5yat - Revision history

OCA at 08:25, 22 November 2023

OCA — Wed, 22 Nov 2023 08:25:33 GMT

←Older revision		Revision as of 08:25, 22 November 2023
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	<StructureSection load='5yat' size='340' side='right'caption='[[5yat]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5yat' size='340' side='right'caption='[[5yat]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yat]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YAT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yat]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_phaffii_GS115 Komagataella phaffii GS115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YAT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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]] 1.745Å</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=5yat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yat OCA], [~~http~~://pdbe.org/5yat PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yat RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yat PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yat ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5yat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yat OCA], [https://pdbe.org/5yat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yat RCSB], [https://www.ebi.ac.uk/pdbsum/5yat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yat ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/C4R0S8_KOMPG C4R0S8_KOMPG]
	<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: Komagataella phaffii GS115]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li, Q]]	+	[[Category: Li Q]]
-	[[Category: Zhang~~, H D]]~~	+	[[Category: Zhang HD]]
-	~~[[Category: Alcohol dehydrogenase]]~~	+
-	~~[[Category: Catalytic zinc]]~~	+
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Yeast~~]]	+

OCA at 09:14, 21 October 2020

OCA — Wed, 21 Oct 2020 09:14:41 GMT

←Older revision		Revision as of 09:14, 21 October 2020
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	==Crystal structure of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115==		==Crystal structure of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115==
-	<StructureSection load='5yat' size='340' side='right' caption='[[5yat]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5yat' size='340' side='right'caption='[[5yat]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yat]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YAT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YAT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yat]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YAT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YAT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5yat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yat OCA], [http://pdbe.org/5yat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yat RCSB], [http://www.ebi.ac.uk/pdbsum/5yat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yat 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=5yat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yat OCA], [http://pdbe.org/5yat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yat RCSB], [http://www.ebi.ac.uk/pdbsum/5yat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yat 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 5yat" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yat" 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: Li, Q]]		[[Category: Li, Q]]
	[[Category: Zhang, H D]]		[[Category: Zhang, H D]]

OCA at 07:34, 21 March 2018

OCA — Wed, 21 Mar 2018 07:34:59 GMT

←Older revision		Revision as of 07:34, 21 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yat is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115==
		+	<StructureSection load='5yat' size='340' side='right' caption='[[5yat]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yat]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YAT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YAT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5yat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yat OCA], [http://pdbe.org/5yat PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yat RCSB], [http://www.ebi.ac.uk/pdbsum/5yat PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yat ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Alcohol dehydrogenases (ADHs) catalyze the reversible oxidation of alcohol using NAD(+) or NADP(+) as cofactor. Three ADH homologues have been identified in Komagataella phaffii GS115 (also named Pichia pastoris GS115), ADH1, ADH2 and ADH3, among which adh3 is the only gene responsible for consumption of ethanol in Komagataella phaffii GS115. However, the relationship between structure and function of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115 (KpADH3) is still not clear yet. METHODS: KpADH3 was purified, identified and characterized by multiple biophysical techniques (Nano LC-MS/MS, Enzymatic activity assay, X-ray crystallography). RESULTS: The crystal structure of KpADH3, which was the first ADH structure from Komagataella phaffii GS115, was solved at 1.745A resolution. Structural analysis indicated that KpADH3 was the sole dimeric ADH structure with face-to-face orientation quaternary structure from yeast. The major structural different conformations located on residues 100-114 (the structural zinc binding loop) and residues 337-344 (the loop between alpha12 and beta15 which covered the catalytic domain). In addition, three channels were observed in KpADH3 crystal structure, channel 2 and channel 3 may be essential for substrate specific recognition, ingress and egress, channel 1 may be the pass-through for cofactor. CONCLUSIONS: KpADH3 plays an important role in the metabolism of alcohols in Komagataella phaffii GS115, and its crystal structure is the only dimeric medium-chain ADH from yeast described so far. GENERAL SIGNIFICANCE: Knowledge of the relationship between structure and function of KpADH3 is crucial for understanding the role of KpADH3 in Komagataella phaffii GS115 mitochondrial metabolism.

-	~~Authors: Zhang~~, H~~.D.~~, Li, Q.	+	Investigation of structure and function of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115.,Zhang H, Li Q, Wang L, Chen Y Biochim Biophys Acta. 2018 Feb 21;1862(5):1199-1208. doi:, 10.1016/j.bbagen.2018.02.012. PMID:29474823<ref>PMID:29474823</ref>

-	~~Description: Crystal structure~~ of ~~mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5yat" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Li, Q]]		[[Category: Li, Q]]
-	[[Category: Zhang, H.D]]	+	[[Category: Zhang, H D]]
		+	[[Category: Alcohol dehydrogenase]]
		+	[[Category: Catalytic zinc]]
		+	[[Category: Dimer]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Yeast]]

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

OCA — Wed, 27 Sep 2017 16:20:56 GMT

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

←Older revision

Revision as of 16:20, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yat is ON HOLD until Paper Publication Authors: Zhang, H.D., Li, Q. Description: Crystal structure of mitochondrial alcohol dehydrogenase isozyme ...

OCA — Wed, 27 Sep 2017 16:20:55 GMT

New page: '''Unreleased structure''' The entry 5yat is ON HOLD until Paper Publication Authors: Zhang, H.D., Li, Q. Description: Crystal structure of mitochondrial alcohol dehydrogenase isozyme ...

New page

'''Unreleased structure'''

The entry 5yat is ON HOLD until Paper Publication

Authors: Zhang, H.D., Li, Q.

Description: Crystal structure of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115
[[Category: Unreleased Structures]]
[[Category: Li, Q]]
[[Category: Zhang, H.D]]