5j8d - Revision history

OCA at 10:54, 6 September 2023

OCA — Wed, 06 Sep 2023 10:54:08 GMT

←Older revision		Revision as of 10:54, 6 September 2023
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	<StructureSection load='5j8d' size='340' side='right'caption='[[5j8d]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5j8d' size='340' side='right'caption='[[5j8d]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter~~ cloacae~~" (jordan 1890) bergey et al. 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J8D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J8D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene~~>, ~~<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]] 1.85Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[1kqb\|1kqb]], [[1kqc\|1kqc]], [[1kqd\|1kqd]], [[5j8g\|5j8g]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">nfsB, nfnB, nfsI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])~~</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=5j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j8d OCA], [https://pdbe.org/5j8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j8d RCSB], [https://www.ebi.ac.uk/pdbsum/5j8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j8d 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=5j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j8d OCA], [~~http~~://pdbe.org/5j8d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j8d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j8d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j8d ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NFSB_ENTCL NFSB_ENTCL]] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.	+	[https://www.uniprot.org/uniprot/NFSB_ENTCL NFSB_ENTCL] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:

	==See Also==		==See Also==
-	*[[Nitroreductase\|Nitroreductase]]	+	*[[Nitroreductase 3D structures\|Nitroreductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enterobacter cloacae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Haynes~~, C A~~]]	+	[[Category: Haynes CA]]
-	[[Category: Koder~~, R L~~]]	+	[[Category: Koder RL]]
-	[[Category: Miller~~, A F~~]]	+	[[Category: Miller AF]]
-	[[Category: Rodgers~~, D W]]~~	+	[[Category: Rodgers DW]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Naad]]~~	+
-	~~[[Category: Nitroreductase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Substrate~~]]	+

OCA at 07:39, 27 November 2019

OCA — Wed, 27 Nov 2019 07:39:17 GMT

←Older revision		Revision as of 07:39, 27 November 2019
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	==Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide==		==Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide==
-	<StructureSection load='5j8d' size='340' side='right' caption='[[5j8d]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5j8d' size='340' side='right'caption='[[5j8d]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J8D FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5j8d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5j8d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitroreductase\|Nitroreductase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Haynes, C A]]		[[Category: Haynes, C A]]
	[[Category: Koder, R L]]		[[Category: Koder, R L]]

OCA at 07:36, 6 December 2017

OCA — Wed, 06 Dec 2017 07:36:55 GMT

←Older revision		Revision as of 07:36, 6 December 2017
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/NFSB_ENTCL NFSB_ENTCL]] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.		[[http://www.uniprot.org/uniprot/NFSB_ENTCL NFSB_ENTCL]] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.
		+
		+	Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase.,Pitsawong W, Haynes CA, Koder RL Jr, Rodgers DW, Miller AF Structure. 2017 Jul 5;25(7):978-987.e4. doi: 10.1016/j.str.2017.05.002. Epub 2017, Jun 1. PMID:28578873<ref>PMID:28578873</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5j8d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:52, 15 November 2017

OCA — Wed, 15 Nov 2017 17:52:14 GMT

←Older revision		Revision as of 17:52, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5j8d' size='340' side='right' caption='[[5j8d]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5j8d' size='340' side='right' caption='[[5j8d]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J8D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J8D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqb\|1kqb]], [[1kqc\|1kqc]], [[1kqd\|1kqd]], [[5j8g\|5j8g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqb\|1kqb]], [[1kqc\|1kqc]], [[1kqd\|1kqd]], [[5j8g\|5j8g]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfsB, nfnB, nfsI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</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=5j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j8d OCA], [http://pdbe.org/5j8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j8d RCSB], [http://www.ebi.ac.uk/pdbsum/5j8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j8d 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=5j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j8d OCA], [http://pdbe.org/5j8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j8d RCSB], [http://www.ebi.ac.uk/pdbsum/5j8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j8d ProSAT]</span></td></tr>
	</table>		</table>

OCA at 15:46, 17 May 2017

OCA — Wed, 17 May 2017 15:46:28 GMT

←Older revision		Revision as of 15:46, 17 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j8d is ~~ON HOLD until Paper Publication~~	+	==Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide==
-		+	<StructureSection load='5j8d' size='340' side='right' caption='[[5j8d]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~Authors~~: ~~Haynes~~, C.A., ~~Koder, R~~.L., ~~Miller~~, A.F., ~~Rodgers~~, D.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5j8d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J8D FirstGlance]. <br>
-	~~Description: Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kqb\|1kqb]], [[1kqc\|1kqc]], [[1kqd\|1kqd]], [[5j8g\|5j8g]]</td></tr>
-	[[Category: Haynes, C.A]]	+	<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=5j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j8d OCA], [http://pdbe.org/5j8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j8d RCSB], [http://www.ebi.ac.uk/pdbsum/5j8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j8d ProSAT]</span></td></tr>
-	[[Category: ~~Rodgers~~, ~~D.W~~]]	+	</table>
-	[[Category: Miller, A.F]]	+	== Function ==
-	[[Category: ~~Koder~~, ~~R.L~~]]	+	[[http://www.uniprot.org/uniprot/NFSB_ENTCL NFSB_ENTCL]] Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Haynes, C A]]
		+	[[Category: Koder, R L]]
		+	[[Category: Miller, A F]]
		+	[[Category: Rodgers, D W]]
		+	[[Category: Complex]]
		+	[[Category: Naad]]
		+	[[Category: Nitroreductase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Substrate]]

OCA at 12:51, 1 February 2017

OCA — Wed, 01 Feb 2017 12:51:56 GMT

←Older revision		Revision as of 12:51, 1 February 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j8d is ON HOLD	+	The entry 5j8d is ON HOLD until Paper Publication

	Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.		Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.

OCA at 11:44, 2 January 2017

OCA — Mon, 02 Jan 2017 11:44:10 GMT

←Older revision		Revision as of 11:44, 2 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j8d is ON HOLD ~~until Paper Publication~~	+	The entry 5j8d is ON HOLD

	Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.		Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.

OCA at 00:39, 4 August 2016

OCA — Thu, 04 Aug 2016 00:39:23 GMT

←Older revision		Revision as of 00:39, 4 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j8d is ON HOLD	+	The entry 5j8d is ON HOLD until Paper Publication

	Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.		Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.

OCA: Protected "5j8d" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:40:13 GMT

Protected "5j8d" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:40, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j8d is ON HOLD Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W. Description: Structure of nitroreductase from E. cloacae complexed ...

OCA — Wed, 11 May 2016 01:40:12 GMT

New page: '''Unreleased structure''' The entry 5j8d is ON HOLD Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W. Description: Structure of nitroreductase from E. cloacae complexed ...

New page

'''Unreleased structure'''

The entry 5j8d is ON HOLD

Authors: Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.

Description: Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide
[[Category: Unreleased Structures]]
[[Category: Haynes, C.A]]
[[Category: Rodgers, D.W]]
[[Category: Miller, A.F]]
[[Category: Koder, R.L]]