5wqs - Revision history

OCA at 16:51, 8 November 2023

2023-11-08T16:51:30Z

←Older revision		Revision as of 16:51, 8 November 2023
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	<StructureSection load='5wqs' size='340' side='right'caption='[[5wqs]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5wqs' size='340' side='right'caption='[[5wqs]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wqs]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ipomoea_batatas Ipomoea batatas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WQS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5WQS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wqs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ipomoea_batatas Ipomoea batatas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WQS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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"~~>[[5wqu\|5wqu]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2]~~ </~~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=5wqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqs OCA], [https://pdbe.org/5wqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wqs RCSB], [https://www.ebi.ac.uk/pdbsum/5wqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqs 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=5wqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqs OCA], [~~http~~://pdbe.org/5wqs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wqs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wqs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqs ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMYB_IPOBA AMYB_IPOBA]
	<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: Beta-amylase]]
	[[Category: Ipomoea batatas]]		[[Category: Ipomoea batatas]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gunasekaran, K]]	+	[[Category: Gunasekaran K]]
-	[[Category: Nandhagopal, N]]	+	[[Category: Nandhagopal N]]
-	[[Category: Sergei, P]]	+	[[Category: Sergei P]]
-	[[Category: Vajravijayan, S]]	+	[[Category: Vajravijayan S]]
-	~~[[Category: Amylase]]~~	+
-	~~[[Category: Apo]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Sweet potato~~]]	+

OCA at 07:14, 7 October 2020

2020-10-07T07:14:43Z

←Older revision		Revision as of 07:14, 7 October 2020
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	==Crystal structure of Apo Beta-Amylase from Sweet potato==		==Crystal structure of Apo Beta-Amylase from Sweet potato==
-	<StructureSection load='5wqs' size='340' side='right' caption='[[5wqs]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5wqs' size='340' side='right'caption='[[5wqs]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wqs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ipomoea_batatas Ipomoea batatas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WQS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WQS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wqs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ipomoea_batatas Ipomoea batatas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WQS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WQS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wqu\|5wqu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wqu\|5wqu]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </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=5wqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqs OCA], [http://pdbe.org/5wqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wqs RCSB], [http://www.ebi.ac.uk/pdbsum/5wqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqs 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=5wqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqs OCA], [http://pdbe.org/5wqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wqs RCSB], [http://www.ebi.ac.uk/pdbsum/5wqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Beta-amylase]]		[[Category: Beta-amylase]]
	[[Category: Ipomoea batatas]]		[[Category: Ipomoea batatas]]
		+	[[Category: Large Structures]]
	[[Category: Gunasekaran, K]]		[[Category: Gunasekaran, K]]
	[[Category: Nandhagopal, N]]		[[Category: Nandhagopal, N]]

OCA at 06:15, 6 June 2018

2018-06-06T06:15:03Z

←Older revision		Revision as of 06:15, 6 June 2018
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	<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=5wqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqs OCA], [http://pdbe.org/5wqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wqs RCSB], [http://www.ebi.ac.uk/pdbsum/5wqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqs 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=5wqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqs OCA], [http://pdbe.org/5wqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wqs RCSB], [http://www.ebi.ac.uk/pdbsum/5wqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqs ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The conversion of starch to maltose is catalysed in plants by beta-amylase. The enzymatic mechanism has been well-characterized for the soybean and barley enzymes, which utilise a glutamic acid-glutamate pair. In the present study, we present a surprise observation of maltotetraose at the active site, the presence of which elucidates the clear role of Thr344 as a conformational "switch" between substrate binding and product release during hydrolysis. This observation is confirmed by the selection of maltotetraose by the crystallized enzyme although that carbohydrate was present in only trace amounts. The conformation of the residues in the substrate-binding site changed upon substrate binding, leading to the movement of threonine, glutamic acid, and the loop conformation, elucidating a missing link in the existing mechanism. By aligning our substrate-free and maltotetraose-bound structures with other existing structures, the sequence of events from substrate binding to hydrolysis can be visualized. Apart from this, the evolutionary relationship among beta-amylases of bacterial and amyloplastic origin could be established. The presence of a sugar-binding domain in the bacterial enzyme and its absence in the plant counterpart could be attributed to a carbohydrate-rich environment. Interestingly, cladogram analysis indicates the presence of N-terminal additions in some plant beta-amylases. Based on sequence similarity, we postulate that the role of such additions is important for the regulation of enzymatic activity, particularly under stress conditions.
		+
		+	Structural insights on starch hydrolysis by plant beta-amylase and its evolutionary relationship with bacterial enzymes.,Vajravijayan S, Pletnev S, Mani N, Pletneva N, Nandhagopal N, Gunasekaran K Int J Biol Macromol. 2018 Jul 1;113:329-337. doi: 10.1016/j.ijbiomac.2018.02.138., Epub 2018 Feb 23. PMID:29481953<ref>PMID:29481953</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5wqs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:18, 6 December 2017

