5z3f - Revision history

OCA at 19:25, 29 May 2024

OCA — Wed, 29 May 2024 19:25:58 GMT

←Older revision		Revision as of 19:25, 29 May 2024
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	<StructureSection load='5z3f' size='340' side='right'caption='[[5z3f]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='5z3f' size='340' side='right'caption='[[5z3f]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z3f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Krifd Krifd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z3F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z3f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Kribbella_flavida_DSM_17836 Kribbella flavida DSM 17836]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z3F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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]] 1.1Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kfla_1896 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=479435 KRIFD])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5z3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3f OCA], [https://pdbe.org/5z3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z3f RCSB], [https://www.ebi.ac.uk/pdbsum/5z3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3f ProSAT]</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=5z3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3f OCA], [https://pdbe.org/5z3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z3f RCSB], [https://www.ebi.ac.uk/pdbsum/5z3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/IMGH_KRIFD IMGH_KRIFD]] Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.<ref>PMID:27302067</ref>	+	[https://www.uniprot.org/uniprot/IMGH_KRIFD IMGH_KRIFD] Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.<ref>PMID:27302067</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Krifd~~]]	+	[[Category: Kribbella flavida DSM 17836]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, M]]	+	[[Category: Chen M]]
-	[[Category: Kimura, A]]	+	[[Category: Kimura A]]
-	[[Category: Tagami, T]]	+	[[Category: Tagami T]]
-	[[Category: Tanaka, Y]]	+	[[Category: Tanaka Y]]
-	[[Category: Yao, M]]	+	[[Category: Yao M]]
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:30, 23 February 2022

OCA — Wed, 23 Feb 2022 08:30:53 GMT

←Older revision		Revision as of 08:30, 23 February 2022
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	<StructureSection load='5z3f' size='340' side='right'caption='[[5z3f]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='5z3f' size='340' side='right'caption='[[5z3f]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z3f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Krifd Krifd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z3F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z3f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Krifd Krifd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z3F 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=CIT:CITRIC+ACID'>CIT</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=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kfla_1896 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=479435 KRIFD])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kfla_1896 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=479435 KRIFD])</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=5z3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3f OCA], [~~http~~://pdbe.org/5z3f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z3f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z3f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3f ProSAT]</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=5z3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3f OCA], [https://pdbe.org/5z3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z3f RCSB], [https://www.ebi.ac.uk/pdbsum/5z3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/IMGH_KRIFD IMGH_KRIFD]] Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.<ref>PMID:27302067</ref>	+	[[https://www.uniprot.org/uniprot/IMGH_KRIFD IMGH_KRIFD]] Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.<ref>PMID:27302067</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside hydrolase family 15 (GH15) inverting enzymes contain two glutamate residues functioning as a general acid catalyst and a general base catalyst, for isomaltose glucohydrolase (IGHase), Glu178 and Glu335, respectively. Generally, a two-catalytic residue-mediated reaction exhibits a typical bell-shaped pH-activity curve. However, IGHase is found to display atypical non-bell-shaped pH-kcat and pH-kcat /Km profiles, theoretically better-fitted to a three-catalytic residue-associated pH-activity curve. We determined the crystal structure of IGHase by the single-wavelength anomalous dispersion method using sulfur atoms and the cocrystal structure of a catalytic base mutant E335A with isomaltose. Although the activity of E335A was undetectable, the electron density observed in its active site pocket did not correspond to an isomaltose but a glycerol and a beta-glucose, cryoprotectant, and hydrolysis product. Our structural and biochemical analyses of several mutant enzymes suggest that Tyr48 acts as a second catalytic base catalyst. Y48F mutant displayed almost equivalent specific activity to a catalytic acid mutant E178A. Tyr48, highly conserved in all GH15 members, is fixed by another Tyr residue in many GH15 enzymes; the latter Tyr is replaced by Phe290 in IGHase. The pH profile of F290Y mutant changed to a bell-shaped curve, suggesting that Phe290 is a key residue distinguishing Tyr48 of IGHase from other GH15 members. Furthermore, F290Y is found to accelerate the condensation of isomaltose from glucose by modifying a hydrogen-bonding network between Tyr290-Tyr48-Glu335. The present study indicates that the atypical Phe290 makes Tyr48 of IGHase unique among GH15 enzymes.
		+
		+	Structural insights reveal the second base catalyst of isomaltose glucohydrolase.,Tagami T, Chen M, Furunaga Y, Kikuchi A, Sadahiro J, Lang W, Okuyama M, Tanaka Y, Iwasaki T, Yao M, Kimura A FEBS J. 2022 Feb;289(4):1118-1134. doi: 10.1111/febs.16237. Epub 2021 Oct 30. PMID:34665923<ref>PMID:34665923</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5z3f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:19, 21 May 2019

