3r5w - Revision history

OCA at 12:11, 14 March 2024

OCA — Thu, 14 Mar 2024 12:11:34 GMT

←Older revision		Revision as of 12:11, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3r5w' size='340' side='right'caption='[[3r5w]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='3r5w' size='340' side='right'caption='[[3r5w]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=F42:COENZYME+F420'>F42</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]] 1.786Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[3r5l\|3r5l]], [[3r5p\|3r5p]], [[3r5r\|3r5r]], [[3r5y\|3r5y]], [[3r5z\|3r5z]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F42:COENZYME+F420'>F42</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ddn, MT3651, Rv3547 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])~~</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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [https://pdbe.org/3r5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [https://www.ebi.ac.uk/pdbsum/3r5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5w 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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [https://pdbe.org/3r5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [https://www.ebi.ac.uk/pdbsum/3r5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DDN_MYCTU DDN_MYCTU]] Nitroreductase involved in the bioreductive activation of the antitubercular prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It converts PA-824 into three primary metabolites; the major one is the des-nitroimidazole (des-nitro) which generated reactive nitrogen species, including nitric oxide (NO). Reactive nitrogen species play a major role in mammalian defense against mycobacterial infections.<ref>PMID:16387854</ref> <ref>PMID:19039139</ref>	+	[https://www.uniprot.org/uniprot/DDN_MYCTU DDN_MYCTU] Nitroreductase involved in the bioreductive activation of the antitubercular prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It converts PA-824 into three primary metabolites; the major one is the des-nitroimidazole (des-nitro) which generated reactive nitrogen species, including nitric oxide (NO). Reactive nitrogen species play a major role in mammalian defense against mycobacterial infections.<ref>PMID:16387854</ref> <ref>PMID:19039139</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F(420) deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F(420) and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.	+
-		+
-	Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824.,Cellitti SE, Shaffer J, Jones DH, Mukherjee T, Gurumurthy M, Bursulaya B, Boshoff HI, Choi I, Nayyar A, Lee YS, Cherian J, Niyomrattanakit P, Dick T, Manjunatha UH, Barry CE 3rd, Spraggon G, Geierstanger BH Structure. 2012 Jan 11;20(1):101-12. PMID:22244759<ref>PMID:22244759</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3r5w" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
-	*[[Nitroreductase\|Nitroreductase]]	+	*[[Nitroreductase 3D structures\|Nitroreductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 18:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barry~~, C E~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Boshoff~~, H I.M~~]]	+	[[Category: Barry CE]]
-	[[Category: Bursulaya, B]]	+	[[Category: Boshoff HIM]]
-	[[Category: Cellitti~~, S E~~]]	+	[[Category: Bursulaya B]]
-	[[Category: Cherian, J]]	+	[[Category: Cellitti SE]]
-	[[Category: Choi, I]]	+	[[Category: Cherian J]]
-	[[Category: Dick, T]]	+	[[Category: Choi I]]
-	[[Category: Geierstanger~~, B H~~]]	+	[[Category: Dick T]]
-	[[Category: Gurumurthy, M]]	+	[[Category: Geierstanger BH]]
-	[[Category: Jones~~, D H~~]]	+	[[Category: Gurumurthy M]]
-	[[Category: Lee~~, Y S~~]]	+	[[Category: Jones DH]]
-	[[Category: Manjunatha~~, U H~~]]	+	[[Category: Lee YS]]
-	[[Category: Mukherjee, T]]	+	[[Category: Manjunatha UH]]
-	[[Category: Nayya, A]]	+	[[Category: Mukherjee T]]
-	[[Category: Niyomrattanakit, P]]	+	[[Category: Nayya A]]
-	[[Category: Shaffer, J]]	+	[[Category: Niyomrattanakit P]]
-	[[Category: Spraggon, G]]	+	[[Category: Shaffer J]]
-	~~[[Category: Deazaflavin-dependent nitroreductase]]~~	+	[[Category: Spraggon G]]
-	~~[[Category: Duf385]]~~	+
-	~~[[Category: F420]]~~	+
-	~~[[Category: Nitroimidazole]]~~	+
-	~~[[Category: Opc-67683]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pa-824]]~~	+
-	~~[[Category: Split barrel-like fold~~]]	+

