6y9g - Revision history

OCA at 13:22, 24 January 2024

OCA — Wed, 24 Jan 2024 13:22:24 GMT

←Older revision		Revision as of 13:22, 24 January 2024
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	==Crystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)==		==Crystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)==
-	<StructureSection load='6y9g' size='340' side='right'caption='[[6y9g]]' scene=''>	+	<StructureSection load='6y9g' size='340' side='right'caption='[[6y9g]], [[Resolution\|resolution]] 1.75Å' 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=6Y9G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y9G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y9g]] 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=6Y9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y9G 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=6y9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y9g OCA], [~~http~~://pdbe.org/6y9g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y9g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y9g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y9g 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]] 1.748Å</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=6y9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y9g OCA], [https://pdbe.org/6y9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y9g RCSB], [https://www.ebi.ac.uk/pdbsum/6y9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y9g ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ancestral sequence reconstruction is a powerful method for inferring ancestors of modern enzymes and for studying structure-function relationships of enzymes. We have previously applied this approach to haloalkane dehalogenases (HLDs) from the subfamily HLD-II and obtained thermodynamically highly stabilized enzymes (DeltaT m up to 24 degrees C), showing improved catalytic properties. Here we combined crystallographic structural analysis and computational molecular dynamics simulations to gain insight into the mechanisms by which ancestral HLDs became more robust enzymes with novel catalytic properties. Reconstructed ancestors exhibited similar structure topology as their descendants with the exception of a few loop deviations. Strikingly, molecular dynamics simulations revealed restricted conformational dynamics of ancestral enzymes, which prefer a single state, in contrast to modern enzymes adopting two different conformational states. The restricted dynamics can potentially be linked to their exceptional stabilization. The study provides molecular insights into protein stabilization due to ancestral sequence reconstruction, which is becoming a widely used approach for obtaining robust protein catalysts.
		+
		+	Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics.,Babkova P, Dunajova Z, Chaloupkova R, Damborsky J, Bednar D, Marek M Comput Struct Biotechnol J. 2020 Jun 19;18:1497-1508. doi:, 10.1016/j.csbj.2020.06.021. eCollection 2020. PMID:32637047<ref>PMID:32637047</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y9g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
	[[Category: Chaloupkova R]]		[[Category: Chaloupkova R]]
	[[Category: Damborsky J]]		[[Category: Damborsky J]]
	[[Category: Marek M]]		[[Category: Marek M]]

OCA at 09:38, 18 November 2020

OCA — Wed, 18 Nov 2020 09:38:20 GMT

←Older revision		Revision as of 09:38, 18 November 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6y9g ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)==
-		+	<StructureSection load='6y9g' size='340' side='right'caption='[[6y9g]]' scene=''>
-	~~Authors~~: ~~Chaloupkova~~, R., ~~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=6Y9G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y9G FirstGlance]. <br>
-	~~Description: Crystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)~~	+	</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=6y9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y9g OCA], [http://pdbe.org/6y9g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y9g RCSB], [http://www.ebi.ac.uk/pdbsum/6y9g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y9g ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Marek, M~~]]	+	__TOC__
-	[[Category: Damborsky, J]]	+	</StructureSection>
-	[[Category: ~~Chaloupkova, R~~]]	+	[[Category: Large Structures]]
		+	[[Category: Chaloupkova R]]
		+	[[Category: Damborsky J]]
		+	[[Category: Marek M]]

OCA at 07:14, 22 July 2020

OCA — Wed, 22 Jul 2020 07:14:06 GMT

←Older revision		Revision as of 07:14, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y9g is ON HOLD	+	The entry 6y9g is ON HOLD until Paper Publication

	Authors: Chaloupkova, R., Damborsky, J., Marek, M.		Authors: Chaloupkova, R., Damborsky, J., Marek, M.
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	Description: Crystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)		Description: Crystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Damborsky, J]]
	[[Category: Marek, M]]		[[Category: Marek, M]]
		+	[[Category: Damborsky, J]]
	[[Category: Chaloupkova, R]]		[[Category: Chaloupkova, R]]

OCA: Protected "6y9g" [edit=sysop:move=sysop]

OCA — Wed, 18 Mar 2020 08:39:06 GMT

Protected "6y9g" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:39, 18 March 2020

OCA: New page: '''Unreleased structure''' The entry 6y9g is ON HOLD Authors: Chaloupkova, R., Damborsky, J., Marek, M. Description: Crystal structure of putative ancestral haloalkane dehalogenase Anc...

OCA — Wed, 18 Mar 2020 08:39:05 GMT

New page: '''Unreleased structure''' The entry 6y9g is ON HOLD Authors: Chaloupkova, R., Damborsky, J., Marek, M. Description: Crystal structure of putative ancestral haloalkane dehalogenase Anc...

New page

'''Unreleased structure'''

The entry 6y9g is ON HOLD

Authors: Chaloupkova, R., Damborsky, J., Marek, M.

Description: Crystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)
[[Category: Unreleased Structures]]
[[Category: Damborsky, J]]
[[Category: Marek, M]]
[[Category: Chaloupkova, R]]