5yqs - Revision history

OCA at 11:25, 13 November 2019

OCA — Wed, 13 Nov 2019 11:25:29 GMT

←Older revision		Revision as of 11:25, 13 November 2019
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	==Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose==		==Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose==
-	<StructureSection load='5yqs' size='340' side='right' caption='[[5yqs]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5yqs' size='340' side='right'caption='[[5yqs]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yqs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YQS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yqs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspor Aspor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YQS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AO090701000274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=510516 ASPOR])</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=5yqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqs OCA], [http://pdbe.org/5yqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yqs RCSB], [http://www.ebi.ac.uk/pdbsum/5yqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqs 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=5yqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqs OCA], [http://pdbe.org/5yqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yqs RCSB], [http://www.ebi.ac.uk/pdbsum/5yqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqs ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isoprimeverose-producing enzymes (IPases) release isoprimeverose (alpha-d-xylopyranosyl-(1-->6)-d-glucopyranose) from the non-reducing end of xyloglucan oligosaccharides. Aspergillus oryzae IPase (IpeA) is classified as a member of the glycoside hydrolase family 3 (GH3); however, it has unusual substrate specificity compared with other GH3 enzymes. Xylopyranosyl branching at the non-reducing ends of xyloglucan oligosaccharides is vital for IpeA activity. We solved the crystal structure of IpeA with isoprimeverose at 2.4A resolution, showing that the structure of IpeA formed a dimer and was composed of three domains: an N-terminal (beta/alpha)8 TIM-barrel domain, alpha/beta/alpha sandwich fold domain, and a C-terminal fibronectin-like domain. The catalytic TIM-barrel domain possessed a catalytic nucleophile (Asp300) and acid/base (Glu524) residues. Interestingly, we found that the cavity of the active site of IpeA was larger than that of other GH3 enzymes, and subsite -1' played an important role in its activity. The glucopyranosyl and xylopyranosyl residues of isoprimeverose were located at subsites -1 and -1', respectively. Gln58 and Tyr89 contributed to the interaction with the xylopyranosyl residue of isoprimeverose through hydrogen bonding and stacking effects, respectively. Our findings provide new insights into the substrate recognition of GH3 enzymes.
		+
		+	Crystal structure and substrate recognition mechanism of Aspergillus oryzae isoprimeverose-producing enzyme.,Matsuzawa T, Watanabe M, Nakamichi Y, Fujimoto Z, Yaoi K J Struct Biol. 2019 Jan 1;205(1):84-90. doi: 10.1016/j.jsb.2018.11.005. Epub 2018, Nov 13. PMID:30445155<ref>PMID:30445155</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yqs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspor]]
		+	[[Category: Large Structures]]
	[[Category: Matsuzawa, T]]		[[Category: Matsuzawa, T]]
	[[Category: Nakamichi, Y]]		[[Category: Nakamichi, Y]]

OCA at 08:03, 14 November 2018

OCA — Wed, 14 Nov 2018 08:03:48 GMT

←Older revision		Revision as of 08:03, 14 November 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yqs ~~is ON HOLD until Paper Publication~~	+	==Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose==
-		+	<StructureSection load='5yqs' size='340' side='right' caption='[[5yqs]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~Yaoi, K~~., ~~Matsuzawa~~, T., ~~Watanabe~~, M., ~~Nakamichi~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yqs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YQS FirstGlance]. <br>
-	~~Description~~: ~~Isoprimeverose~~-~~producing enzyme from Aspergillus oryzae in complex with isoprimeverose~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5yqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqs OCA], [http://pdbe.org/5yqs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yqs RCSB], [http://www.ebi.ac.uk/pdbsum/5yqs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqs ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Matsuzawa, T]]
	[[Category: Nakamichi, Y]]		[[Category: Nakamichi, Y]]
	[[Category: Watanabe, M]]		[[Category: Watanabe, M]]
-	[[Category: Matsuzawa, T]]
	[[Category: Yaoi, K]]		[[Category: Yaoi, K]]
		+	[[Category: Glycoside hydrolase family 3]]
		+	[[Category: Hydrolase]]

OCA at 05:45, 23 May 2018

OCA — Wed, 23 May 2018 05:45:03 GMT

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

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

	Authors: Yaoi, K., Matsuzawa, T., Watanabe, M., Nakamichi, Y.		Authors: Yaoi, K., Matsuzawa, T., Watanabe, M., Nakamichi, Y.

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

OCA — Wed, 15 Nov 2017 06:16:38 GMT

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

←Older revision

Revision as of 06:16, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yqs is ON HOLD Authors: Yaoi, K., Matsuzawa, T., Watanabe, M., Nakamichi, Y. Description: Isoprimeverose-producing enzyme from Aspergillus oryzae ...

OCA — Wed, 15 Nov 2017 06:16:37 GMT

New page: '''Unreleased structure''' The entry 5yqs is ON HOLD Authors: Yaoi, K., Matsuzawa, T., Watanabe, M., Nakamichi, Y. Description: Isoprimeverose-producing enzyme from Aspergillus oryzae ...

New page

'''Unreleased structure'''

The entry 5yqs is ON HOLD

Authors: Yaoi, K., Matsuzawa, T., Watanabe, M., Nakamichi, Y.

Description: Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose
[[Category: Unreleased Structures]]
[[Category: Nakamichi, Y]]
[[Category: Watanabe, M]]
[[Category: Matsuzawa, T]]
[[Category: Yaoi, K]]