OCA at 05:50, 15 June 2022

OCA — Wed, 15 Jun 2022 05:50:12 GMT

←Older revision		Revision as of 05:50, 15 June 2022
Line 1:		Line 1:

	==Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420==		==Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420==
-	<StructureSection load='3r5w' size='340' side='right' caption='[[3r5w]], [[Resolution\|resolution]] 1.79Å' scene=''>	+	<StructureSection load='3r5w' size='340' side='right'caption='[[3r5w]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3R5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F42:COENZYME+F420'>F42</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F42:COENZYME+F420'>F42</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5l\|3r5l]], [[3r5p\|3r5p]], [[3r5r\|3r5r]], [[3r5y\|3r5y]], [[3r5z\|3r5z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r5l\|3r5l]], [[3r5p\|3r5p]], [[3r5r\|3r5r]], [[3r5y\|3r5y]], [[3r5z\|3r5z]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddn, MT3651, Rv3547 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddn, MT3651, Rv3547 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [~~http~~://pdbe.org/3r5w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3r5w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5w 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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [https://pdbe.org/3r5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [https://www.ebi.ac.uk/pdbsum/3r5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DDN_MYCTU DDN_MYCTU]] Nitroreductase involved in the bioreductive activation of the antitubercular prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It converts PA-824 into three primary metabolites; the major one is the des-nitroimidazole (des-nitro) which generated reactive nitrogen species, including nitric oxide (NO). Reactive nitrogen species play a major role in mammalian defense against mycobacterial infections.<ref>PMID:16387854</ref> <ref>PMID:19039139</ref>	+	[[https://www.uniprot.org/uniprot/DDN_MYCTU DDN_MYCTU]] Nitroreductase involved in the bioreductive activation of the antitubercular prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It converts PA-824 into three primary metabolites; the major one is the des-nitroimidazole (des-nitro) which generated reactive nitrogen species, including nitric oxide (NO). Reactive nitrogen species play a major role in mammalian defense against mycobacterial infections.<ref>PMID:16387854</ref> <ref>PMID:19039139</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3r5w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3r5w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitroreductase\|Nitroreductase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Barry, C E]]		[[Category: Barry, C E]]
	[[Category: Boshoff, H I.M]]		[[Category: Boshoff, H I.M]]

OCA at 09:23, 8 November 2017

OCA — Wed, 08 Nov 2017 09:23:08 GMT

←Older revision		Revision as of 09:23, 8 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3r5w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3r5w" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nitroreductase\|Nitroreductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:50, 5 August 2016

OCA — Fri, 05 Aug 2016 04:50:38 GMT

←Older revision		Revision as of 04:50, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420==		==Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420==
	<StructureSection load='3r5w' size='340' side='right' caption='[[3r5w]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='3r5w' size='340' side='right' caption='[[3r5w]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F42:COENZYME+F420'>F42</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F42:COENZYME+F420'>F42</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5l\|3r5l]], [[3r5p\|3r5p]], [[3r5r\|3r5r]], [[3r5y\|3r5y]], [[3r5z\|3r5z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5l\|3r5l]], [[3r5p\|3r5p]], [[3r5r\|3r5r]], [[3r5y\|3r5y]], [[3r5z\|3r5z]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddn, MT3651, Rv3547 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddn, MT3651, Rv3547 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [http://www.ebi.ac.uk/pdbsum/3r5w PDBsum]</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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [http://pdbe.org/3r5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [http://www.ebi.ac.uk/pdbsum/3r5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3r5w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Barry, C E]]		[[Category: Barry, C E]]
	[[Category: Boshoff, H I.M]]		[[Category: Boshoff, H I.M]]

