3iep - Revision history

OCA at 10:05, 21 February 2024

OCA — Wed, 21 Feb 2024 10:05:06 GMT

←Older revision		Revision as of 10:05, 21 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEP FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[3ier\|3ier]]~~, [[~~3ies~~\|~~3ies~~]]~~</div></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]] 2.1Å</td></tr>
-	~~<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en~~.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1~~.13.12.7 1.13.12.7] </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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [https://pdbe.org/3iep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [https://www.ebi.ac.uk/pdbsum/3iep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iep 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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [https://pdbe.org/3iep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [https://www.ebi.ac.uk/pdbsum/3iep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iep ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LUCI_PHOPY LUCI_PHOPY]] Produces green light with a wavelength of 562 nm.	+	[https://www.uniprot.org/uniprot/LUCI_PHOPY LUCI_PHOPY] Produces green light with a wavelength of 562 nm.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iep ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iep ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Firefly luciferase (FLuc), an ATP-dependent bioluminescent reporter enzyme, is broadly used in chemical biology and drug discovery assays. PTC124 (Ataluren; (3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid) discovered in an FLuc-based assay targeting nonsense codon suppression, is an unusually potent FLuc-inhibitor. Paradoxically, PTC124 and related analogs increase cellular FLuc activity levels by posttranslational stabilization. In this study, we show that FLuc inhibition and stabilization is the result of an inhibitory product formed during the FLuc-catalyzed reaction between its natural substrate, ATP, and PTC124. A 2.0 A cocrystal structure revealed the inhibitor to be the acyl-AMP mixed-anhydride adduct PTC124-AMP, which was subsequently synthesized and shown to be a high-affinity multisubstrate adduct inhibitor (MAI; K(D) = 120 pM) of FLuc. Biochemical assays, liquid chromatography/mass spectrometry, and near-attack conformer modeling demonstrate that formation of this novel MAI is absolutely dependent upon the precise positioning and reactivity of a key meta-carboxylate of PTC124 within the FLuc active site. We also demonstrate that the inhibitory activity of PTC124-AMP is relieved by free coenzyme A, a component present at high concentrations in luciferase detection reagents used for cell-based assays. This explains why PTC124 can appear to increase, instead of inhibit, FLuc activity in cell-based reporter gene assays. To our knowledge, this is an unusual example in which the "off-target" effect of a small molecule is mediated by an MAI mechanism.
-
-	Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124.,Auld DS, Lovell S, Thorne N, Lea WA, Maloney DJ, Shen M, Rai G, Battaile KP, Thomas CJ, Simeonov A, Hanzlik RP, Inglese J Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4878-83. Epub 2010 Mar 1. PMID:20194791<ref>PMID:20194791</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3iep" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Luciferase\|Luciferase]]		*[[Luciferase\|Luciferase]]
	*[[Luciferase 3D structures\|Luciferase 3D structures]]		*[[Luciferase 3D structures\|Luciferase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Photinus pyralis]]		[[Category: Photinus pyralis]]
-	[[Category: Auld~~, D S~~]]	+	[[Category: Auld DS]]
-	[[Category: Battaile~~, K P~~]]	+	[[Category: Battaile KP]]
-	[[Category: Hanzlik~~, R P~~]]	+	[[Category: Hanzlik RP]]
-	[[Category: Inglese, J]]	+	[[Category: Inglese J]]
-	[[Category: Lea~~, W A~~]]	+	[[Category: Lea WA]]
-	[[Category: Lovell, S]]	+	[[Category: Lovell S]]
-	[[Category: Maloney~~, D J~~]]	+	[[Category: Maloney DJ]]
-	[[Category: Raj, G]]	+	[[Category: Raj G]]
-	[[Category: Shen, M]]	+	[[Category: Shen M]]
-	[[Category: Simeonov, A]]	+	[[Category: Simeonov A]]
-	[[Category: Thomas~~, C J~~]]	+	[[Category: Thomas CJ]]
-	[[Category: Thorne, N]]	+	[[Category: Thorne N]]
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Luminescence]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Monooxygenase]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxisome]]~~	+
-	~~[[Category: Photoprotein~~]]	+

