5fmc - Revision history

OCA at 06:57, 19 July 2023

OCA — Wed, 19 Jul 2023 06:57:11 GMT

←Older revision		Revision as of 06:57, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5fmc' size='340' side='right'caption='[[5fmc]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5fmc' size='340' side='right'caption='[[5fmc]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fmc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cbs_7918 Cbs 7918~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FMC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fmc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phaffia_rhodozyma Phaffia rhodozyma]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FMC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.84Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ann\|5ann]], [[5fix\|5fix]], [[5fk7\|5fk7]], [[5fk8\|5fk8]], [[5fkb\|5fkb]], [[5fkc\|5fkc]], [[5fmb\|5fmb]], [[5fmd\|5fmd]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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-fructofuranosidase Beta-fructofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.26 3.2.1.26] </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=5fmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fmc OCA], [https://pdbe.org/5fmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fmc RCSB], [https://www.ebi.ac.uk/pdbsum/5fmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fmc 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=5fmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fmc OCA], [~~http~~://pdbe.org/5fmc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fmc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fmc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fmc ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/J7HDY4_PHARH J7HDY4_PHARH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-fructofuranosidase]]
-	[[Category: Cbs 7918]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ramirez-Escudero, M~~]]	+	[[Category: Phaffia rhodozyma]]
-	[[Category: ~~Sanz~~-~~Aparicio, J~~]]	+	[[Category: Ramirez-Escudero M]]
-	[[Category: ~~Bis~~-~~tris propane]]~~	+	[[Category: Sanz-Aparicio J]]
-	~~[[Category: Buffer]]~~	+
-	~~[[Category: Catalysis]]~~	+
-	~~[[Category: Catalytic domain]]~~	+
-	~~[[Category: Cloning]]~~	+
-	~~[[Category: Dimerization]]~~	+
-	~~[[Category: Fructose]]~~	+
-	~~[[Category: Fungal protein]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Invertase]]~~	+
-	~~[[Category: Kinetic]]~~	+
-	~~[[Category: Molecular]]~~	+
-	~~[[Category: Molecular conformation]]~~	+
-	~~[[Category: Pichia pastori]]~~	+
-	~~[[Category: Prebiotic]]~~	+
-	~~[[Category: Protein conformation]]~~	+
-	~~[[Category: Protein structure]]~~	+
-	~~[[Category: Quaternary]]~~	+
-	~~[[Category: Secondary]]~~	+
-	~~[[Category: Substrate specificity~~]]	+

OCA at 07:25, 6 May 2020

OCA — Wed, 06 May 2020 07:25:40 GMT

←Older revision		Revision as of 07:25, 6 May 2020
Line 1:		Line 1:

	==Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS-TRIS propane buffer==		==Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS-TRIS propane buffer==
-	<StructureSection load='5fmc' size='340' side='right' caption='[[5fmc]], [[Resolution\|resolution]] 1.84Å' scene=''>	+	<StructureSection load='5fmc' size='340' side='right'caption='[[5fmc]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fmc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FMC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fmc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_7918 Cbs 7918]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FMC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FMC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ann\|5ann]], [[5fix\|5fix]], [[5fk7\|5fk7]], [[5fk8\|5fk8]], [[5fkb\|5fkb]], [[5fkc\|5fkc]], [[5fmb\|5fmb]], [[5fmd\|5fmd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ann\|5ann]], [[5fix\|5fix]], [[5fk7\|5fk7]], [[5fk8\|5fk8]], [[5fkb\|5fkb]], [[5fkc\|5fkc]], [[5fmb\|5fmb]], [[5fmd\|5fmd]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-fructofuranosidase Beta-fructofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.26 3.2.1.26] </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-fructofuranosidase Beta-fructofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.26 3.2.1.26] </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=5fmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fmc OCA], [http://pdbe.org/5fmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fmc RCSB], [http://www.ebi.ac.uk/pdbsum/5fmc PDBsum]</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=5fmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fmc OCA], [http://pdbe.org/5fmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fmc RCSB], [http://www.ebi.ac.uk/pdbsum/5fmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fmc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Beta-fructofuranosidase]]		[[Category: Beta-fructofuranosidase]]
		+	[[Category: Cbs 7918]]
		+	[[Category: Large Structures]]
	[[Category: Ramirez-Escudero, M]]		[[Category: Ramirez-Escudero, M]]
	[[Category: Sanz-Aparicio, J]]		[[Category: Sanz-Aparicio, J]]

OCA at 17:36, 10 May 2016

OCA — Tue, 10 May 2016 17:36:24 GMT

←Older revision		Revision as of 17:36, 10 May 2016
Line 1:		Line 1:
		+
	==Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS-TRIS propane buffer==		==Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS-TRIS propane buffer==
	<StructureSection load='5fmc' size='340' side='right' caption='[[5fmc]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5fmc' size='340' side='right' caption='[[5fmc]], [[Resolution\|resolution]] 1.84Å' scene=''>

