7qni - Revision history

OCA at 07:57, 7 February 2024

2024-02-07T07:57:55Z

←Older revision		Revision as of 07:57, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7qni]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QNI FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qni]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QNI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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]] 1.73Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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=7qni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qni OCA], [https://pdbe.org/7qni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qni RCSB], [https://www.ebi.ac.uk/pdbsum/7qni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qni 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=7qni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qni OCA], [https://pdbe.org/7qni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qni RCSB], [https://www.ebi.ac.uk/pdbsum/7qni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qni ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/FUCO_ECO57 FUCO_ECO57]		[https://www.uniprot.org/uniprot/FUCO_ECO57 FUCO_ECO57]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A group-III iron containing 1,2-propanediol oxidoreductase, FucO, (also known as lactaldehyde reductase) from Escherichia coli was examined regarding its structure-dynamics-function relationships in the catalysis of the NADH-dependent reduction of (2S)-lactaldehyde. Crystal structures of FucO variants in the presence or absence of cofactors have been determined, illustrating large domain movements between the apo and holo enzyme structures. Different structures of FucO variants co-crystallized with NAD(+) or NADH together with substrate further suggest dynamic properties of the nicotinamide moiety of the coenzyme that are important for the reaction mechanism. Modelling of the native substrate (2S)-lactaldehyde into the active site can explain the stereoselectivity exhibited by the enzyme, with a critical hydrogen bond interaction between the (2S)-hydroxyl and the side-chain of N151, as well as the previously experimentally demonstrated pro-(R) selectivity in hydride transfer from NADH to the aldehydic carbon. Furthermore, the deuterium kinetic isotope effect of hydride transfer suggests that reduction chemistry is the main rate-limiting step for turnover which is not the case in FucO catalysed alcohol oxidation. We further propose that a water molecule in the active site - hydrogen bonded to a conserved histidine (H267) and the 2'-hydroxyl of the coenzyme ribose - functions as a catalytic proton donor in the protonation of the product alcohol. A hydrogen bond network of water molecules and the side-chains of amino acid residues D360 and H267 links bulk solvent to this proposed catalytic water molecule.
-
-	Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics.,Zavarise A, Sridhar S, Kiema TR, Wierenga RK, Widersten M FEBS J. 2022 Aug 24. doi: 10.1111/febs.16603. PMID:36002154<ref>PMID:36002154</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7qni" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:18, 19 October 2022

2022-10-19T19:18:59Z

←Older revision		Revision as of 19:18, 19 October 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7qni is ~~ON HOLD until Paper~~ Publication	+	==CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT L259V==
		+	<StructureSection load='7qni' size='340' side='right'caption='[[7qni]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7qni]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QNI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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=7qni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qni OCA], [https://pdbe.org/7qni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qni RCSB], [https://www.ebi.ac.uk/pdbsum/7qni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qni ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/FUCO_ECO57 FUCO_ECO57]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A group-III iron containing 1,2-propanediol oxidoreductase, FucO, (also known as lactaldehyde reductase) from Escherichia coli was examined regarding its structure-dynamics-function relationships in the catalysis of the NADH-dependent reduction of (2S)-lactaldehyde. Crystal structures of FucO variants in the presence or absence of cofactors have been determined, illustrating large domain movements between the apo and holo enzyme structures. Different structures of FucO variants co-crystallized with NAD(+) or NADH together with substrate further suggest dynamic properties of the nicotinamide moiety of the coenzyme that are important for the reaction mechanism. Modelling of the native substrate (2S)-lactaldehyde into the active site can explain the stereoselectivity exhibited by the enzyme, with a critical hydrogen bond interaction between the (2S)-hydroxyl and the side-chain of N151, as well as the previously experimentally demonstrated pro-(R) selectivity in hydride transfer from NADH to the aldehydic carbon. Furthermore, the deuterium kinetic isotope effect of hydride transfer suggests that reduction chemistry is the main rate-limiting step for turnover which is not the case in FucO catalysed alcohol oxidation. We further propose that a water molecule in the active site - hydrogen bonded to a conserved histidine (H267) and the 2'-hydroxyl of the coenzyme ribose - functions as a catalytic proton donor in the protonation of the product alcohol. A hydrogen bond network of water molecules and the side-chains of amino acid residues D360 and H267 links bulk solvent to this proposed catalytic water molecule.

-	~~Authors: Sridhar~~, S., ~~Kiema~~, ~~T.R.~~, Wierenga~~, R.K.~~, Widersten, M.	+	Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics.,Zavarise A, Sridhar S, Kiema TR, Wierenga RK, Widersten M FEBS J. 2022 Aug 24. doi: 10.1111/febs.16603. PMID:36002154<ref>PMID:36002154</ref>

-	~~Description: CRYSTAL STRUCTURE OF E~~.~~coli ALCOHOL DEHYDROGENASE~~ -~~FucO MUTANT L259V~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Kiema, T.R~~]]	+	<div class="pdbe-citations 7qni" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Wierenga, R.K~~]]	+	== References ==
-	[[Category: Sridhar, S]]	+	<references/>
-	[[Category: Widersten, M]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli str. K-12 substr. MG1655]]
		+	[[Category: Large Structures]]
		+	[[Category: Kiema TR]]
		+	[[Category: Sridhar S]]
		+	[[Category: Widersten M]]
		+	[[Category: Wierenga RK]]

OCA at 06:04, 9 February 2022

2022-02-09T06:04:30Z

←Older revision		Revision as of 06:04, 9 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7qni is ON HOLD	+	The entry 7qni is ON HOLD until Paper Publication

	Authors: Sridhar, S., Kiema, T.R., Wierenga, R.K., Widersten, M.		Authors: Sridhar, S., Kiema, T.R., Wierenga, R.K., Widersten, M.
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	Description: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE -FucO MUTANT L259V		Description: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE -FucO MUTANT L259V
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Kiema, T.R]]
	[[Category: Wierenga, R.K]]		[[Category: Wierenga, R.K]]
	[[Category: Sridhar, S]]		[[Category: Sridhar, S]]
	[[Category: Widersten, M]]		[[Category: Widersten, M]]
-	[[Category: Kiema, T.R]]

OCA: Protected "7qni" [edit=sysop:move=sysop]

2021-12-29T11:56:27Z

Protected "7qni" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:56, 29 December 2021

OCA: New page: '''Unreleased structure''' The entry 7qni is ON HOLD Authors: Sridhar, S., Kiema, T.R., Wierenga, R.K., Widersten, M. Description: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE -Fu...

2021-12-29T11:56:26Z

New page: '''Unreleased structure''' The entry 7qni is ON HOLD Authors: Sridhar, S., Kiema, T.R., Wierenga, R.K., Widersten, M. Description: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE -Fu...

New page

'''Unreleased structure'''

The entry 7qni is ON HOLD

Authors: Sridhar, S., Kiema, T.R., Wierenga, R.K., Widersten, M.

Description: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE -FucO MUTANT L259V
[[Category: Unreleased Structures]]
[[Category: Wierenga, R.K]]
[[Category: Sridhar, S]]
[[Category: Widersten, M]]
[[Category: Kiema, T.R]]