5zec - Revision history

OCA at 08:52, 22 November 2023

OCA — Wed, 22 Nov 2023 08:52:18 GMT

←Older revision		Revision as of 08:52, 22 November 2023
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	<StructureSection load='5zec' size='340' side='right'caption='[[5zec]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='5zec' size='340' side='right'caption='[[5zec]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zec]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZEC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zec]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vanderwaltozyma_polyspora_DSM_70294 Vanderwaltozyma polyspora DSM 70294]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZEC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.779Å</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=5zec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zec OCA], [~~http~~://pdbe.org/5zec PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zec RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zec PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zec ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5zec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zec OCA], [https://pdbe.org/5zec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zec RCSB], [https://www.ebi.ac.uk/pdbsum/5zec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zec ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A7TM80_VANPO A7TM80_VANPO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hou~~, X D~~]]	+	[[Category: Vanderwaltozyma polyspora DSM 70294]]
-	[[Category: Ni, Y]]	+	[[Category: Hou XD]]
-	[[Category: Rao~~, Y J~~]]	+	[[Category: Ni Y]]
-	[[Category: Wang, Y]]	+	[[Category: Rao YJ]]
-	[[Category: Wu, L]]	+	[[Category: Wang Y]]
-	[[Category: Xu~~, G C~~]]	+	[[Category: Wu L]]
-	[[Category: ZHou~~, J Y~~]]	+	[[Category: Xu GC]]
-	[[Category: Zhou~~, J H]]~~	+	[[Category: ZHou JY]]
-	~~[[Category: Isomerase]]~~	+	[[Category: Zhou JH]]
-	~~[[Category: Nadph~~]]	+

OCA at 21:18, 28 October 2020

OCA — Wed, 28 Oct 2020 21:18:46 GMT

←Older revision		Revision as of 21:18, 28 October 2020
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	==Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Q136N/F161V/S196G/E214G/S237C)==		==Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Q136N/F161V/S196G/E214G/S237C)==
-	<StructureSection load='5zec' size='340' side='right' caption='[[5zec]], [[Resolution\|resolution]] 1.78Å' scene=''>	+	<StructureSection load='5zec' size='340' side='right'caption='[[5zec]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zec]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZEC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zec]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZEC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5zec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zec OCA], [http://pdbe.org/5zec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zec RCSB], [http://www.ebi.ac.uk/pdbsum/5zec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zec ProSAT]</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=5zec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zec OCA], [http://pdbe.org/5zec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zec RCSB], [http://www.ebi.ac.uk/pdbsum/5zec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zec ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hou, X D]]		[[Category: Hou, X D]]
	[[Category: Ni, Y]]		[[Category: Ni, Y]]

OCA at 06:07, 2 January 2019

OCA — Wed, 02 Jan 2019 06:07:54 GMT

←Older revision		Revision as of 06:07, 2 January 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 5zec is ~~ON HOLD until Feb 27 2020~~	+	==Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Q136N/F161V/S196G/E214G/S237C)==
		+	<StructureSection load='5zec' size='340' side='right' caption='[[5zec]], [[Resolution\|resolution]] 1.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zec]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZEC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5zec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zec OCA], [http://pdbe.org/5zec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zec RCSB], [http://www.ebi.ac.uk/pdbsum/5zec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zec ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Diaryl ketones are important building blocks for synthesizing pharmaceuticals and are generally regarded as "difficult-to-reduce" ketones due to the large steric hindrance of their two bulky aromatic side chains. Alcohol dehydrogenase from Kluyveromyces polyspora ( KpADH) has been identified as a robust biocatalyst due to its high conversion of diaryl ketone substrate (4-chlorophenyl)(pyridine-2-yl)ketone (CPMK) with a moderate R-selectivity of 82% ee. To modulate the stereoselectivity of KpADH, a "polarity scanning" strategy was proposed, in which six key residues inside and at the entrance of the substrate binding pocket were identified. After iterative combinatorial mutagenesis, variants Mu-R2 and Mu-S5 with enhanced (99.2% ee, R) and inverted (97.8% ee, S) stereoselectivity were obtained. The crystal structures of KpADH and two mutants in complex with NADPH were resolved to elucidate the evolution of enantioselective inversion. Based on MD simulation, Mu-R2-CPMKProR and Mu-S5-CPMKProS were more favorable in the formation of prereaction states. Interestingly, a quadrilateral plane formed by alpha-carbons of four residues (N136, V161, C237, and G214) was identified at the entrance of the substrate binding pocket of Mu-S5; this plane acts as a "polar gate" for substrates. Due to the discrepancy in charge characteristics between chlorophenyl and pyridine substituents, the pro- S orientation of CPMK is defined when it passes through the "polar gate" in Mu-S5, whereas the similar plane in wild-type is blocked by several aromatic residues. Our result paves the way for engineering stereocomplementary ADH toward bulky diaryl ketones and provides structural insight into the mechanism of stereoselective inversion.

