6dnj - Revision history

OCA at 06:10, 11 October 2023

OCA — Wed, 11 Oct 2023 06:10:21 GMT

←Older revision		Revision as of 06:10, 11 October 2023
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	==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5==		==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5==
-	<StructureSection load='6dnj' size='340' side='right' caption='[[6dnj]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='6dnj' size='340' side='right'caption='[[6dnj]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dnj]] is a 1 chain structure with sequence from [~~http~~://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=6DNJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DNJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dnj]] is a 1 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=6DNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DNJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H5J:5-nitro-1,2-benzoxazole'>H5J</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.65Å</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=6dnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dnj OCA], [~~http~~://pdbe.org/6dnj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dnj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dnj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dnj ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H5J:5-nitro-1,2-benzoxazole'>H5J</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6dnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dnj OCA], [https://pdbe.org/6dnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dnj RCSB], [https://www.ebi.ac.uk/pdbsum/6dnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dnj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 6dnj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dnj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Kemp eliminase\|Kemp eliminase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Large Structures]]
-	[[Category: Carr~~, P D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Hong, N S]]	+	[[Category: Carr PD]]
-	[[Category: Jackson~~, C J]]~~	+	[[Category: Hong N-S]]
-	~~[[Category: De novo protein]]~~	+	[[Category: Jackson CJ]]
-	~~[[Category: Directed evolution]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 09:46, 13 February 2019

OCA — Wed, 13 Feb 2019 09:46:22 GMT

←Older revision		Revision as of 09:46, 13 February 2019
Line 3:		Line 3:
	<StructureSection load='6dnj' size='340' side='right' caption='[[6dnj]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='6dnj' size='340' side='right' caption='[[6dnj]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dnj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DNJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dnj]] is a 1 chain structure with sequence from [http://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=6DNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DNJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H5J:5-nitro-1,2-benzoxazole'>H5J</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H5J:5-nitro-1,2-benzoxazole'>H5J</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=6dnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dnj OCA], [http://pdbe.org/6dnj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dnj RCSB], [http://www.ebi.ac.uk/pdbsum/6dnj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dnj ProSAT]</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=6dnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dnj OCA], [http://pdbe.org/6dnj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dnj RCSB], [http://www.ebi.ac.uk/pdbsum/6dnj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dnj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.
		+
		+	The evolution of multiple active site configurations in a designed enzyme.,Hong NS, Petrovic D, Lee R, Gryn'ova G, Purg M, Saunders J, Bauer P, Carr PD, Lin CY, Mabbitt PD, Zhang W, Altamore T, Easton C, Coote ML, Kamerlin SCL, Jackson CJ Nat Commun. 2018 Sep 25;9(1):3900. doi: 10.1038/s41467-018-06305-y. PMID:30254369<ref>PMID:30254369</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dnj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Carr, P D]]		[[Category: Carr, P D]]
	[[Category: Hong, N S]]		[[Category: Hong, N S]]

OCA at 18:51, 1 August 2018

OCA — Wed, 01 Aug 2018 18:51:00 GMT

←Older revision		Revision as of 18:51, 1 August 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6dnj is ~~ON HOLD until Paper Publication~~	+	==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5==
-		+	<StructureSection load='6dnj' size='340' side='right' caption='[[6dnj]], [[Resolution\|resolution]] 1.65Å' scene=''>
-	~~Authors~~: ~~Jackson~~, C.J., ~~Hong~~, N.-S., ~~Carr~~, P.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dnj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DNJ FirstGlance]. <br>
-	~~Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 28 round 5~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H5J:5-nitro-1,2-benzoxazole'>H5J</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6dnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dnj OCA], [http://pdbe.org/6dnj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dnj RCSB], [http://www.ebi.ac.uk/pdbsum/6dnj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dnj ProSAT]</span></td></tr>
-	[[Category: Hong, N.-S]]	+	</table>
-	[[Category: Jackson, C.J]]	+	__TOC__
-	[[Category: ~~Carr, P.D~~]]	+	</StructureSection>
		+	[[Category: Carr, P D]]
		+	[[Category: Hong, N S]]
		+	[[Category: Jackson, C J]]
		+	[[Category: De novo protein]]
		+	[[Category: Directed evolution]]
		+	[[Category: Lyase]]

OCA at 05:21, 18 July 2018

OCA — Wed, 18 Jul 2018 05:21:01 GMT

←Older revision		Revision as of 05:21, 18 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Jackson, C.J., Hong, N.-S., Carr, P.D.		Authors: Jackson, C.J., Hong, N.-S., Carr, P.D.

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

OCA — Thu, 14 Jun 2018 05:47:49 GMT

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

←Older revision

Revision as of 05:47, 14 June 2018

OCA: New page: '''Unreleased structure''' The entry 6dnj is ON HOLD Authors: Jackson, C.J., Hong, N.-S., Carr, P.D. Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 28 round...

OCA — Thu, 14 Jun 2018 05:47:48 GMT

New page: '''Unreleased structure''' The entry 6dnj is ON HOLD Authors: Jackson, C.J., Hong, N.-S., Carr, P.D. Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 28 round...

New page

'''Unreleased structure'''

The entry 6dnj is ON HOLD

Authors: Jackson, C.J., Hong, N.-S., Carr, P.D.

Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 28 round 5
[[Category: Unreleased Structures]]
[[Category: Hong, N.-S]]
[[Category: Jackson, C.J]]
[[Category: Carr, P.D]]