2017-12-06T07:18:20Z

←Older revision		Revision as of 07:18, 6 December 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5wqs is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Apo Beta-Amylase from Sweet potato==
-		+	<StructureSection load='5wqs' size='340' side='right' caption='[[5wqs]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~: ~~Vajravijayan~~, S., ~~Sergei~~, P., ~~Nandhagopal~~, N., ~~Gunasekaran, K~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5wqs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ipomoea_batatas Ipomoea batatas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WQS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WQS FirstGlance]. <br>
-	~~Description: Crystal structure of Apo Beta-Amylase from Sweet potato~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wqu\|5wqu]]</td></tr>
-	[[Category: ~~Vajravijayan, S~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </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=5wqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqs OCA], [http://pdbe.org/5wqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wqs RCSB], [http://www.ebi.ac.uk/pdbsum/5wqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqs ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-amylase]]
		+	[[Category: Ipomoea batatas]]
	[[Category: Gunasekaran, K]]		[[Category: Gunasekaran, K]]
		+	[[Category: Nandhagopal, N]]
	[[Category: Sergei, P]]		[[Category: Sergei, P]]
-	[[Category: ~~Nandhagopal~~, N]]	+	[[Category: Vajravijayan, S]]
		+	[[Category: Amylase]]
		+	[[Category: Apo]]
		+	[[Category: Hydrolase]]
		+	[[Category: Sweet potato]]

OCA at 15:04, 27 September 2017

2017-09-27T15:04:50Z

←Older revision		Revision as of 15:04, 27 September 2017
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	Description: Crystal structure of Apo Beta-Amylase from Sweet potato		Description: Crystal structure of Apo Beta-Amylase from Sweet potato
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Vajravijayan, S]]
	[[Category: Gunasekaran, K]]		[[Category: Gunasekaran, K]]
	[[Category: Sergei, P]]		[[Category: Sergei, P]]
	[[Category: Nandhagopal, N]]		[[Category: Nandhagopal, N]]
-	[[Category: Vajravijayan, S]]

OCA at 19:47, 15 March 2017

2017-03-15T19:47:17Z

←Older revision		Revision as of 19:47, 15 March 2017
Line 7:		Line 7:
	Description: Crystal structure of Apo Beta-Amylase from Sweet potato		Description: Crystal structure of Apo Beta-Amylase from Sweet potato
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Vajravijayan, S]]
	[[Category: Gunasekaran, K]]		[[Category: Gunasekaran, K]]
	[[Category: Sergei, P]]		[[Category: Sergei, P]]
	[[Category: Nandhagopal, N]]		[[Category: Nandhagopal, N]]
		+	[[Category: Vajravijayan, S]]

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

2016-12-09T18:18:07Z

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

←Older revision

Revision as of 18:18, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5wqs is ON HOLD until Paper Publication Authors: Vajravijayan, S., Sergei, P., Nandhagopal, N., Gunasekaran, K. Description: Crystal structure of A...

2016-12-09T18:18:06Z

New page: '''Unreleased structure''' The entry 5wqs is ON HOLD until Paper Publication Authors: Vajravijayan, S., Sergei, P., Nandhagopal, N., Gunasekaran, K. Description: Crystal structure of A...

New page

'''Unreleased structure'''

The entry 5wqs is ON HOLD until Paper Publication

Authors: Vajravijayan, S., Sergei, P., Nandhagopal, N., Gunasekaran, K.

Description: Crystal structure of Apo Beta-Amylase from Sweet potato
[[Category: Unreleased Structures]]
[[Category: Vajravijayan, S]]
[[Category: Gunasekaran, K]]
[[Category: Sergei, P]]
[[Category: Nandhagopal, N]]