5vjg - Revision history

OCA at 13:49, 4 October 2023

OCA — Wed, 04 Oct 2023 13:49:56 GMT

←Older revision		Revision as of 13:49, 4 October 2023
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	<StructureSection load='5vjg' size='340' side='right'caption='[[5vjg]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5vjg' size='340' side='right'caption='[[5vjg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vjg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VJG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vjg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VJG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=0BP:2,2~~-~~BIPYRIDINE'>0BP</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5vj5\|5vj5]], [[5vkr\|5vkr]], [[5vl0\|5vl0]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0BP:2,2-BIPYRIDINE'>0BP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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 Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1]~~ </~~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=5vjg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjg OCA], [https://pdbe.org/5vjg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vjg RCSB], [https://www.ebi.ac.uk/pdbsum/5vjg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjg ProSAT]</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=5vjg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjg OCA], [~~http~~://pdbe.org/5vjg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vjg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vjg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjg ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ADH1E_HORSE ADH1E_HORSE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Plapp, B V]]~~	+	[[Category: Baskar Raj S]]
-	~~[[Category:~~ Raj, S ~~Baskar~~]]	+	[[Category: Plapp BV]]
-	[[Category: ~~2'bipyridine]]~~	+
-	~~[[Category: Horse liver]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Zinc chelation~~]]	+

OCA at 17:18, 11 December 2019

OCA — Wed, 11 Dec 2019 17:18:17 GMT

←Older revision		Revision as of 17:18, 11 December 2019
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	==horse liver alcohol dehydrogenase complexed with 2,2'bipyridine==		==horse liver alcohol dehydrogenase complexed with 2,2'bipyridine==
-	<StructureSection load='5vjg' size='340' side='right' caption='[[5vjg]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5vjg' size='340' side='right'caption='[[5vjg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vjg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJG FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vjg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJG FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5vjg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vjg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Alcohol dehydrogenase]]		[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
		+	[[Category: Large Structures]]
	[[Category: Plapp, B V]]		[[Category: Plapp, B V]]
	[[Category: Raj, S Baskar]]		[[Category: Raj, S Baskar]]

OCA at 04:10, 4 August 2017

OCA — Fri, 04 Aug 2017 04:10:41 GMT

←Older revision		Revision as of 04:10, 4 August 2017
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~We have studied~~ the ~~binding~~ of ~~two inhibitor molecules, imidazole and 1,10~~-~~phenanthroline~~, ~~to liver alcohol dehydrogenase~~ by ~~crystallographic methods~~. X-ray ~~data for the imidazole complex were collected to 0~~.~~29-nm resolution~~ and ~~for~~ the 1,10-~~phenanthroline complex to 0.45~~-~~nm resolution. In both cases we found only one peak in the difference electron density maps close to the active zinc atom~~. The ~~peak corresponding to~~ 1,10-phenanthroline ~~overlaps~~ the ~~site~~ of the ~~density~~ of the zinc~~-bound water~~ in the apoenzyme ~~and~~ the ~~imidazole density partly overlaps this density~~. ~~We can not discern any additional peaks close to~~ the ~~zinc atom~~ which ~~would correspond to new positions of bound water. We thus conclude that both these inhibitors bind~~ to the catalytic zinc ~~atom~~ and ~~that upon binding they displace~~ the water ~~molecule that~~ is ~~firmly~~ bound to ~~this~~ zinc ~~atom in~~ the ~~apoenzyme~~. ~~We do not see any structural changes~~ in the ~~remaining part~~ of the ~~molecule~~.	+	During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism might involve a pentacoordinated zinc or a double-displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. The apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators 2,2'-bipyridine and 1,10-phenanthroline displace the water and form a pentacoordinated zinc. The enzyme-NADH complex has a closed conformation similar to that of ternary complexes with coenzyme and substrate analogues; the coordination of the catalytic zinc is similar to that found in the apoenzyme, except that a minor, alternative position for the catalytic zinc is approximately 1.3 A from the major position and closer to Glu-68, which could form the alternative coordination to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide or N-benzylformamide (or with NAD+ and fluoro alcohols) have the classical tetracoordinated zinc, and no water is bound to the zinc or the nicotinamide rings. The major forms of the enzyme in the mechanism have a tetracoordinated zinc, where the carboxylate group of Glu-68 could participate in the exchange of water and substrates on the zinc. Hydride transfer in the Michaelis complexes does not involve a nearby water.

