5rgf - Revision history

OCA at 13:48, 1 March 2024

2024-03-01T13:48:02Z

←Older revision		Revision as of 13:48, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='5rgf' size='340' side='right'caption='[[5rgf]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='5rgf' size='340' side='right'caption='[[5rgf]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5rgf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Theau Theau~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RGF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5rgf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RGF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=6NT:6~~-~~NITROBENZOTRIAZOLE'>6NT</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.46Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Endo-1~~,~~4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NT:6-NITROBENZOTRIAZOLE'>6NT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgf OCA], [https://pdbe.org/5rgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rgf RCSB], [https://www.ebi.ac.uk/pdbsum/5rgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgf ProSAT]</span></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=5rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgf OCA], [https://pdbe.org/5rgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rgf RCSB], [https://www.ebi.ac.uk/pdbsum/5rgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgf ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/XYNA_THEAU XYNA_THEAU]
-	The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M(-1)s(-1)). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M(-1)s(-1)) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.	+
-		+
-	Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.,Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA Nat Commun. 2020 Sep 23;11(1):~~4808. doi: 10.1038~~/~~s41467-020-18619-x. PMID:32968058<ref>PMID:32968058<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5rgf" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Kemp eliminase\|Kemp eliminase]]		*[[Kemp eliminase\|Kemp eliminase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Theau~~]]	+	[[Category: Thermoascus aurantiacus]]
-	[[Category: Broom, A]]	+	[[Category: Broom A]]
-	[[Category: Chica~~, R A~~]]	+	[[Category: Chica RA]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Fraser JS]]
-	[[Category: Rakotoharisoa~~, R V~~]]	+	[[Category: Rakotoharisoa RV]]
-	[[Category: Thompson~~, M C]]~~	+	[[Category: Thompson MC]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:30, 12 May 2021

2021-05-12T09:30:18Z

←Older revision		Revision as of 09:30, 12 May 2021
Line 3:		Line 3:
	<StructureSection load='5rgf' size='340' side='right'caption='[[5rgf]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='5rgf' size='340' side='right'caption='[[5rgf]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5rgf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Theau Theau]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5RGF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5rgf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Theau Theau]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RGF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NT:6-NITROBENZOTRIAZOLE'>6NT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NT:6-NITROBENZOTRIAZOLE'>6NT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=5rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgf OCA], [~~http~~://pdbe.org/5rgf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5rgf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5rgf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgf ProSAT]</span></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=5rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgf OCA], [https://pdbe.org/5rgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rgf RCSB], [https://www.ebi.ac.uk/pdbsum/5rgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:59, 2 December 2020

2020-12-02T07:59:59Z

←Older revision		Revision as of 07:59, 2 December 2020
Line 1:		Line 1:

	==Crystal Structure of Kemp Eliminase HG4 with bound transition state analogue, 277K==		==Crystal Structure of Kemp Eliminase HG4 with bound transition state analogue, 277K==
-	<StructureSection load='5rgf' size='340' side='right'caption='[[5rgf]]' scene=''>	+	<StructureSection load='5rgf' size='340' side='right'caption='[[5rgf]], [[Resolution\|resolution]] 1.46Å' 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=5RGF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5RGF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5rgf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Theau Theau]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5RGF 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=5rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgf OCA], [http://pdbe.org/5rgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5rgf RCSB], [http://www.ebi.ac.uk/pdbsum/5rgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgf 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=6NT:6-NITROBENZOTRIAZOLE'>6NT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=5rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgf OCA], [http://pdbe.org/5rgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5rgf RCSB], [http://www.ebi.ac.uk/pdbsum/5rgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M(-1)s(-1)). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M(-1)s(-1)) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.
		+
		+	Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.,Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA Nat Commun. 2020 Sep 23;11(1):4808. doi: 10.1038/s41467-020-18619-x. PMID:32968058<ref>PMID:32968058</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5rgf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Kemp eliminase\|Kemp eliminase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Broom A]]	+	[[Category: Theau]]
-	[[Category: Chica RA]]	+	[[Category: Broom, A]]
-	[[Category: Fraser JS]]	+	[[Category: Chica, R A]]
-	[[Category: Rakotoharisoa RV]]	+	[[Category: Fraser, J S]]
-	[[Category: Thompson MC]]	+	[[Category: Rakotoharisoa, R V]]
		+	[[Category: Thompson, M C]]
		+	[[Category: Hydrolase]]

OCA at 10:44, 22 July 2020

2020-07-22T10:44:42Z

←Older revision		Revision as of 10:44, 22 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5rgf ~~is ON HOLD~~	+	==Crystal Structure of Kemp Eliminase HG4 with bound transition state analogue, 277K==
-		+	<StructureSection load='5rgf' size='340' side='right'caption='[[5rgf]]' scene=''>
-	~~Authors~~: ~~Broom, A~~., ~~Rakotoharisoa, R~~.V., ~~Thompson~~, M.C., ~~Fraser, J~~.S., ~~Chica, R~~.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5RGF FirstGlance]. <br>
-	~~Description: Crystal Structure of Kemp Eliminase HG4 with bound transition state analogue, 277K~~	+	</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=5rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgf OCA], [http://pdbe.org/5rgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5rgf RCSB], [http://www.ebi.ac.uk/pdbsum/5rgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgf ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Rakotoharisoa, R.V~~]]	+	__TOC__
-	[[Category: ~~Broom, A~~]]	+	</StructureSection>
-	[[Category: ~~Thompson, M.C~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Chica, R.A~~]]	+	[[Category: Broom A]]
-	[[Category: ~~Fraser, J.S~~]]	+	[[Category: Chica RA]]
		+	[[Category: Fraser JS]]
		+	[[Category: Rakotoharisoa RV]]
		+	[[Category: Thompson MC]]

OCA: Protected "5rgf" [edit=sysop:move=sysop]

2020-03-27T08:12:32Z

Protected "5rgf" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:12, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 5rgf is ON HOLD Authors: Broom, A., Rakotoharisoa, R.V., Thompson, M.C., Fraser, J.S., Chica, R.A. Description: Crystal Structure of Kemp Eliminase...

2020-03-27T08:12:30Z

New page: '''Unreleased structure''' The entry 5rgf is ON HOLD Authors: Broom, A., Rakotoharisoa, R.V., Thompson, M.C., Fraser, J.S., Chica, R.A. Description: Crystal Structure of Kemp Eliminase...

New page

'''Unreleased structure'''

The entry 5rgf is ON HOLD

Authors: Broom, A., Rakotoharisoa, R.V., Thompson, M.C., Fraser, J.S., Chica, R.A.

Description: Crystal Structure of Kemp Eliminase HG4 with bound transition state analogue, 277K
[[Category: Unreleased Structures]]
[[Category: Rakotoharisoa, R.V]]
[[Category: Broom, A]]
[[Category: Thompson, M.C]]
[[Category: Chica, R.A]]
[[Category: Fraser, J.S]]