3nz1 - Revision history

OCA at 10:02, 14 February 2024

OCA — Wed, 14 Feb 2024 10:02:20 GMT

←Older revision		Revision as of 10:02, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='3nz1' size='340' side='right'caption='[[3nz1]], [[Resolution\|resolution]] 1.56Å' scene=''>		<StructureSection load='3nz1' size='340' side='right'caption='[[3nz1]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_35091 Atcc 35091~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=3NY:5~~-~~NITRO-1H-BENZOTRIAZOLE'>3NY</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 1.56Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3nyz\|3nyz]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE~~, ~~SSO0895, trpC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48]~~ </~~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=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [https://pdbe.org/3nz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [https://www.ebi.ac.uk/pdbsum/3nz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nz1 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=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [https://pdbe.org/3nz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [https://www.ebi.ac.uk/pdbsum/3nz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nz1 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/TRPC_SACS2 TRPC_SACS2]
-	A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes.	+
-		+
-	~~Iterative approach to computational enzyme design.,Privett HK, Kiss G, Lee TM, Blomberg R, Chica RA, Thomas LM, Hilvert D, Houk KN, Mayo SL Proc Natl Acad Sci U S A. 2012 Mar 6;109(10)~~:~~3790-5. Epub 2012 Feb 22. PMID:22357762<ref>PMID:22357762<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3nz1" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
-	*[[~~Indole-3-glycerol phosphate synthase~~\|~~Indole-3-glycerol phosphate synthase~~]]	+	*[[IGPS 3D structures\|IGPS 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 35091]]
-	[[Category: Indole-3-glycerol-phosphate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kaiser, J T~~]]	+	[[Category: Saccharolobus solfataricus]]
-	[[Category: ~~Lee, T M~~]]	+	[[Category: Kaiser JT]]
-	[[Category: ~~Mayo, S L~~]]	+	[[Category: Lee TM]]
-	[[Category: ~~Privett, H K~~]]	+	[[Category: Mayo SL]]
-	[[Category: ~~Kemp elimination enzyme]]~~	+	[[Category: Privett HK]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 07:12, 12 May 2022

OCA — Thu, 12 May 2022 07:12:09 GMT

←Older revision		Revision as of 07:12, 12 May 2022
Line 1:		Line 1:

	==Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole==		==Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole==
-	<StructureSection load='3nz1' size='340' side='right' caption='[[3nz1]], [[Resolution\|resolution]] 1.56Å' scene=''>	+	<StructureSection load='3nz1' size='340' side='right'caption='[[3nz1]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nyz\|3nyz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nyz\|3nyz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </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=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [~~http~~://pdbe.org/3nz1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3nz1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3nz1 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=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [https://pdbe.org/3nz1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [https://www.ebi.ac.uk/pdbsum/3nz1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nz1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	[[Category: Atcc 35091]]		[[Category: Atcc 35091]]
	[[Category: Indole-3-glycerol-phosphate synthase]]		[[Category: Indole-3-glycerol-phosphate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Kaiser, J T]]		[[Category: Kaiser, J T]]
	[[Category: Lee, T M]]		[[Category: Lee, T M]]

OCA at 16:46, 4 August 2016

OCA — Thu, 04 Aug 2016 16:46:07 GMT

←Older revision		Revision as of 16:46, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole==		==Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole==
	<StructureSection load='3nz1' size='340' side='right' caption='[[3nz1]], [[Resolution\|resolution]] 1.56Å' scene=''>		<StructureSection load='3nz1' size='340' side='right' caption='[[3nz1]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus Sulfolobus solfataricus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nyz\|3nyz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nyz\|3nyz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ~~Sulfolobus solfataricus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </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=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3nz1 PDBsum]</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=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [http://pdbe.org/3nz1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3nz1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nz1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3nz1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 35091]]
	[[Category: Indole-3-glycerol-phosphate synthase]]		[[Category: Indole-3-glycerol-phosphate synthase]]
-	[[Category: Sulfolobus solfataricus]]
	[[Category: Kaiser, J T]]		[[Category: Kaiser, J T]]
	[[Category: Lee, T M]]		[[Category: Lee, T M]]

OCA at 23:22, 3 January 2015

OCA — Sat, 03 Jan 2015 23:22:12 GMT

←Older revision		Revision as of 23:22, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nyz\|3nyz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nyz\|3nyz]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3nz1 PDBsum]</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=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3nz1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 15:
	Iterative approach to computational enzyme design.,Privett HK, Kiss G, Lee TM, Blomberg R, Chica RA, Thomas LM, Hilvert D, Houk KN, Mayo SL Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3790-5. Epub 2012 Feb 22. PMID:22357762<ref>PMID:22357762</ref>		Iterative approach to computational enzyme design.,Privett HK, Kiss G, Lee TM, Blomberg R, Chica RA, Thomas LM, Hilvert D, Houk KN, Mayo SL Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3790-5. Epub 2012 Feb 22. PMID:22357762<ref>PMID:22357762</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+
		+	==See Also==
		+	*[[Indole-3-glycerol phosphate synthase\|Indole-3-glycerol phosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	[[Category: Indole-3-glycerol-phosphate synthase]]		[[Category: Indole-3-glycerol-phosphate synthase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
-	[[Category: Kaiser, J T.]]	+	[[Category: Kaiser, J T]]
-	[[Category: Lee, T M.]]	+	[[Category: Lee, T M]]
-	[[Category: Mayo, S L.]]	+	[[Category: Mayo, S L]]
-	[[Category: Privett, H K.]]	+	[[Category: Privett, H K]]
	[[Category: Kemp elimination enzyme]]		[[Category: Kemp elimination enzyme]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 10:41, 28 May 2014