-	~~X-ray investigation of the binding of 1,10-phenanthroline~~ and ~~imidazole to horse-liver alcohol dehydrogenase~~.,~~Boiwe T~~, ~~Branden CI Eur J Biochem~~. ~~1977~~ Jul 1;77(1):~~173~~-9. PMID:~~561693~~<ref>PMID:~~561693~~</ref>	+	Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.,Plapp BV, Savarimuthu BR, Ferraro DJ, Rubach JK, Brown EN, Ramaswamy S Biochemistry. 2017 Jul 18;56(28):3632-3646. doi: 10.1021/acs.biochem.7b00446., Epub 2017 Jul 7. PMID:28640600<ref>PMID:28640600</ref>

	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>

OCA at 12:59, 4 May 2017

OCA — Thu, 04 May 2017 12:59:35 GMT

←Older revision		Revision as of 12:59, 4 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vjg is ~~ON HOLD~~	+	==horse liver alcohol dehydrogenase complexed with 2,2'bipyridine==
		+	<StructureSection load='5vjg' size='340' side='right' caption='[[5vjg]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vjg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0BP:2,2-BIPYRIDINE'>0BP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vj5\|5vj5]], [[5vkr\|5vkr]], [[5vl0\|5vl0]]</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 Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=5vjg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjg OCA], [http://pdbe.org/5vjg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjg RCSB], [http://www.ebi.ac.uk/pdbsum/5vjg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjg ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We have studied the binding of two inhibitor molecules, imidazole and 1,10-phenanthroline, to liver alcohol dehydrogenase by crystallographic methods. X-ray data for the imidazole complex were collected to 0.29-nm resolution and for the 1,10-phenanthroline complex to 0.45-nm resolution. In both cases we found only one peak in the difference electron density maps close to the active zinc atom. The peak corresponding to 1,10-phenanthroline overlaps the site of the density of the zinc-bound water in the apoenzyme and the imidazole density partly overlaps this density. We can not discern any additional peaks close to the zinc atom which would correspond to new positions of bound water. We thus conclude that both these inhibitors bind to the catalytic zinc atom and that upon binding they displace the water molecule that is firmly bound to this zinc atom in the apoenzyme. We do not see any structural changes in the remaining part of the molecule.

-	~~Authors: Plapp~~, ~~B.V~~., ~~Baskar Raj~~, S.	+	X-ray investigation of the binding of 1,10-phenanthroline and imidazole to horse-liver alcohol dehydrogenase.,Boiwe T, Branden CI Eur J Biochem. 1977 Jul 1;77(1):173-9. PMID:561693<ref>PMID:561693</ref>

-	~~Description~~: ~~horse liver alcohol~~ dehydrogenase ~~complexed with 2~~,2'bipyridine	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Baskar Raj, S~~]]	+	<div class="pdbe-citations 5vjg" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Plapp, B.V~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alcohol dehydrogenase]]
		+	[[Category: Equus caballus]]
		+	[[Category: Plapp, B V]]
		+	[[Category: Raj, S Baskar]]
		+	[[Category: 2'bipyridine]]
		+	[[Category: Horse liver]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Zinc chelation]]

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

OCA — Thu, 27 Apr 2017 12:21:34 GMT

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

←Older revision

Revision as of 12:21, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vjg is ON HOLD Authors: Plapp, B.V., Baskar Raj, S. Description: horse liver alcohol dehydrogenase complexed with 2,2'bipyridine [[Category: Unrel...

OCA — Thu, 27 Apr 2017 12:21:33 GMT

New page: '''Unreleased structure''' The entry 5vjg is ON HOLD Authors: Plapp, B.V., Baskar Raj, S. Description: horse liver alcohol dehydrogenase complexed with 2,2'bipyridine [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 5vjg is ON HOLD

Authors: Plapp, B.V., Baskar Raj, S.

Description: horse liver alcohol dehydrogenase complexed with 2,2'bipyridine
[[Category: Unreleased Structures]]
[[Category: Baskar Raj, S]]
[[Category: Plapp, B.V]]