6s6e - Revision history

OCA at 12:36, 24 January 2024

OCA — Wed, 24 Jan 2024 12:36:08 GMT

←Older revision		Revision as of 12:36, 24 January 2024
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	<StructureSection load='6s6e' size='340' side='right'caption='[[6s6e]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6s6e' size='340' side='right'caption='[[6s6e]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s6e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S6E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s6e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S6E FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6s6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s6e OCA], [https://pdbe.org/6s6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s6e RCSB], [https://www.ebi.ac.uk/pdbsum/6s6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s6e ProSAT]</span></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]] 2.001Å</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=6s6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s6e OCA], [https://pdbe.org/6s6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s6e RCSB], [https://www.ebi.ac.uk/pdbsum/6s6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s6e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Damborsky, J]]	+	[[Category: Damborsky J]]
-	[[Category: Marek, M]]	+	[[Category: Marek M]]
-	[[Category: Schenkmayerova, A]]	+	[[Category: Schenkmayerova A]]
-	~~[[Category: Bioluminscence]]~~	+
-	~~[[Category: Coelenterazine-utilizing enzyme]]~~	+
-	~~[[Category: Engineered ancestral enzyme]]~~	+
-	~~[[Category: Luminescent protein~~]]	+

OCA at 09:03, 8 September 2021

OCA — Wed, 08 Sep 2021 09:03:08 GMT

←Older revision		Revision as of 09:03, 8 September 2021
Line 1:		Line 1:

	==Crystal structure of the engineered ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc I161_F162PinsL)==		==Crystal structure of the engineered ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc I161_F162PinsL)==
-	<StructureSection load='6s6e' size='340' side='right'caption='[[6s6e]]' scene=''>	+	<StructureSection load='6s6e' size='340' side='right'caption='[[6s6e]], [[Resolution\|resolution]] 2.00Å' 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=6S6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S6E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s6e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S6E FirstGlance]. <br>
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6s6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s6e OCA], [https://pdbe.org/6s6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s6e RCSB], [https://www.ebi.ac.uk/pdbsum/6s6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s6e ProSAT]</span></td></tr>		</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=6s6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s6e OCA], [https://pdbe.org/6s6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s6e RCSB], [https://www.ebi.ac.uk/pdbsum/6s6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s6e ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein Anc(HLD-RLuc) which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of Anc(HLD-RLuc) challenged the scaffold dynamics. Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). An anisotropic network model highlights the importance of the conformational flexibility of a loop-helix fragment of Renilla luciferases for ligand binding. Transplantation of this dynamic fragment leads to lower product inhibition and highly stable glow-type bioluminescence. The success of our approach suggests that a strategy comprising (i) constructing a stable and evolvable template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation of dynamic features, can lead to functionally innovative proteins.
		+
		+	Engineering the protein dynamics of an ancestral luciferase.,Schenkmayerova A, Pinto GP, Toul M, Marek M, Hernychova L, Planas-Iglesias J, Daniel Liskova V, Pluskal D, Vasina M, Emond S, Dorr M, Chaloupkova R, Bednar D, Prokop Z, Hollfelder F, Bornscheuer UT, Damborsky J Nat Commun. 2021 Jun 14;12(1):3616. doi: 10.1038/s41467-021-23450-z. PMID:34127663<ref>PMID:34127663</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6s6e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Damborsky J]]	+	[[Category: Synthetic construct sequences]]
-	[[Category: Marek M]]	+	[[Category: Damborsky, J]]
-	[[Category: Schenkmayerova A]]	+	[[Category: Marek, M]]
		+	[[Category: Schenkmayerova, A]]
		+	[[Category: Bioluminscence]]
		+	[[Category: Coelenterazine-utilizing enzyme]]
		+	[[Category: Engineered ancestral enzyme]]
		+	[[Category: Luminescent protein]]

OCA at 07:53, 27 January 2021

OCA — Wed, 27 Jan 2021 07:53:09 GMT

←Older revision		Revision as of 07:53, 27 January 2021
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-	'''Unreleased structure'''

-	~~The entry 6s6e is ON HOLD until Paper Publication~~	+	==Crystal structure of the engineered ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc I161_F162PinsL)==
-		+	<StructureSection load='6s6e' size='340' side='right'caption='[[6s6e]]' scene=''>
-	~~Authors: Schenkmayerova, A., Damborsky, J., Marek, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S6E FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the engineered ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc I161_F162PinsL)	+	</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=6s6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s6e OCA], [https://pdbe.org/6s6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s6e RCSB], [https://www.ebi.ac.uk/pdbsum/6s6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s6e ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Damborsky, J]]	+	__TOC__
-	[[Category: ~~Schenkmayerova, A~~]]	+	</StructureSection>
-	[[Category: ~~Marek, M~~]]	+	[[Category: Large Structures]]
		+	[[Category: Damborsky J]]
		+	[[Category: Marek M]]
		+	[[Category: Schenkmayerova A]]

OCA at 03:48, 13 May 2020

OCA — Wed, 13 May 2020 03:48:39 GMT

←Older revision		Revision as of 03:48, 13 May 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6s6e is ON HOLD	+	The entry 6s6e is ON HOLD until Paper Publication

	Authors: Schenkmayerova, A., Damborsky, J., Marek, M.		Authors: Schenkmayerova, A., Damborsky, J., Marek, M.

OCA: Protected "6s6e" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:27:58 GMT

Protected "6s6e" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:27, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6s6e is ON HOLD Authors: Schenkmayerova, A., Damborsky, J., Marek, M. Description: Crystal structure of the engineered ancestor of haloalkane dehal...

OCA — Wed, 10 Jul 2019 04:27:57 GMT

New page: '''Unreleased structure''' The entry 6s6e is ON HOLD Authors: Schenkmayerova, A., Damborsky, J., Marek, M. Description: Crystal structure of the engineered ancestor of haloalkane dehal...

New page

'''Unreleased structure'''

The entry 6s6e is ON HOLD

Authors: Schenkmayerova, A., Damborsky, J., Marek, M.

Description: Crystal structure of the engineered ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc I161_F162PinsL)
[[Category: Unreleased Structures]]
[[Category: Damborsky, J]]
[[Category: Schenkmayerova, A]]
[[Category: Marek, M]]