OCA — Tue, 21 May 2019 07:19:22 GMT

←Older revision		Revision as of 07:19, 21 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z3f ~~is ON HOLD until May 05 2020~~	+	==Glycosidase E335A in complex with glucose==
-		+	<StructureSection load='5z3f' size='340' side='right'caption='[[5z3f]], [[Resolution\|resolution]] 1.10Å' scene=''>
-	~~Authors~~: ~~Tanaka, Y~~., ~~Chen~~, M., ~~Tagami~~, T., ~~Yao~~, M., ~~Kimura, A~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5z3f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Krifd Krifd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z3F FirstGlance]. <br>
-	~~Description~~: ~~Glycosidase E335A~~ in ~~complex with~~ glucose	+	</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=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kfla_1896 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=479435 KRIFD])</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=5z3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3f OCA], [http://pdbe.org/5z3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z3f RCSB], [http://www.ebi.ac.uk/pdbsum/5z3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3f ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IMGH_KRIFD IMGH_KRIFD]] Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.<ref>PMID:27302067</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Krifd]]
		+	[[Category: Large Structures]]
		+	[[Category: Chen, M]]
	[[Category: Kimura, A]]		[[Category: Kimura, A]]
-	[[Category: Chen, M]]
	[[Category: Tagami, T]]		[[Category: Tagami, T]]
		+	[[Category: Tanaka, Y]]
	[[Category: Yao, M]]		[[Category: Yao, M]]
-	[[Category: ~~Tanaka, Y~~]]	+	[[Category: Glycosidase]]
		+	[[Category: Hydrolase]]

OCA at 04:44, 2 January 2019

OCA — Wed, 02 Jan 2019 04:44:48 GMT

←Older revision		Revision as of 04:44, 2 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z3f is ON HOLD until ~~Paper Publication~~	+	The entry 5z3f is ON HOLD until May 05 2020

	Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.		Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

OCA at 03:50, 20 June 2018

OCA — Wed, 20 Jun 2018 03:50:27 GMT

←Older revision		Revision as of 03:50, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z3f is ON HOLD	+	The entry 5z3f is ON HOLD until Paper Publication

	Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.		Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

OCA at 17:10, 24 January 2018

OCA — Wed, 24 Jan 2018 17:10:45 GMT

←Older revision		Revision as of 17:10, 24 January 2018
Line 5:		Line 5:
	Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.		Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

-	Description: Glycosidase ~~Wild Type~~	+	Description: Glycosidase E335A in complex with glucose
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Tagami, T]]
-	[[Category: Yao, M]]
	[[Category: Kimura, A]]		[[Category: Kimura, A]]
	[[Category: Chen, M]]		[[Category: Chen, M]]
		+	[[Category: Tagami, T]]
		+	[[Category: Yao, M]]
	[[Category: Tanaka, Y]]		[[Category: Tanaka, Y]]

OCA: Protected "5z3f" [edit=sysop:move=sysop]

OCA — Wed, 17 Jan 2018 05:32:24 GMT

Protected "5z3f" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:32, 17 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z3f is ON HOLD Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A. Description: Glycosidase Wild Type [[Category: Unreleased Structures...

OCA — Wed, 17 Jan 2018 05:32:23 GMT

New page: '''Unreleased structure''' The entry 5z3f is ON HOLD Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A. Description: Glycosidase Wild Type [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 5z3f is ON HOLD

Authors: Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

Description: Glycosidase Wild Type
[[Category: Unreleased Structures]]
[[Category: Tagami, T]]
[[Category: Yao, M]]
[[Category: Kimura, A]]
[[Category: Chen, M]]
[[Category: Tanaka, Y]]