OCA at 17:18, 10 February 2016

OCA — Wed, 10 Feb 2016 17:18:56 GMT

←Older revision		Revision as of 17:18, 10 February 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS-TRIS propane buffer==
		+	<StructureSection load='5fmc' size='340' side='right' caption='[[5fmc]], [[Resolution\|resolution]] 1.84Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fmc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FMC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ann\|5ann]], [[5fix\|5fix]], [[5fk7\|5fk7]], [[5fk8\|5fk8]], [[5fkb\|5fkb]], [[5fkc\|5fkc]], [[5fmb\|5fmb]], [[5fmd\|5fmd]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-fructofuranosidase Beta-fructofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.26 3.2.1.26] </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=5fmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fmc OCA], [http://pdbe.org/5fmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fmc RCSB], [http://www.ebi.ac.uk/pdbsum/5fmc PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xanthophyllomyces dendrorhous beta-fructofuranosidase (XdINV) is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. It also catalyzes the synthesis of FOS, prebiotics that stimulate the growth of beneficial bacteria in human gut. In contrast to most fructosylating enzymes, XdINV produces neo-FOS, which makes it an interesting biotechnology target. We present here its three-dimensional structure, which shows the expected bimodular arrangement but, also, a long extension of its C-terminus that together with a N-linked glycan mediate the formation of an unusual dimer. This dimer shapes two active sites communicated by a long channel, which might indicate its potential ability to house branched fructans. This arrangement could be representative of a group of GH32 yeast enzymes having the traits observed in XdINV. Inactivated D80A mutant was used to obtain complexes with relevant substrates and products, their crystals structures showing at least four binding subsites at each active site. Moreover, two different positions are observed from subsite +2 depending of the substrate and, thus, a flexible loop (Glu334-His343) is essential in binding sucrose and beta(2-1) linked oligosaccharides. Conversely, beta(2-6) and neo-type substrates are accommodated mainly by stacking to Trp105, explaining the production of neokestose and the efficient fructosylating activity of XdINV on alpha-glucosides. The role of relevant residues has been investigated by mutagenesis and kinetics measurements and a model for the transfructosylating reaction has been proposed. The plasticity of its active site makes XdINV a valuable and flexible biocatalyst to produce novel bioconjugates.

-	~~The entry 5fmc is ON HOLD until Paper Publication~~	+	Structural analysis of beta-fructofuranosidase from Xanthophyllomyces dendrorhous reveals unique features and the crucial role of N-glycosylation in oligomerization and activity.,Ramirez-Escudero M, Gimeno-Perez M, Gonzalez B, Linde D, Merdzo Z, Fernandez-Lobato M, Sanz-Aparicio J J Biol Chem. 2016 Jan 28. pii: jbc.M115.708495. PMID:26823463<ref>PMID:26823463</ref>

-	~~Authors: Ramirez-Escudero~~, M.~~, Sanz-Aparicio, J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Structure of D80A~~-~~fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS~~-~~TRIS propane buffer~~	+	<div class="pdbe-citations 5fmc" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-fructofuranosidase]]
	[[Category: Ramirez-Escudero, M]]		[[Category: Ramirez-Escudero, M]]
	[[Category: Sanz-Aparicio, J]]		[[Category: Sanz-Aparicio, J]]
		+	[[Category: Bis-tris propane]]
		+	[[Category: Buffer]]
		+	[[Category: Catalysis]]
		+	[[Category: Catalytic domain]]
		+	[[Category: Cloning]]
		+	[[Category: Dimerization]]
		+	[[Category: Fructose]]
		+	[[Category: Fungal protein]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Invertase]]
		+	[[Category: Kinetic]]
		+	[[Category: Molecular]]
		+	[[Category: Molecular conformation]]
		+	[[Category: Pichia pastori]]
		+	[[Category: Prebiotic]]
		+	[[Category: Protein conformation]]
		+	[[Category: Protein structure]]
		+	[[Category: Quaternary]]
		+	[[Category: Secondary]]
		+	[[Category: Substrate specificity]]

OCA at 12:45, 9 December 2015

OCA — Wed, 09 Dec 2015 12:45:56 GMT

←Older revision		Revision as of 12:45, 9 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Ramirez-Escudero, M., Sanz-Aparicio, J.		Authors: Ramirez-Escudero, M., Sanz-Aparicio, J.

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

OCA — Tue, 01 Dec 2015 03:35:38 GMT

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

←Older revision

Revision as of 03:35, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fmc is ON HOLD Authors: Ramirez-Escudero, M., Sanz-Aparicio, J. Description: Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorho...

OCA — Tue, 01 Dec 2015 03:35:37 GMT

New page: '''Unreleased structure''' The entry 5fmc is ON HOLD Authors: Ramirez-Escudero, M., Sanz-Aparicio, J. Description: Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorho...

New page

'''Unreleased structure'''

The entry 5fmc is ON HOLD

Authors: Ramirez-Escudero, M., Sanz-Aparicio, J.

Description: Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS-TRIS propane buffer
[[Category: Unreleased Structures]]
[[Category: Ramirez-Escudero, M]]
[[Category: Sanz-Aparicio, J]]