OCA at 03:30, 21 April 2022

OCA — Thu, 21 Apr 2022 03:30:46 GMT

←Older revision		Revision as of 03:30, 21 April 2022
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	<StructureSection load='3iep' size='340' side='right'caption='[[3iep]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3iep' size='340' side='right'caption='[[3iep]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IEP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEP FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ier\|3ier]], [[3ies\|3ies]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [~~http~~://pdbe.org/3iep PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3iep PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3iep 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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [https://pdbe.org/3iep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [https://www.ebi.ac.uk/pdbsum/3iep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iep ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LUCI_PHOPY LUCI_PHOPY]] Produces green light with a wavelength of 562 nm.	+	[[https://www.uniprot.org/uniprot/LUCI_PHOPY LUCI_PHOPY]] Produces green light with a wavelength of 562 nm.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Luciferase\|Luciferase]]		*[[Luciferase\|Luciferase]]
-	*[[Luciferase ~~(Hebrew)~~\|Luciferase ~~(Hebrew)~~]]	+	*[[Luciferase 3D structures\|Luciferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:19, 7 August 2019

OCA — Wed, 07 Aug 2019 07:19:48 GMT

←Older revision		Revision as of 07:19, 7 August 2019
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	==Firefly luciferase apo structure (P41 form)==		==Firefly luciferase apo structure (P41 form)==
-	<StructureSection load='3iep' size='340' side='right' caption='[[3iep]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3iep' size='340' side='right'caption='[[3iep]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEP FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ie/3iep_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ie/3iep_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 31:		Line 31:

	==See Also==		==See Also==
		+	*[[Luciferase\|Luciferase]]
	*[[Luciferase (Hebrew)\|Luciferase (Hebrew)]]		*[[Luciferase (Hebrew)\|Luciferase (Hebrew)]]
	== References ==		== References ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Photinus pyralis]]		[[Category: Photinus pyralis]]
	[[Category: Auld, D S]]		[[Category: Auld, D S]]

OCA at 08:04, 1 November 2017

OCA — Wed, 01 Nov 2017 08:04:41 GMT

←Older revision		Revision as of 08:04, 1 November 2017
Line 1:		Line 1:
		+
	==Firefly luciferase apo structure (P41 form)==		==Firefly luciferase apo structure (P41 form)==
	<StructureSection load='3iep' size='340' side='right' caption='[[3iep]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3iep' size='340' side='right' caption='[[3iep]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [http://pdbe.org/3iep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [http://www.ebi.ac.uk/pdbsum/3iep 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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [http://pdbe.org/3iep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [http://www.ebi.ac.uk/pdbsum/3iep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iep ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	==See Also==		==See Also==
-	*[[Luciferase\|Luciferase]]	+	*[[Luciferase (Hebrew)\|Luciferase (Hebrew)]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:54, 10 February 2016

OCA — Wed, 10 Feb 2016 03:54:39 GMT

←Older revision		Revision as of 03:54, 10 February 2016
Line 5:		Line 5:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [http://www.ebi.ac.uk/pdbsum/3iep 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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [http://pdbe.org/3iep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [http://www.ebi.ac.uk/pdbsum/3iep PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iep ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3iep" style="background-color:#fffaf0;"></div>

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

OCA at 11:37, 25 December 2014

OCA — Thu, 25 Dec 2014 11:37:13 GMT

←Older revision		Revision as of 11:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [http://www.ebi.ac.uk/pdbsum/3iep 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=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [http://www.ebi.ac.uk/pdbsum/3iep PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LUCI_PHOPY LUCI_PHOPY]] Produces green light with a wavelength of 562 nm.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Photinus pyralis]]		[[Category: Photinus pyralis]]
-	[[Category: Auld, D S.]]	+	[[Category: Auld, D S]]
-	[[Category: Battaile, K P.]]	+	[[Category: Battaile, K P]]
-	[[Category: Hanzlik, R P.]]	+	[[Category: Hanzlik, R P]]
-	[[Category: Inglese, J.]]	+	[[Category: Inglese, J]]
-	[[Category: Lea, W A.]]	+	[[Category: Lea, W A]]
-	[[Category: Lovell, S.]]	+	[[Category: Lovell, S]]
-	[[Category: Maloney, D J.]]	+	[[Category: Maloney, D J]]
-	[[Category: Raj, G.]]	+	[[Category: Raj, G]]
-	[[Category: Shen, M.]]	+	[[Category: Shen, M]]
-	[[Category: Simeonov, A.]]	+	[[Category: Simeonov, A]]
-	[[Category: Thomas, C J.]]	+	[[Category: Thomas, C J]]
-	[[Category: Thorne, N.]]	+	[[Category: Thorne, N]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Luminescence]]		[[Category: Luminescence]]