-	~~Authors: Wang, Y~~., ~~ZHou~~, J.Y., ~~Hou~~, ~~X.D.~~, Xu, ~~G.C.~~, Rao, Y~~.J.~~, ~~Wu, L.~~, Zhou, J.H., ~~Ni, Y~~.	+	Structural Insight into Enantioselective Inversion of an Alcohol Dehydrogenase Reveals a "Polar Gate" in Stereorecognition of Diaryl Ketones.,Zhou J, Wang Y, Xu G, Wu L, Han R, Schwaneberg U, Rao Y, Zhao YL, Zhou J, Ni Y J Am Chem Soc. 2018 Oct 3;140(39):12645-12654. doi: 10.1021/jacs.8b08640. Epub, 2018 Sep 24. PMID:30247889<ref>PMID:30247889</ref>

-	~~Description: Crystal structure~~ of ~~Kluyveromyces polyspora ADH (KpADH) mutant (Q136N~~/~~F161V~~/~~S196G~~/~~E214G/S237C)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Xu, G.C]]~~	+	<div class="pdbe-citations 5zec" style="background-color:#fffaf0;"></div>
-	[[Category: Wu, ~~L]]~~	+	== References ==
-	~~[[Category: Zhou, J.Y~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hou, X D]]
	[[Category: Ni, Y]]		[[Category: Ni, Y]]
-	[[Category: ~~Hou~~, ~~X.D~~]]	+	[[Category: Rao, Y J]]
	[[Category: Wang, Y]]		[[Category: Wang, Y]]
-	[[Category: ~~Rao~~, Y.J]]	+	[[Category: Wu, L]]
-	[[Category: Zhou, J.H]]	+	[[Category: Xu, G C]]
		+	[[Category: ZHou, J Y]]
		+	[[Category: Zhou, J H]]
		+	[[Category: Isomerase]]
		+	[[Category: Nadph]]

OCA at 03:48, 25 April 2018

OCA — Wed, 25 Apr 2018 03:48:44 GMT

←Older revision		Revision as of 03:48, 25 April 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zec is ON HOLD	+	The entry 5zec is ON HOLD until Feb 27 2020

	Authors: Wang, Y., ZHou, J.Y., Hou, X.D., Xu, G.C., Rao, Y.J., Wu, L., Zhou, J.H., Ni, Y.		Authors: Wang, Y., ZHou, J.Y., Hou, X.D., Xu, G.C., Rao, Y.J., Wu, L., Zhou, J.H., Ni, Y.
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	Description: Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Q136N/F161V/S196G/E214G/S237C)		Description: Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Q136N/F161V/S196G/E214G/S237C)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Xu, G.C]]
	[[Category: Wu, L]]		[[Category: Wu, L]]
		+	[[Category: Zhou, J.Y]]
	[[Category: Ni, Y]]		[[Category: Ni, Y]]
	[[Category: Hou, X.D]]		[[Category: Hou, X.D]]
Line 13:		Line 15:
	[[Category: Rao, Y.J]]		[[Category: Rao, Y.J]]
	[[Category: Zhou, J.H]]		[[Category: Zhou, J.H]]
-	[[Category: Xu, G.C]]
-	[[Category: Zhou, J.Y]]

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

OCA — Thu, 08 Mar 2018 03:38:25 GMT

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

←Older revision

Revision as of 03:38, 8 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zec is ON HOLD Authors: Wang, Y., ZHou, J.Y., Hou, X.D., Xu, G.C., Rao, Y.J., Wu, L., Zhou, J.H., Ni, Y. Description: Crystal structure of Kluyver...

OCA — Thu, 08 Mar 2018 03:38:24 GMT

New page: '''Unreleased structure''' The entry 5zec is ON HOLD Authors: Wang, Y., ZHou, J.Y., Hou, X.D., Xu, G.C., Rao, Y.J., Wu, L., Zhou, J.H., Ni, Y. Description: Crystal structure of Kluyver...

New page

'''Unreleased structure'''

The entry 5zec is ON HOLD

Authors: Wang, Y., ZHou, J.Y., Hou, X.D., Xu, G.C., Rao, Y.J., Wu, L., Zhou, J.H., Ni, Y.

Description: Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Q136N/F161V/S196G/E214G/S237C)
[[Category: Unreleased Structures]]
[[Category: Wu, L]]
[[Category: Ni, Y]]
[[Category: Hou, X.D]]
[[Category: Wang, Y]]
[[Category: Rao, Y.J]]
[[Category: Zhou, J.H]]
[[Category: Xu, G.C]]
[[Category: Zhou, J.Y]]