steps of their degradation and detoxification. However, the determinants of the specificity of NfnB for these herbicides are unknown. In this study, we performed structural and biochemical analyses of NfnB to decipher its substrate specificity. The homodimer NfnB is a member of the PnbA subgroup of the nitroreductase family. Each monomer displays a central alpha + beta fold for the core domain, with a protruding middle region and an extended C-terminal region. The protruding middle region of Val75-Tyr129 represents a structural extension that is a common feature to members of the PnbA subgroup and functions as an opening wall connecting the coenzyme FMN-binding site to the surface, therefore serving as a substrate binding site. We performed mutational, kinetic, and structural analyses of mutant enzymes and found that Tyr88 in the middle region plays a pivotal role in substrate specificity by determining the dimensions of the wall opening. The mutation of Tyr88 to phenylalanine or alanine caused significant changes in substrate selectivity toward bulkier dinitroaniline herbicides such as oryzalin and isopropalin without compromising its activity. These results provide a framework to modify the substrate specificity of nitroreductase in the PnbA subgroup, which has been a challenging issue for its biotechnological and bioremediation applications.
		+
		+	Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide-catabolizing nitroreductase from Sphingopyxis sp. strain HMH.,Kim SH, Park S, Park E, Kim JH, Ghatge S, Hur HG, Rhee S J Biol Chem. 2021 Oct;297(4):101143. doi: 10.1016/j.jbc.2021.101143. Epub 2021, Aug 30. PMID:34473996<ref>PMID:34473996</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dp2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitroreductase\|Nitroreductase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim SH]]	+	[[Category: Sphingopyxis sp]]
-	[[Category: Park S]]	+	[[Category: Kim, S H]]
-	[[Category: Rhee S]]	+	[[Category: Park, S]]
		+	[[Category: Rhee, S]]
		+	[[Category: Dinitroaniline herbicides reductase]]
		+	[[Category: Oxidoreductase]]

OCA at 08:56, 8 September 2021

OCA — Wed, 08 Sep 2021 08:56:34 GMT

←Older revision		Revision as of 08:56, 8 September 2021
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-	'''Unreleased structure'''

-	~~The entry 7dp2 is ON HOLD until Paper Publication~~	+	==Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH==
-		+	<StructureSection load='7dp2' size='340' side='right'caption='[[7dp2]]' scene=''>
-	~~Authors: Kim, S.H., Park, S., Rhee, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DP2 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH	+	</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=7dp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dp2 OCA], [https://pdbe.org/7dp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dp2 RCSB], [https://www.ebi.ac.uk/pdbsum/7dp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dp2 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kim~~, S.H~~]]	+	__TOC__
-	[[Category: Park, S]]	+	</StructureSection>
-	[[Category: Rhee, S]]	+	[[Category: Large Structures]]
		+	[[Category: Kim SH]]
		+	[[Category: Park S]]
		+	[[Category: Rhee S]]

OCA at 02:21, 2 July 2021

OCA — Fri, 02 Jul 2021 02:21:36 GMT

←Older revision		Revision as of 02:21, 2 July 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dp2 is ON HOLD	+	The entry 7dp2 is ON HOLD until Paper Publication

	Authors: Kim, S.H., Park, S., Rhee, S.		Authors: Kim, S.H., Park, S., Rhee, S.
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	Description: Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH		Description: Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Rhee, S]]
	[[Category: Kim, S.H]]		[[Category: Kim, S.H]]
	[[Category: Park, S]]		[[Category: Park, S]]
		+	[[Category: Rhee, S]]

OCA: Protected "7dp2" [edit=sysop:move=sysop]

OCA — Thu, 24 Dec 2020 07:57:16 GMT

Protected "7dp2" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:57, 24 December 2020

OCA: New page: '''Unreleased structure''' The entry 7dp2 is ON HOLD Authors: Kim, S.H., Park, S., Rhee, S. Description: Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F de...

OCA — Thu, 24 Dec 2020 07:57:14 GMT

New page: '''Unreleased structure''' The entry 7dp2 is ON HOLD Authors: Kim, S.H., Park, S., Rhee, S. Description: Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F de...

New page

'''Unreleased structure'''

The entry 7dp2 is ON HOLD

Authors: Kim, S.H., Park, S., Rhee, S.

Description: Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH
[[Category: Unreleased Structures]]
[[Category: Rhee, S]]
[[Category: Kim, S.H]]
[[Category: Park, S]]