5xfm - Revision history

OCA at 08:01, 22 November 2023

OCA — Wed, 22 Nov 2023 08:01:20 GMT

←Older revision		Revision as of 08:01, 22 November 2023
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	<StructureSection load='5xfm' size='340' side='right'caption='[[5xfm]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5xfm' size='340' side='right'caption='[[5xfm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xfm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xfm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XFM FirstGlance]. <br>
-	</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></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]] 2.3Å</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=5xfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfm OCA], [~~http~~://pdbe.org/5xfm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xfm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xfm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfm ProSAT]</span></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></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=5xfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfm OCA], [https://pdbe.org/5xfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xfm RCSB], [https://www.ebi.ac.uk/pdbsum/5xfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8A1K0_BACTN Q8A1K0_BACTN]
	<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: Bacteroides thetaiotaomicron]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kato, K]]	+	[[Category: Kato K]]
-	[[Category: Okuyama, M]]	+	[[Category: Okuyama M]]
-	[[Category: Yao, M]]	+	[[Category: Yao M]]
-	~~[[Category: Arabinopyranosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:48, 14 October 2020

OCA — Wed, 14 Oct 2020 06:48:30 GMT

←Older revision		Revision as of 06:48, 14 October 2020
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	==Crystal structure of beta-arabinopyranosidase==		==Crystal structure of beta-arabinopyranosidase==
-	<StructureSection load='5xfm' size='340' side='right' caption='[[5xfm]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5xfm' size='340' side='right'caption='[[5xfm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xfm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xfm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XFM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</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></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=5xfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfm OCA], [http://pdbe.org/5xfm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfm RCSB], [http://www.ebi.ac.uk/pdbsum/5xfm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfm 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=5xfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfm OCA], [http://pdbe.org/5xfm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfm RCSB], [http://www.ebi.ac.uk/pdbsum/5xfm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5xfm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xfm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Okuyama, M]]		[[Category: Okuyama, M]]

OCA at 06:27, 28 February 2018

OCA — Wed, 28 Feb 2018 06:27:27 GMT

←Older revision		Revision as of 06:27, 28 February 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5xfm is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of beta-arabinopyranosidase==
		+	<StructureSection load='5xfm' size='340' side='right' caption='[[5xfm]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xfm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XFM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5xfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfm OCA], [http://pdbe.org/5xfm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfm RCSB], [http://www.ebi.ac.uk/pdbsum/5xfm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside hydrolase family 97 (GH97) is one of the most interesting glycosidase families, which contains inverting and retaining glycosidases. Currently, only two enzyme types, alpha-glucoside hydrolase and alpha-galactosidase, are registered in the carbohydrate active enzyme database as GH97 function-known proteins. To explore new specificities, BT3661 and BT3664, which have distinct amino acid sequences when compared with that of GH97 alpha-glucoside hydrolase and alpha-galactosidase, were characterized in this study. BT3664 was identified to be an alpha-galactosidase, whereas BT3661 exhibits hydrolytic activity toward both beta-l-arabinopyranoside and alpha-d-galactopyranoside, and thus we designate BT3661 as a beta-l-arabinopyranosidase/alpha-d-galactosidase. Since this is the first dual substrate specificity enzyme in GH97, we investigated the substrate recognition mechanism of BT3661 by determining its three-dimensional structure and based on this structural data generated a number of mutants to probe the enzymatic mechanism. Structural comparison shows that the active-site pocket of BT3661 is similar to GH97 alpha-galactosidase BT1871, but the environment around the hydroxymethyl group of the galactopyranoside is different. While BT1871 bears Glu361 to stabilize the hydroxy group of C6 through a hydrogen bond with its carboxy group, BT3661 has Asn338 at the equivalent position. Amino acid mutation analysis indicates that the length of the side chain at Asn338 is important for defining specificity of BT3661. The kcat/Km value for the hydrolysis of p-nitrophenyl alpha-galactoside decreases when Asn338 is substituted with Glu, whereas an increase is observed when the mutation is Ala. Interestingly, mutation of Asn338 to Ala reduces the kcat/Km value for hydrolysis of p-nitrophenyl beta-l-arabinopyranoside.

-	~~Authors~~:	+	A novel glycoside hydrolase family 97 enzyme: Bifunctional beta-l-arabinopyranosidase/alpha-galactosidase from Bacteroides thetaiotaomicron.,Kikuchi A, Okuyama M, Kato K, Osaki S, Ma M, Kumagai Y, Matsunaga K, Klahan P, Tagami T, Yao M, Kimura A Biochimie. 2017 Nov;142:41-50. doi: 10.1016/j.biochi.2017.08.003. Epub 2017 Aug, 10. PMID:28804002<ref>PMID:28804002</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xfm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kato, K]]
		+	[[Category: Okuyama, M]]
		+	[[Category: Yao, M]]
		+	[[Category: Arabinopyranosidase]]
		+	[[Category: Hydrolase]]

OCA at 13:01, 27 April 2017

OCA — Thu, 27 Apr 2017 13:01:24 GMT

←Older revision		Revision as of 13:01, 27 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 19 Apr 2017 12:08:33 GMT

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

←Older revision

Revision as of 12:08, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xfm is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Apr 2017 12:08:31 GMT

New page: '''Unreleased structure''' The entry 5xfm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xfm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]