5zai - Revision history

OCA at 08:50, 22 November 2023

OCA — Wed, 22 Nov 2023 08:50:51 GMT

←Older revision		Revision as of 08:50, 22 November 2023
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	<StructureSection load='5zai' size='340' side='right'caption='[[5zai]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5zai' size='340' side='right'caption='[[5zai]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zai]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mets5 Mets5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zai]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Metallosphaera_sedula_DSM_5348 Metallosphaera sedula DSM 5348]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZAI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=COA:COENZYME+A'>COA</scene>~~, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Msed_2001 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=399549 METS5])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/3-hydroxypropionyl-CoA_dehydratase 3-hydroxypropionyl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.116 4.2.1.116]~~ </~~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=5zai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zai OCA], [https://pdbe.org/5zai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zai RCSB], [https://www.ebi.ac.uk/pdbsum/5zai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zai 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=5zai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zai OCA], [~~http~~://pdbe.org/5zai PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zai RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zai PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zai ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HPCD_METS5 HPCD_METS5]] Plays a role in autotrophic carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle. Catalyzes the reversible dehydration of 3-hydroxypropionyl-CoA to form acryloyl-CoA, and the reversible dehydration of (S)-3-hydroxybutyryl-CoA to form crotonyl-CoA. Inactive towards (R)-3-hydroxybutyryl-CoA.<ref>PMID:19429610</ref>	+	[https://www.uniprot.org/uniprot/HPCD_METS5 HPCD_METS5] Plays a role in autotrophic carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle. Catalyzes the reversible dehydration of 3-hydroxypropionyl-CoA to form acryloyl-CoA, and the reversible dehydration of (S)-3-hydroxybutyryl-CoA to form crotonyl-CoA. Inactive towards (R)-3-hydroxybutyryl-CoA.<ref>PMID:19429610</ref>
	<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: 3-hydroxypropionyl-CoA dehydratase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mets5~~]]	+	[[Category: Metallosphaera sedula DSM 5348]]
-	[[Category: Kim~~, K J~~]]	+	[[Category: Kim KJ]]
-	[[Category: Lee, D]]	+	[[Category: Lee D]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:46, 9 September 2020

OCA — Wed, 09 Sep 2020 09:46:51 GMT

←Older revision		Revision as of 09:46, 9 September 2020
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-	==Crystal ~~strcuture~~ of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula==	+	==Crystal structure of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula==
-	<StructureSection load='5zai' size='340' side='right' caption='[[5zai]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5zai' size='340' side='right'caption='[[5zai]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zai]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zai]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mets5 Mets5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Msed_2001 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=399549 METS5])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxypropionyl-CoA_dehydratase 3-hydroxypropionyl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.116 4.2.1.116] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxypropionyl-CoA_dehydratase 3-hydroxypropionyl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.116 4.2.1.116] </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=5zai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zai OCA], [http://pdbe.org/5zai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zai RCSB], [http://www.ebi.ac.uk/pdbsum/5zai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zai 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=5zai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zai OCA], [http://pdbe.org/5zai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zai RCSB], [http://www.ebi.ac.uk/pdbsum/5zai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zai ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: 3-hydroxypropionyl-CoA dehydratase]]		[[Category: 3-hydroxypropionyl-CoA dehydratase]]
		+	[[Category: Large Structures]]
		+	[[Category: Mets5]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Lee, D]]		[[Category: Lee, D]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 18:40, 1 August 2018

