5yvm - Revision history

OCA at 08:38, 22 November 2023

2023-11-22T08:38:53Z

←Older revision		Revision as of 08:38, 22 November 2023
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	==Crystal Structure of the archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase ADH/D1 bound to NZQ==		==Crystal Structure of the archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase ADH/D1 bound to NZQ==
-	<StructureSection load='5yvm' size='340' side='right' caption='[[5yvm]], [[Resolution\|resolution]] 2.12Å' scene=''>	+	<StructureSection load='5yvm' size='340' side='right'caption='[[5yvm]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yvm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Candidate_divison_msbl1_archaeon_scgc~~-~~aaa259e19~~ Candidate ~~divison msbl1~~ archaeon ~~scgc~~-~~aaa259e19~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YVM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yvm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidate_division_MSBL1_archaeon_SCGC-AAA259E19 Candidate division MSBL1 archaeon SCGC-AAA259E19]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YVM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</scene~~>, ~~<scene name='pdbligand=NZQ:5,6-DIHYDROXY-NADP'>NZQ</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]] 2.12Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~AKJ65_00115 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=1698264 candidate divison MSBL1 archaeon SCGC~~-~~AAA259E19])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZQ:5,6-DIHYDROXY-NADP'>NZQ</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=5yvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvm OCA], [~~http~~://pdbe.org/5yvm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yvm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yvm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvm 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=5yvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvm OCA], [https://pdbe.org/5yvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yvm RCSB], [https://www.ebi.ac.uk/pdbsum/5yvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A133UP32_9EURY A0A133UP32_9EURY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5yvm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yvm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Candidate ~~divison msbl1~~ archaeon ~~scgc~~-~~aaa259e19~~]]	+	[[Category: Candidate division MSBL1 archaeon SCGC-AAA259E19]]
-	[[Category: Arold~~, S T~~]]	+	[[Category: Large Structures]]
-	[[Category: Eppinger, J]]	+	[[Category: Arold ST]]
-	[[Category: Frank, A]]	+	[[Category: Eppinger J]]
-	[[Category: Groetzinger~~, S W~~]]	+	[[Category: Frank A]]
-	[[Category: Groll, M]]	+	[[Category: Groetzinger SW]]
-	[[Category: Strillinger, E]]	+	[[Category: Groll M]]
-	~~[[Category: Dehydrogenase]]~~	+	[[Category: Strillinger E]]
-	~~[[Category: Halophilic]]~~	+
-	~~[[Category: Nzq]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein-cofactor complex]]~~	+
-	~~[[Category: Thermophilic~~]]	+

OCA at 06:47, 7 February 2018

2018-02-07T06:47:15Z

←Older revision		Revision as of 06:47, 7 February 2018
Line 25:		Line 25:
	[[Category: Eppinger, J]]		[[Category: Eppinger, J]]
	[[Category: Frank, A]]		[[Category: Frank, A]]
		+	[[Category: Groetzinger, S W]]
	[[Category: Groll, M]]		[[Category: Groll, M]]
-	[[Category: Grotzinger, S W]]
	[[Category: Strillinger, E]]		[[Category: Strillinger, E]]
	[[Category: Dehydrogenase]]		[[Category: Dehydrogenase]]

OCA at 07:10, 31 January 2018

2018-01-31T07:10:05Z

←Older revision		Revision as of 07:10, 31 January 2018
Line 1:		Line 1:

-	==Crystal Structure of ~~ADH/D1, an~~ archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase==	+	==Crystal Structure of the archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase ADH/D1 bound to NZQ==
	<StructureSection load='5yvm' size='340' side='right' caption='[[5yvm]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='5yvm' size='340' side='right' caption='[[5yvm]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yvm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidate_divison_msbl1_archaeon_scgc-aaa259e19 Candidate divison msbl1 archaeon scgc-aaa259e19]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZQ:5,6-DIHYDROXY-NADP'>NZQ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZQ:5,6-DIHYDROXY-NADP'>NZQ</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AKJ65_00115 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1698264 candidate divison MSBL1 archaeon SCGC-AAA259E19])</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=5yvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvm OCA], [http://pdbe.org/5yvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvm RCSB], [http://www.ebi.ac.uk/pdbsum/5yvm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvm 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=5yvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvm OCA], [http://pdbe.org/5yvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvm RCSB], [http://www.ebi.ac.uk/pdbsum/5yvm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvm ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Candidate divison msbl1 archaeon scgc-aaa259e19]]
	[[Category: Arold, S T]]		[[Category: Arold, S T]]
	[[Category: Eppinger, J]]		[[Category: Eppinger, J]]

