6c7v - Revision history

OCA at 14:57, 4 October 2023

OCA — Wed, 04 Oct 2023 14:57:54 GMT

←Older revision		Revision as of 14:57, 4 October 2023
Line 1:		Line 1:

	==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 22 round 5==		==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 22 round 5==
-	<StructureSection load='6c7v' size='340' side='right' caption='[[6c7v]], [[Resolution\|resolution]] 1.64Å' scene=''>	+	<StructureSection load='6c7v' size='340' side='right'caption='[[6c7v]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c7v]] 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=6C7V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6C7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c7v]] 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=6C7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C7V FirstGlance]. <br>
-	</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=6c7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c7v OCA], [~~http~~://pdbe.org/6c7v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6c7v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6c7v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6c7v 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]] 1.64Å</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=6c7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c7v OCA], [https://pdbe.org/6c7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c7v RCSB], [https://www.ebi.ac.uk/pdbsum/6c7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c7v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 6c7v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6c7v" 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: Ke07]]~~	+
-	~~[[Category: Kemp eliminase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 09:44, 13 February 2019

OCA — Wed, 13 Feb 2019 09:44:40 GMT

←Older revision		Revision as of 09:44, 13 February 2019
Line 3:		Line 3:
	<StructureSection load='6c7v' size='340' side='right' caption='[[6c7v]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='6c7v' size='340' side='right' caption='[[6c7v]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c7v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c7v]] 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=6C7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C7V FirstGlance]. <br>
	</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=6c7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c7v OCA], [http://pdbe.org/6c7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c7v RCSB], [http://www.ebi.ac.uk/pdbsum/6c7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c7v ProSAT]</span></td></tr>		</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=6c7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c7v OCA], [http://pdbe.org/6c7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c7v RCSB], [http://www.ebi.ac.uk/pdbsum/6c7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c7v 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 6c7v" 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 18:46, 1 August 2018

OCA — Wed, 01 Aug 2018 18:46:13 GMT

←Older revision		Revision as of 18:46, 1 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6c7v ~~is ON HOLD until Paper Publication~~	+	==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 22 round 5==
-		+	<StructureSection load='6c7v' size='340' side='right' caption='[[6c7v]], [[Resolution\|resolution]] 1.64Å' scene=''>
-	~~Authors~~: ~~Jackson~~, C.J., ~~Hong~~, N.-S., ~~Carr~~, P.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6c7v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C7V FirstGlance]. <br>
-	~~Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 22 round 5~~	+	</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=6c7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c7v OCA], [http://pdbe.org/6c7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c7v RCSB], [http://www.ebi.ac.uk/pdbsum/6c7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c7v ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Hong, N.-S]]	+	__TOC__
-	[[Category: Jackson, C.J]]	+	</StructureSection>
-	[[Category: ~~Carr, P.D~~]]	+	[[Category: Carr, P D]]
		+	[[Category: Hong, N S]]
		+	[[Category: Jackson, C J]]
		+	[[Category: De novo protein]]
		+	[[Category: Directed evolution]]
		+	[[Category: Ke07]]
		+	[[Category: Kemp eliminase]]
		+	[[Category: Lyase]]

OCA at 04:14, 6 June 2018

OCA — Wed, 06 Jun 2018 04:14:14 GMT

←Older revision		Revision as of 04:14, 6 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6c7v is ON HOLD	+	The entry 6c7v 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 "6c7v" [edit=sysop:move=sysop]

OCA — Wed, 31 Jan 2018 04:49:51 GMT

Protected "6c7v" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:49, 31 January 2018

OCA: New page: '''Unreleased structure''' The entry 6c7v is ON HOLD Authors: Jackson, C.J., Hong, N.-S., Carr, P.D. Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 22 round...

OCA — Wed, 31 Jan 2018 04:49:50 GMT

New page: '''Unreleased structure''' The entry 6c7v is ON HOLD Authors: Jackson, C.J., Hong, N.-S., Carr, P.D. Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 22 round...

New page

'''Unreleased structure'''

The entry 6c7v is ON HOLD

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

Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 22 round 5
[[Category: Unreleased Structures]]
[[Category: Hong, N.-S]]
[[Category: Jackson, C.J]]
[[Category: Carr, P.D]]