OCA at 15:54, 25 December 2014

OCA — Thu, 25 Dec 2014 15:54:55 GMT

←Older revision		Revision as of 15:54, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3r5w.~~png~~\|~~left~~\|~~200px~~]]	+	==Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420==
		+	<StructureSection load='3r5w' size='340' side='right' caption='[[3r5w]], [[Resolution\|resolution]] 1.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F42:COENZYME+F420'>F42</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5l\|3r5l]], [[3r5p\|3r5p]], [[3r5r\|3r5r]], [[3r5y\|3r5y]], [[3r5z\|3r5z]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ddn, MT3651, Rv3547 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</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=3r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r5w RCSB], [http://www.ebi.ac.uk/pdbsum/3r5w PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDN_MYCTU DDN_MYCTU]] Nitroreductase involved in the bioreductive activation of the antitubercular prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It converts PA-824 into three primary metabolites; the major one is the des-nitroimidazole (des-nitro) which generated reactive nitrogen species, including nitric oxide (NO). Reactive nitrogen species play a major role in mammalian defense against mycobacterial infections.<ref>PMID:16387854</ref> <ref>PMID:19039139</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F(420) deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F(420) and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.

-	~~{{STRUCTURE_3r5w\| PDB=3r5w \| SCENE= }}~~	+	Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824.,Cellitti SE, Shaffer J, Jones DH, Mukherjee T, Gurumurthy M, Bursulaya B, Boshoff HI, Choi I, Nayyar A, Lee YS, Cherian J, Niyomrattanakit P, Dick T, Manjunatha UH, Barry CE 3rd, Spraggon G, Geierstanger BH Structure. 2012 Jan 11;20(1):101-12. PMID:22244759<ref>PMID:22244759</ref>

-	~~===Structure~~ of ~~Ddn,~~ the ~~Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22244759}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3r5w]] is a 10 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].~~	+

	==See Also==		==See Also==
	*[[Nitroreductase\|Nitroreductase]]		*[[Nitroreductase\|Nitroreductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:022244759<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Barry, C E.]]	+	[[Category: Barry, C E]]
-	[[Category: Boshoff, H I.M.]]	+	[[Category: Boshoff, H I.M]]
-	[[Category: Bursulaya, B.]]	+	[[Category: Bursulaya, B]]
-	[[Category: Cellitti, S E.]]	+	[[Category: Cellitti, S E]]
-	[[Category: Cherian, J.]]	+	[[Category: Cherian, J]]
-	[[Category: Choi, I.]]	+	[[Category: Choi, I]]
-	[[Category: Dick, T.]]	+	[[Category: Dick, T]]
-	[[Category: Geierstanger, B H.]]	+	[[Category: Geierstanger, B H]]
-	[[Category: Gurumurthy, M.]]	+	[[Category: Gurumurthy, M]]
-	[[Category: Jones, D H.]]	+	[[Category: Jones, D H]]
-	[[Category: Lee, Y S.]]	+	[[Category: Lee, Y S]]
-	[[Category: Manjunatha, U H.]]	+	[[Category: Manjunatha, U H]]
-	[[Category: Mukherjee, T.]]	+	[[Category: Mukherjee, T]]
-	[[Category: Nayya, A.]]	+	[[Category: Nayya, A]]
-	[[Category: Niyomrattanakit, P.]]	+	[[Category: Niyomrattanakit, P]]
-	[[Category: Shaffer, J.]]	+	[[Category: Shaffer, J]]
-	[[Category: Spraggon, G.]]	+	[[Category: Spraggon, G]]
	[[Category: Deazaflavin-dependent nitroreductase]]		[[Category: Deazaflavin-dependent nitroreductase]]
	[[Category: Duf385]]		[[Category: Duf385]]

OCA at 18:35, 20 October 2012

OCA — Sat, 20 Oct 2012 18:35:33 GMT

←Older revision		Revision as of 18:35, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3r5w]] is a 10 chain structure ~~of [[Nitroreductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].	+	[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].