OCA — Wed, 01 Aug 2018 18:40:10 GMT

←Older revision		Revision as of 18:40, 1 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zai is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal strcuture of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula==
		+	<StructureSection load='5zai' size='340' side='right' caption='[[5zai]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zai]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZAI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxypropionyl-CoA_dehydratase 3-hydroxypropionyl-CoA dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.116 4.2.1.116] </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=5zai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zai OCA], [http://pdbe.org/5zai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zai RCSB], [http://www.ebi.ac.uk/pdbsum/5zai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zai ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HPCD_METS5 HPCD_METS5]] Plays a role in autotrophic carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle. Catalyzes the reversible dehydration of 3-hydroxypropionyl-CoA to form acryloyl-CoA, and the reversible dehydration of (S)-3-hydroxybutyryl-CoA to form crotonyl-CoA. Inactive towards (R)-3-hydroxybutyryl-CoA.<ref>PMID:19429610</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Metallosphaera sedula is a thermoacidophilic autotrophic archaeon known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as carbon fixation pathway. 3-Hydroxypropionyl-CoA dehydratase (3HPCD) is an enzyme involved in the 3-HP/4-HB cycle by converting 3-hydroxypropionyl-CoA to acryloyl-CoA. To elucidate the molecular mechanism of 3HPCD from M. sedula (Ms3HPCD), we determined its crystal structure in complex with Coenzyme A (CoA). Ms3HPCD showed an overall structure and the CoA-binding mode similar to other enoyl-CoA hydratase (ECH) family enzymes. However, compared with the other ECHs, Ms3HPCD has a tightly formed alpha3 helix near the active site, and bulky aromatic residues are located at the enoyl-group binding site, resulting in the enzyme having an optimal substrate binding site for accepting short-chain 3-hydroxyacyl-CoA as a substrate. Moreover, based on the phylogenetic tree analysis, we propose that the 3HPCD homologues from the phylum Crenarchaeota have an enoyl-group binding pocket similar to that of bacterial short-chain ECHs.

-	~~Authors: Lee~~, D., Kim~~, K~~.J.	+	Structural Insight into Substrate Specificity of 3-Hydroxypropionyl-Coenzyme A Dehydratase from Metallosphaera sedula.,Lee D, Kim KJ Sci Rep. 2018 Jul 16;8(1):10692. doi: 10.1038/s41598-018-29070-w. PMID:30013155<ref>PMID:30013155</ref>

-	~~Description: Crystal strcuture~~ of 3-~~Hydroxypropionyl~~-CoA dehydratase ~~from Metallosphaera sedula~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5zai" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 3-hydroxypropionyl-CoA dehydratase]]
		+	[[Category: Kim, K J]]
	[[Category: Lee, D]]		[[Category: Lee, D]]
-	[[Category: ~~Kim, K.J~~]]	+	[[Category: Hydrolase]]

OCA at 03:49, 30 May 2018

OCA — Wed, 30 May 2018 03:49:04 GMT

←Older revision		Revision as of 03:49, 30 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zai is ON HOLD	+	The entry 5zai is ON HOLD until Paper Publication

	Authors: Lee, D., Kim, K.J.		Authors: Lee, D., Kim, K.J.

OCA at 05:45, 23 May 2018

OCA — Wed, 23 May 2018 05:45:30 GMT

←Older revision		Revision as of 05:45, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zai is ON HOLD ~~until Paper Publication~~	+	The entry 5zai is ON HOLD

	Authors: Lee, D., Kim, K.J.		Authors: Lee, D., Kim, K.J.

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

OCA — Thu, 15 Feb 2018 05:12:07 GMT

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

←Older revision

Revision as of 05:12, 15 February 2018

OCA: New page: '''Unreleased structure''' The entry 5zai is ON HOLD until Paper Publication Authors: Lee, D., Kim, K.J. Description: Crystal strcuture of 3-Hydroxypropionyl-CoA dehydratase from Metal...

OCA — Thu, 15 Feb 2018 05:12:05 GMT

New page: '''Unreleased structure''' The entry 5zai is ON HOLD until Paper Publication Authors: Lee, D., Kim, K.J. Description: Crystal strcuture of 3-Hydroxypropionyl-CoA dehydratase from Metal...

New page

'''Unreleased structure'''

The entry 5zai is ON HOLD until Paper Publication

Authors: Lee, D., Kim, K.J.

Description: Crystal strcuture of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula
[[Category: Unreleased Structures]]
[[Category: Lee, D]]
[[Category: Kim, K.J]]