5z2x - Revision history

OCA at 08:44, 22 November 2023

OCA — Wed, 22 Nov 2023 08:44:31 GMT

←Older revision		Revision as of 08:44, 22 November 2023
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	<StructureSection load='5z2x' size='340' side='right'caption='[[5z2x]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='5z2x' size='340' side='right'caption='[[5z2x]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z2x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Z2X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z2x]] 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=5Z2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z2X 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=GOL:GLYCEROL'>GOL</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]] 1.98Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(NADP(+)) Alcohol dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.2 1.1.1.2] </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=GOL:GLYCEROL'>GOL</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~~://proteopedia.org/fgij/fg.htm?mol=5z2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2x OCA], [~~http~~://pdbe.org/5z2x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z2x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z2x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2x 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=5z2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2x OCA], [https://pdbe.org/5z2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z2x RCSB], [https://www.ebi.ac.uk/pdbsum/5z2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2x 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 H~~]]	+	[[Category: Xu GC]]
-	[[Category: Zhou~~, J Y]]~~	+	[[Category: ZHou JH]]
-	~~[[Category: Nadph]]~~	+	[[Category: Zhou JY]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 21:13, 28 October 2020

OCA — Wed, 28 Oct 2020 21:13:51 GMT

←Older revision		Revision as of 21:13, 28 October 2020
Line 1:		Line 1:

	==Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)==		==Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)==
-	<StructureSection load='5z2x' size='340' side='right' caption='[[5z2x]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='5z2x' size='340' side='right'caption='[[5z2x]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z2x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z2X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z2x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z2X 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=GOL:GLYCEROL'>GOL</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=GOL:GLYCEROL'>GOL</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(NADP(+)) Alcohol dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.2 1.1.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(NADP(+)) Alcohol dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.2 1.1.1.2] </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=5z2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2x OCA], [http://pdbe.org/5z2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2x RCSB], [http://www.ebi.ac.uk/pdbsum/5z2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2x 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=5z2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2x OCA], [http://pdbe.org/5z2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2x RCSB], [http://www.ebi.ac.uk/pdbsum/5z2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2x 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 5z2x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5z2x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__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 06:07:07 GMT

←Older revision		Revision as of 06:07, 2 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z2x is ~~ON HOLD~~	+	==Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)==
		+	<StructureSection load='5z2x' size='340' side='right' caption='[[5z2x]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z2x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z2X 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=GOL:GLYCEROL'>GOL</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(NADP(+)) Alcohol dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.2 1.1.1.2] </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=5z2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2x OCA], [http://pdbe.org/5z2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2x RCSB], [http://www.ebi.ac.uk/pdbsum/5z2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2x 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.~~, Wu, L., Rao, Y~~.J.~~, ~~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: Structure~~ of ~~Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)~~	+	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 5z2x" 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 H]]
		+	[[Category: Zhou, J Y]]
		+	[[Category: Nadph]]
		+	[[Category: Oxidoreductase]]

OCA at 04:57, 7 February 2018

OCA — Wed, 07 Feb 2018 04:57:52 GMT

←Older revision		Revision as of 04:57, 7 February 2018
Line 3:		Line 3:
	The entry 5z2x is ON HOLD		The entry 5z2x is ON HOLD

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

	Description: Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)		Description: Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)
Line 10:		Line 10:
	[[Category: Wu, L]]		[[Category: Wu, L]]
	[[Category: Zhou, J.Y]]		[[Category: Zhou, J.Y]]
-	[[Category: Hou, X.D]]
	[[Category: Ni, Y]]		[[Category: Ni, Y]]
		+	[[Category: Hou, X.D]]
	[[Category: Wang, Y]]		[[Category: Wang, Y]]
	[[Category: Rao, Y.J]]		[[Category: Rao, Y.J]]
	[[Category: Zhou, J.H]]		[[Category: Zhou, J.H]]

OCA: Protected "5z2x" [edit=sysop:move=sysop]

OCA — Wed, 10 Jan 2018 07:07:07 GMT

Protected "5z2x" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:07, 10 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z2x is ON HOLD Authors: Ni, Y., Zhou, J.H., Wang, Y., ZHou, J.Y., Hou, X.D., Rao, Y.J., Xu, G.C., Wu, l. Description: Structure of Alcohol dehydro...

OCA — Wed, 10 Jan 2018 07:07:06 GMT

New page: '''Unreleased structure''' The entry 5z2x is ON HOLD Authors: Ni, Y., Zhou, J.H., Wang, Y., ZHou, J.Y., Hou, X.D., Rao, Y.J., Xu, G.C., Wu, l. Description: Structure of Alcohol dehydro...

New page

'''Unreleased structure'''

The entry 5z2x is ON HOLD

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

Description: Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)
[[Category: Unreleased Structures]]
[[Category: Xu, G.C]]
[[Category: Wu, L]]
[[Category: Zhou, J.Y]]
[[Category: Hou, X.D]]
[[Category: Ni, Y]]
[[Category: Wang, Y]]
[[Category: Rao, Y.J]]
[[Category: Zhou, J.H]]