OCA — Wed, 28 May 2014 10:41:35 GMT

←Older revision		Revision as of 10:41, 28 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3nz1.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole==
		+	<StructureSection load='3nz1' size='340' side='right' caption='[[3nz1]], [[Resolution\|resolution]] 1.56Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NZ1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3NY:5-NITRO-1H-BENZOTRIAZOLE'>3NY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nyz\|3nyz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE, SSO0895, trpC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indole-3-glycerol-phosphate_synthase Indole-3-glycerol-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.48 4.1.1.48] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nz1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nz1 RCSB], [http://www.ebi.ac.uk/pdbsum/3nz1 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes.

-	~~<!--~~	+	Iterative approach to computational enzyme design.,Privett HK, Kiss G, Lee TM, Blomberg R, Chica RA, Thomas LM, Hilvert D, Houk KN, Mayo SL Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3790-5. Epub 2012 Feb 22. PMID:22357762<ref>PMID:22357762</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3nz1"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_3nz1\| PDB=3nz1 \| SCENE= }}~~	+

-	~~===Crystal Structure~~ of ~~Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22357762}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22357762 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22357762}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3nz1]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022357762<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Indole-3-glycerol-phosphate synthase]]		[[Category: Indole-3-glycerol-phosphate synthase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]

OCA at 08:23, 25 April 2012

OCA — Wed, 25 Apr 2012 08:23:16 GMT

←Older revision		Revision as of 08:23, 25 April 2012
Line 1:		Line 1:
-	[[Image:3nz1.~~jpg~~\|left\|200px]]	+	[[Image:3nz1.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole===		===Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22357762}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22357762 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22357762}}

	==About this Structure==		==About this Structure==
	[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA].		[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022357762</ref><references group="xtra"/>
	[[Category: Indole-3-glycerol-phosphate synthase]]		[[Category: Indole-3-glycerol-phosphate synthase]]
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]

OCA: Protected "3nz1" [edit=sysop:move=sysop]

OCA — Wed, 29 Jun 2011 06:19:11 GMT

Protected "3nz1" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:19, 29 June 2011

OCA at 06:19, 29 June 2011

OCA — Wed, 29 Jun 2011 06:19:07 GMT

←Older revision		Revision as of 06:19, 29 June 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3nz1.jpg\|left\|200px]]

-	The ~~entry 3nz1~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3nz1", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3nz1\| PDB=3nz1 \| SCENE= }}

-	~~Authors: Lee, T.M., Privett, H.K., Kaiser, J.T., Mayo, S.L.~~	+	===Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole===

-	Description: Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Aug 4 08~~:50:~~47 2010''~~	+	==About this Structure==
		+	[[3nz1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NZ1 OCA].
		+	[[Category: Indole-3-glycerol-phosphate synthase]]
		+	[[Category: Sulfolobus solfataricus]]
		+	[[Category: Kaiser, J T.]]
		+	[[Category: Lee, T M.]]
		+	[[Category: Mayo, S L.]]
		+	[[Category: Privett, H K.]]
		+	[[Category: Kemp elimination enzyme]]
		+	[[Category: Lyase]]
		+	[[Category: Tim barrel]]

OCA at 04:43, 4 August 2010

OCA — Wed, 04 Aug 2010 04:43:48 GMT

←Older revision		Revision as of 04:43, 4 August 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3nz1 is ON HOLD	+	The entry 3nz1 is ON HOLD until Paper Publication

	Authors: Lee, T.M., Privett, H.K., Kaiser, J.T., Mayo, S.L.		Authors: Lee, T.M., Privett, H.K., Kaiser, J.T., Mayo, S.L.
Line 7:		Line 7:
	Description: Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole		Description: Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 28 12~~:26:49 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 4 08:50:47 2010''

OCA: New page: '''Unreleased structure''' The entry 3nz1 is ON HOLD Authors: Lee, T.M., Privett, H.K., Kaiser, J.T., Mayo, S.L. Description: Crystal Structure of Kemp Elimination Catalyst 1A53-2 Comp...

OCA — Wed, 28 Jul 2010 08:20:07 GMT

New page: '''Unreleased structure''' The entry 3nz1 is ON HOLD Authors: Lee, T.M., Privett, H.K., Kaiser, J.T., Mayo, S.L. Description: Crystal Structure of Kemp Elimination Catalyst 1A53-2 Comp...

New page

'''Unreleased structure'''

The entry 3nz1 is ON HOLD

Authors: Lee, T.M., Privett, H.K., Kaiser, J.T., Mayo, S.L.

Description: Crystal Structure of Kemp Elimination Catalyst 1A53-2 Complexed with Transition State Analog 5-Nitro Benzotriazole

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:26:49 2010''