6yqa - Revision history

OCA at 13:33, 24 January 2024

2024-01-24T13:33:16Z

←Older revision		Revision as of 13:33, 24 January 2024
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	==Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor==		==Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor==
-	<StructureSection load='6yqa' size='340' side='right'caption='[[6yqa]]' scene=''>	+	<StructureSection load='6yqa' size='340' side='right'caption='[[6yqa]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQA FirstGlance]. <br>
-	</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=6yqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqa OCA], [https://pdbe.org/6yqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqa RCSB], [https://www.ebi.ac.uk/pdbsum/6yqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqa ProSAT]</span></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]] 1.67Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=P9Q:(1~{S},2~{R},3~{R},4~{R},5~{R})-5-(8-azanyloctylamino)-4-(hydroxymethyl)cyclohexane-1,2,3-triol'>P9Q</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=6yqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqa OCA], [https://pdbe.org/6yqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqa RCSB], [https://www.ebi.ac.uk/pdbsum/6yqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1S9DH83_ASPOZ A0A1S9DH83_ASPOZ]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Amylases are key enzymes in the processing of starch in many kingdoms of life. They are important catalysts in industrial biotechnology where they are applied in, among others, food processing and the production of detergents. In man amylases are the first enzymes in the digestion of starch to glucose and arguably also the preferred target in therapeutic strategies aimed at the treatment of type 2 diabetes patients through down-tuning glucose assimilation. Efficient and sensitive assays that report selectively on retaining amylase activities irrespective of the nature and complexity of the biomaterial studied are of great value both in finding new and effective human amylase inhibitors and in the discovery of new microbial amylases with potentially advantageous features for biotechnological application. Activity-based protein profiling (ABPP) of retaining glycosidases is inherently suited for the development of such an assay format. We here report on the design and synthesis of 1,6-epi-cyclophellitol-based pseudodisaccharides equipped with a suite of reporter entities and their use in ABPP of retaining amylases from human saliva, murine tissue as well as secretomes from fungi grown on starch. The activity and efficiency of the inhibitors and probes are substantiated by extensive biochemical analysis, and the selectivity for amylases over related retaining endoglycosidases is validated by structural studies.
		+
		+	Activity-Based Protein Profiling of Retaining alpha-Amylases in Complex Biological Samples.,Chen Y, Armstrong Z, Artola M, Florea BI, Kuo CL, de Boer C, Rasmussen MS, Abou Hachem M, van der Marel GA, Codee JDC, Aerts JMFG, Davies GJ, Overkleeft HS J Am Chem Soc. 2021 Jan 26. doi: 10.1021/jacs.0c13059. PMID:33497208<ref>PMID:33497208</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yqa" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Amylase 3D structures\|Amylase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus oryzae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Armstrong Z]]		[[Category: Armstrong Z]]

OCA at 06:39, 24 February 2021

2021-02-24T06:39:18Z

←Older revision		Revision as of 06:39, 24 February 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6yqa ~~is ON HOLD~~	+	==Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor==
-		+	<StructureSection load='6yqa' size='340' side='right'caption='[[6yqa]]' scene=''>
-	~~Authors~~: ~~Armstrong~~, Z., ~~Chen, Y~~., ~~Artola, M~~., ~~Overkleeft, H~~., ~~Davies, G~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQA FirstGlance]. <br>
-	~~Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor~~	+	</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=6yqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqa OCA], [https://pdbe.org/6yqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqa RCSB], [https://www.ebi.ac.uk/pdbsum/6yqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqa ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Overkleeft, H~~]]	+	__TOC__
-	[[Category: Artola, M]]	+	</StructureSection>
-	[[Category: ~~Armstrong, Z~~]]	+	[[Category: Large Structures]]
-	[[Category: Davies, G]]	+	[[Category: Armstrong Z]]
-	[[Category: ~~Chen, Y~~]]	+	[[Category: Artola M]]
		+	[[Category: Chen Y]]
		+	[[Category: Davies G]]
		+	[[Category: Overkleeft H]]

OCA at 09:04, 10 February 2021

2021-02-10T09:04:07Z

←Older revision		Revision as of 09:04, 10 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6yqa is ON HOLD ~~until Paper Publication~~	+	The entry 6yqa is ON HOLD

	Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.		Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.
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	Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor		Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chen, Y]]
	[[Category: Overkleeft, H]]		[[Category: Overkleeft, H]]
	[[Category: Artola, M]]		[[Category: Artola, M]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]
	[[Category: Davies, G]]		[[Category: Davies, G]]
		+	[[Category: Chen, Y]]

OCA at 07:32, 22 July 2020

2020-07-22T07:32:13Z

←Older revision		Revision as of 07:32, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6yqa is ON HOLD	+	The entry 6yqa is ON HOLD until Paper Publication

	Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.		Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.
Line 7:		Line 7:
	Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor		Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Artola, M]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
	[[Category: Overkleeft, H]]		[[Category: Overkleeft, H]]
		+	[[Category: Artola, M]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]
	[[Category: Davies, G]]		[[Category: Davies, G]]

OCA: Protected "6yqa" [edit=sysop:move=sysop]

2020-04-22T04:33:36Z

Protected "6yqa" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:33, 22 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yqa is ON HOLD Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G. Description: Taka-amylase in complex with alpha-glucosyl e...

2020-04-22T04:33:34Z

New page: '''Unreleased structure''' The entry 6yqa is ON HOLD Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G. Description: Taka-amylase in complex with alpha-glucosyl e...

New page

'''Unreleased structure'''

The entry 6yqa is ON HOLD

Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.

Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor
[[Category: Unreleased Structures]]
[[Category: Artola, M]]
[[Category: Chen, Y]]
[[Category: Overkleeft, H]]
[[Category: Armstrong, Z]]
[[Category: Davies, G]]