	==See Also==		==See Also==

OCA at 04:34, 27 July 2012

OCA — Fri, 27 Jul 2012 04:34:10 GMT

←Older revision		Revision as of 04:34, 27 July 2012
Line 1:		Line 1:
	[[Image:3r5w.png\|left\|200px]]		[[Image:3r5w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3r5w", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3r5w\| PDB=3r5w \| SCENE= }}		{{STRUCTURE_3r5w\| PDB=3r5w \| SCENE= }}

	===Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420===		===Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22244759}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22244759 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22244759}}		{{ABSTRACT_PUBMED_22244759}}

	==About this Structure==		==About this Structure==
-	[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].	+	[[3r5w]] is a 10 chain structure of [[Nitroreductase]] with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].
		+
		+	==See Also==
		+	*[[Nitroreductase\|Nitroreductase]]

	==Reference==		==Reference==

OCA at 06:25, 21 March 2012

OCA — Wed, 21 Mar 2012 06:25:58 GMT

←Older revision		Revision as of 06:25, 21 March 2012
Line 1:		Line 1:
-	[[Image:3r5w.~~jpg~~\|left\|200px]]	+	[[Image:3r5w.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420===		===Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22244759}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22244759 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22244759}}

	==About this Structure==		==About this Structure==
	[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].		[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022244759</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Barry, C E.]]		[[Category: Barry, C E.]]

OCA at 10:52, 18 January 2012

OCA — Wed, 18 Jan 2012 10:52:37 GMT

←Older revision		Revision as of 10:52, 18 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3r5w.jpg\|left\|200px]]

-	The ~~entry 3r5w~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3r5w", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3r5w\| PDB=3r5w \| SCENE= }}

-	~~Authors: Cellitti~~, ~~S.E.~~, Shaffer, J., Jones, D.H., Mukherjee, T., Gurumurthy, M., Bursulaya, B., Boshoff, H.I.M., Choi, I., Nayya, A., Lee, Y.S., Cherian, J., Niyomrattanakit, P., Dick, T., Manjunatha, U.H., Barry, C.E., Spraggon, G., Geierstanger, B.H.	+	===Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420===

-	~~Description:~~ Structure ~~of Ddn~~, ~~the~~ Deazaflavin-dependent nitroreductase ~~from Mycobacterium tuberculosis involved in bioreductive activation of PA~~-824~~, with co~~-~~factor F420~~	+
		+	==About this Structure==
		+	[[3r5w]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5W OCA].
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Barry, C E.]]
		+	[[Category: Boshoff, H I.M.]]
		+	[[Category: Bursulaya, B.]]
		+	[[Category: Cellitti, S E.]]
		+	[[Category: Cherian, J.]]
		+	[[Category: Choi, I.]]
		+	[[Category: Dick, T.]]
		+	[[Category: Geierstanger, B H.]]
		+	[[Category: Gurumurthy, M.]]
		+	[[Category: Jones, D H.]]
		+	[[Category: Lee, Y S.]]
		+	[[Category: Manjunatha, U H.]]
		+	[[Category: Mukherjee, T.]]
		+	[[Category: Nayya, A.]]
		+	[[Category: Niyomrattanakit, P.]]
		+	[[Category: Shaffer, J.]]
		+	[[Category: Spraggon, G.]]
		+	[[Category: Deazaflavin-dependent nitroreductase]]
		+	[[Category: Duf385]]
		+	[[Category: F420]]
		+	[[Category: Nitroimidazole]]
		+	[[Category: Opc-67683]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pa-824]]
		+	[[Category: Split barrel-like fold]]

OCA at 05:49, 15 June 2011

OCA — Wed, 15 Jun 2011 05:49:58 GMT

←Older revision		Revision as of 05:49, 15 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3r5w is ON HOLD	+	The entry 3r5w is ON HOLD until Paper Publication

	Authors: Cellitti, S.E., Shaffer, J., Jones, D.H., Mukherjee, T., Gurumurthy, M., Bursulaya, B., Boshoff, H.I.M., Choi, I., Nayya, A., Lee, Y.S., Cherian, J., Niyomrattanakit, P., Dick, T., Manjunatha, U.H., Barry, C.E., Spraggon, G., Geierstanger, B.H.		Authors: Cellitti, S.E., Shaffer, J., Jones, D.H., Mukherjee, T., Gurumurthy, M., Bursulaya, B., Boshoff, H.I.M., Choi, I., Nayya, A., Lee, Y.S., Cherian, J., Niyomrattanakit, P., Dick, T., Manjunatha, U.H., Barry, C.E., Spraggon, G., Geierstanger, B.H.

	Description: Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420		Description: Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420