OCA at 11:22, 29 September 2014

OCA — Mon, 29 Sep 2014 11:22:23 GMT

←Older revision		Revision as of 11:22, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3iep.~~png~~\|~~left~~\|200px]]	+	==Firefly luciferase apo structure (P41 form)==
		+	<StructureSection load='3iep' size='340' side='right' caption='[[3iep]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3iep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IEP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ier\|3ier]], [[3ies\|3ies]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photinus-luciferin_4-monooxygenase_(ATP-hydrolyzing) Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.7 1.13.12.7] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3iep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iep OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iep RCSB], [http://www.ebi.ac.uk/pdbsum/3iep PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ie/3iep_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Firefly luciferase (FLuc), an ATP-dependent bioluminescent reporter enzyme, is broadly used in chemical biology and drug discovery assays. PTC124 (Ataluren; (3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid) discovered in an FLuc-based assay targeting nonsense codon suppression, is an unusually potent FLuc-inhibitor. Paradoxically, PTC124 and related analogs increase cellular FLuc activity levels by posttranslational stabilization. In this study, we show that FLuc inhibition and stabilization is the result of an inhibitory product formed during the FLuc-catalyzed reaction between its natural substrate, ATP, and PTC124. A 2.0 A cocrystal structure revealed the inhibitor to be the acyl-AMP mixed-anhydride adduct PTC124-AMP, which was subsequently synthesized and shown to be a high-affinity multisubstrate adduct inhibitor (MAI; K(D) = 120 pM) of FLuc. Biochemical assays, liquid chromatography/mass spectrometry, and near-attack conformer modeling demonstrate that formation of this novel MAI is absolutely dependent upon the precise positioning and reactivity of a key meta-carboxylate of PTC124 within the FLuc active site. We also demonstrate that the inhibitory activity of PTC124-AMP is relieved by free coenzyme A, a component present at high concentrations in luciferase detection reagents used for cell-based assays. This explains why PTC124 can appear to increase, instead of inhibit, FLuc activity in cell-based reporter gene assays. To our knowledge, this is an unusual example in which the "off-target" effect of a small molecule is mediated by an MAI mechanism.

-	~~{{STRUCTURE_3iep\| PDB=3iep \| SCENE= }}~~	+	Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124.,Auld DS, Lovell S, Thorne N, Lea WA, Maloney DJ, Shen M, Rai G, Battaile KP, Thomas CJ, Simeonov A, Hanzlik RP, Inglese J Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4878-83. Epub 2010 Mar 1. PMID:20194791<ref>PMID:20194791</ref>

-	~~===Firefly luciferase apo structure (P41 form)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20194791}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3iep]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Photinus_pyralis Photinus pyralis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA].~~	+

	==See Also==		==See Also==
	*[[Luciferase\|Luciferase]]		*[[Luciferase\|Luciferase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020194791<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Photinus pyralis]]		[[Category: Photinus pyralis]]
	[[Category: Auld, D S.]]		[[Category: Auld, D S.]]

OCA at 16:14, 20 October 2012

OCA — Sat, 20 Oct 2012 16:14:33 GMT

←Older revision		Revision as of 16:14, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3iep]] is a 1 chain structure ~~of [[Luciferase]]~~ with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA].	+	[[3iep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA].

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

OCA: Protected "3iep" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 21:02:32 GMT

Protected "3iep" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:02, 26 July 2012

OCA at 21:02, 26 July 2012

OCA — Thu, 26 Jul 2012 21:02:30 GMT

←Older revision		Revision as of 21:02, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3iep.png\|left\|200px]]		[[Image:3iep.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3iep", 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_3iep\| PDB=3iep \| SCENE= }}		{{STRUCTURE_3iep\| PDB=3iep \| SCENE= }}

	===Firefly luciferase apo structure (P41 form)===		===Firefly luciferase apo structure (P41 form)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20194791}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20194791 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20194791}}		{{ABSTRACT_PUBMED_20194791}}

	==About this Structure==		==About this Structure==
-	~~3IEP~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA].	+	[[3iep]] is a 1 chain structure of [[Luciferase]] with sequence from [http://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEP OCA].
		+
		+	==See Also==
		+	*[[Luciferase\|Luciferase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20194791~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020194791</ref><references group="xtra"/>
	[[Category: Photinus pyralis]]		[[Category: Photinus pyralis]]
	[[Category: Auld, D S.]]		[[Category: Auld, D S.]]
Line 46:		Line 37:
	[[Category: Peroxisome]]		[[Category: Peroxisome]]
	[[Category: Photoprotein]]		[[Category: Photoprotein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 24 08:26:53 2010''