6k4d - Revision history

OCA at 10:26, 22 November 2023

OCA — Wed, 22 Nov 2023 10:26:29 GMT

←Older revision		Revision as of 10:26, 22 November 2023
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	<StructureSection load='6k4d' size='340' side='right'caption='[[6k4d]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6k4d' size='340' side='right'caption='[[6k4d]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k4d]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lampyridae Lampyridae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6K4D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k4d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lampyridae Lampyridae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K4D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4F:[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+(4S)-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate'>D4F</scene>, <scene name='pdbligand=ESJ:(4S)-2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-4,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>ESJ</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]] 1.7Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6k4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4d OCA], [~~http~~://pdbe.org/6k4d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k4d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k4d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4d ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4F:[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+(4S)-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate'>D4F</scene>, <scene name='pdbligand=ESJ:(4S)-2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-4,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>ESJ</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=6k4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4d OCA], [https://pdbe.org/6k4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k4d RCSB], [https://www.ebi.ac.uk/pdbsum/6k4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Lampyridae]]		[[Category: Lampyridae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kato, D]]	+	[[Category: Kato D]]
-	[[Category: Konishi, K]]	+	[[Category: Konishi K]]
-	[[Category: Oba, Y]]	+	[[Category: Oba Y]]
-	[[Category: Shirai, T]]	+	[[Category: Shirai T]]
-	[[Category: Yano, D]]	+	[[Category: Yano D]]
-	~~[[Category: Ancestral protein]]~~	+
-	~~[[Category: Bioluminescence]]~~	+
-	~~[[Category: Luciferase]]~~	+
-	~~[[Category: Molecular evolution]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 12:40, 16 December 2020

OCA — Wed, 16 Dec 2020 12:40:13 GMT

←Older revision		Revision as of 12:40, 16 December 2020
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4d OCA], [http://pdbe.org/6k4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4d RCSB], [http://www.ebi.ac.uk/pdbsum/6k4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4d ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4d OCA], [http://pdbe.org/6k4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4d RCSB], [http://www.ebi.ac.uk/pdbsum/6k4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4d ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The color of firefly bioluminescence is determined by the structure of luciferase. Firefly luciferase genes have been isolated from more than 30 species, producing light ranging in color from green to orange-yellow. Here, we reconstructed seven ancestral firefly luciferase genes, characterized the enzymatic properties of the recombinant proteins, and determined the crystal structures of the gene from ancestral Lampyridae. Results showed that the synthetic luciferase for the last common firefly ancestor exhibited green light caused by a spatial constraint on the luciferin molecule in enzyme, while fatty acyl-CoA synthetic activity, an original function of firefly luciferase, was diminished in exchange. All known firefly species are bioluminescent in the larvae, with a common ancestor arising approximately 100 million years ago. Combined, our findings propose that, within the mid-Cretaceous forest, the common ancestor of fireflies evolved green light luciferase via trade-off of the original function, which was likely aposematic warning display against nocturnal predation.
		+
		+	Resurrecting the ancient glow of the fireflies.,Oba Y, Konishi K, Yano D, Shibata H, Kato D, Shirai T Sci Adv. 2020 Dec 2;6(49). pii: 6/49/eabc5705. doi: 10.1126/sciadv.abc5705. Print, 2020 Dec. PMID:33268373<ref>PMID:33268373</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k4d" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Luciferase 3D structures\|Luciferase 3D structures]]		*[[Luciferase 3D structures\|Luciferase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:45, 9 December 2020

OCA — Wed, 09 Dec 2020 06:45:04 GMT

←Older revision		Revision as of 06:45, 9 December 2020
Line 1:		Line 1:

	==Ancestral luciferase AncLamp in complex with ATP and D-luciferin==		==Ancestral luciferase AncLamp in complex with ATP and D-luciferin==
-	<StructureSection load='6k4d' size='340' side='right'caption='[[6k4d]]' scene=''>	+	<StructureSection load='6k4d' size='340' side='right'caption='[[6k4d]], [[Resolution\|resolution]] 1.70Å' 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=6K4D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K4D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k4d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lampyridae Lampyridae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K4D FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4d OCA], [http://pdbe.org/6k4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4d RCSB], [http://www.ebi.ac.uk/pdbsum/6k4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4d 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=D4F:[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+(4S)-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate'>D4F</scene>, <scene name='pdbligand=ESJ:(4S)-2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-4,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>ESJ</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4d OCA], [http://pdbe.org/6k4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4d RCSB], [http://www.ebi.ac.uk/pdbsum/6k4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4d ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Luciferase 3D structures\|Luciferase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lampyridae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kato D]]	+	[[Category: Kato, D]]
-	[[Category: Konishi K]]	+	[[Category: Konishi, K]]
-	[[Category: Oba Y]]	+	[[Category: Oba, Y]]
-	[[Category: Shirai T]]	+	[[Category: Shirai, T]]
-	[[Category: Yano D]]	+	[[Category: Yano, D]]
		+	[[Category: Ancestral protein]]
		+	[[Category: Bioluminescence]]
		+	[[Category: Luciferase]]
		+	[[Category: Molecular evolution]]
		+	[[Category: Oxidoreductase]]

OCA at 06:52, 27 May 2020

OCA — Wed, 27 May 2020 06:52:02 GMT

←Older revision		Revision as of 06:52, 27 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k4d is ~~ON HOLD until Paper Publication~~	+	==Ancestral luciferase AncLamp in complex with ATP and D-luciferin==
-		+	<StructureSection load='6k4d' size='340' side='right'caption='[[6k4d]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K4D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K4D FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k4d OCA], [http://pdbe.org/6k4d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k4d RCSB], [http://www.ebi.ac.uk/pdbsum/6k4d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k4d ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kato D]]
		+	[[Category: Konishi K]]
		+	[[Category: Oba Y]]
		+	[[Category: Shirai T]]
		+	[[Category: Yano D]]

OCA at 04:01, 3 July 2019

OCA — Wed, 03 Jul 2019 04:01:25 GMT

←Older revision		Revision as of 04:01, 3 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k4d is ON HOLD	+	The entry 6k4d is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6k4d" [edit=sysop:move=sysop]

OCA — Wed, 29 May 2019 04:27:31 GMT

Protected "6k4d" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:27, 29 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k4d is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 29 May 2019 04:27:30 GMT

New page: '''Unreleased structure''' The entry 6k4d is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6k4d is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]