OCA at 08:35, 27 December 2017

2017-12-27T08:35:52Z

←Older revision		Revision as of 08:35, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yvm is ~~ON HOLD~~	+	==Crystal Structure of ADH/D1, an archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase==
		+	<StructureSection load='5yvm' size='340' side='right' caption='[[5yvm]], [[Resolution\|resolution]] 2.12Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yvm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZQ:5,6-DIHYDROXY-NADP'>NZQ</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=5yvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvm OCA], [http://pdbe.org/5yvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvm RCSB], [http://www.ebi.ac.uk/pdbsum/5yvm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Because only 0.01% of prokaryotic genospecies can be cultured and in situ observations are often impracticable, culture-independent methods are required to understand microbial life and harness potential applications of microbes. Here, we report a methodology for the production of proteins with desired functions based on single amplified genomes (SAGs) from unculturable species. We use this method to resurrect an alcohol dehydrogenase (ADH/D1) from an uncharacterized halo-thermophilic archaeon collected from a brine pool at the bottom of the Red Sea. Our crystal structure of 5,6-dihydroxy NADPH-bound ADH/D1 combined with biochemical analyses reveal the molecular features of its halo-thermophily, its unique habitat adaptations, and its possible reaction mechanism for atypical oxygen activation. Our strategy offers a general guide for using SAGs as a source for scientific and industrial investigations of "microbial dark matter."

-	~~Authors:~~ Grotzinger, ~~S.W.~~, Strillinger, E., Frank, A., ~~Eppinger~~, J., ~~Groll~~, M., ~~Arold~~, S.T.	+	Identification and Experimental Characterization of an Extremophilic Brine Pool Alcohol Dehydrogenase from Single Amplified Genomes.,Grotzinger SW, Karan R, Strillinger E, Bader S, Frank A, Al Rowaihi IS, Akal A, Wackerow W, Archer JA, Rueping M, Weuster-Botz D, Groll M, Eppinger J, Arold ST ACS Chem Biol. 2017 Dec 18. doi: 10.1021/acschembio.7b00792. PMID:29188989<ref>PMID:29188989</ref>

-	~~Description: Crystal Structure of ADH~~/D1, ~~an archaeal halo~~-~~thermophilic Red Sea brine pool alcohol dehydrogenase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yvm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arold, S T]]
		+	[[Category: Eppinger, J]]
	[[Category: Frank, A]]		[[Category: Frank, A]]
-	[[Category: Strillinger, E]]
	[[Category: Groll, M]]		[[Category: Groll, M]]
-	[[Category: ~~Eppinger~~, J]]	+	[[Category: Grotzinger, S W]]
-	[[Category: ~~Grotzinger~~, ~~S.W~~]]	+	[[Category: Strillinger, E]]
-	[[Category: ~~Arold, S.T~~]]	+	[[Category: Dehydrogenase]]
		+	[[Category: Halophilic]]
		+	[[Category: Nzq]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Protein-cofactor complex]]
		+	[[Category: Thermophilic]]

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

2017-12-06T05:58:25Z

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

←Older revision

Revision as of 05:58, 6 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yvm is ON HOLD Authors: Grotzinger, S.W., Strillinger, E., Frank, A., Eppinger, J., Groll, M., Arold, S.T. Description: Crystal Structure of ADH/D...

2017-12-06T05:58:24Z

New page: '''Unreleased structure''' The entry 5yvm is ON HOLD Authors: Grotzinger, S.W., Strillinger, E., Frank, A., Eppinger, J., Groll, M., Arold, S.T. Description: Crystal Structure of ADH/D...

New page

'''Unreleased structure'''

The entry 5yvm is ON HOLD

Authors: Grotzinger, S.W., Strillinger, E., Frank, A., Eppinger, J., Groll, M., Arold, S.T.

Description: Crystal Structure of ADH/D1, an archaeal halo-thermophilic Red Sea brine pool alcohol dehydrogenase
[[Category: Unreleased Structures]]
[[Category: Frank, A]]
[[Category: Strillinger, E]]
[[Category: Groll, M]]
[[Category: Eppinger, J]]
[[Category: Grotzinger, S.W]]
[[Category: Arold, S.T]]