5ifp - Revision history

OCA at 13:49, 30 August 2023

OCA — Wed, 30 Aug 2023 13:49:45 GMT

←Older revision		Revision as of 13:49, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='5ifp' size='340' side='right'caption='[[5ifp]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='5ifp' size='340' side='right'caption='[[5ifp]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ifp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IFP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ifp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger_CBS_513.88 Aspergillus niger CBS 513.88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IFP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.71Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5ifp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifp OCA], [~~http~~://pdbe.org/5ifp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ifp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ifp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifp 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=5ifp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifp OCA], [https://pdbe.org/5ifp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ifp RCSB], [https://www.ebi.ac.uk/pdbsum/5ifp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BGALA_ASPNC BGALA_ASPNC]] Cleaves beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans.	+	[https://www.uniprot.org/uniprot/BGALA_ASPNC BGALA_ASPNC] Cleaves beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-galactosidase~~]]	+	[[Category: Aspergillus niger CBS 513 88]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Becerra, M]]	+	[[Category: Becerra M]]
-	[[Category: Cerdan~~, M E~~]]	+	[[Category: Cerdan ME]]
-	[[Category: Ramirez-Escudero, M]]	+	[[Category: Ramirez-Escudero M]]
-	[[Category: Rico-Diaz, A]]	+	[[Category: Rico-Diaz A]]
-	[[Category: Sanz-Aparicio, J]]	+	[[Category: Sanz-Aparicio J]]
-	[[Category: Vazquez, A ~~Vizoso]]~~	+	[[Category: Vizoso Vazquez A]]
-	~~[[Category: Aspergillus niger]]~~	+
-	~~[[Category: B-galactosidase]]~~	+
-	~~[[Category: Carbohydrate metabolism]]~~	+
-	~~[[Category: Fungal protein]]~~	+
-	~~[[Category: Galactooligosaccharide]]~~	+
-	~~[[Category: Gh35]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Go]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Kinetic]]~~	+
-	~~[[Category: Native]]~~	+
-	~~[[Category: Prebiotic]]~~	+
-	~~[[Category: Protein conformation]]~~	+
-	~~[[Category: Substrate specificity]]~~	+
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: Wildtype~~]]	+

OCA at 07:17, 3 June 2020

OCA — Wed, 03 Jun 2020 07:17:00 GMT

←Older revision		Revision as of 07:17, 3 June 2020
Line 1:		Line 1:

	==STRUCTURE OF BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER==		==STRUCTURE OF BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER==
-	<StructureSection load='5ifp' size='340' side='right' caption='[[5ifp]], [[Resolution\|resolution]] 1.71Å' scene=''>	+	<StructureSection load='5ifp' size='340' side='right'caption='[[5ifp]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ifp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IFP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ifp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IFP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=5ifp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifp OCA], [http://pdbe.org/5ifp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifp RCSB], [http://www.ebi.ac.uk/pdbsum/5ifp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifp 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=5ifp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifp OCA], [http://pdbe.org/5ifp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifp RCSB], [http://www.ebi.ac.uk/pdbsum/5ifp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ifp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ifp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
		+	[[Category: Large Structures]]
	[[Category: Becerra, M]]		[[Category: Becerra, M]]
	[[Category: Cerdan, M E]]		[[Category: Cerdan, M E]]

OCA at 12:41, 6 November 2017

OCA — Mon, 06 Nov 2017 12:41:11 GMT

←Older revision		Revision as of 12:41, 6 November 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ifp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ifp" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Galactosidase\|Galactosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:37, 3 August 2017

OCA — Thu, 03 Aug 2017 10:37:34 GMT

←Older revision		Revision as of 10:37, 3 August 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ifp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ifp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase\|Galactosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:57, 19 April 2017

OCA — Wed, 19 Apr 2017 12:57:30 GMT

←Older revision		Revision as of 12:57, 19 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ifp is ~~ON HOLD until Paper~~ Publication	+	==STRUCTURE OF BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER==
		+	<StructureSection load='5ifp' size='340' side='right' caption='[[5ifp]], [[Resolution\|resolution]] 1.71Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ifp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IFP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=5ifp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifp OCA], [http://pdbe.org/5ifp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifp RCSB], [http://www.ebi.ac.uk/pdbsum/5ifp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BGALA_ASPNC BGALA_ASPNC]] Cleaves beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	beta-galactosidases are biotechnologically interesting enzymes that catalyze the hydrolysis or transgalactosylation of beta-galactosides. Among them, the Aspergillus niger beta-galactosidase (AnbetaGal) belongs to the glycoside hydrolase family 35 (GH35) and is widely used in the industry due to its high hydrolytic activity degrading lactose. We present here its three-dimensional structure in complex with different oligosaccharides, to illustrate the structural determinants of the broad specificity of the enzyme against different glycoside linkages. Remarkably, the residues Phe264, Tyr304 and Trp806 make a dynamic hydrophobic platform that accommodates the sugar at subsite +1 suggesting a main role on the recognition of structurally different substrates. Moreover, complexes with the trisaccharides show two potential subsites +2 depending on the substrate type. This feature and the peculiar shape of its wide cavity suggest that AnbetaGal might accommodate branched substrates from the complex net of polysaccharides composing the plant material in its natural environment. Relevant residues were selected and mutagenesis analyses were performed to evaluate their role in the catalytic performance and the hydrolase/transferase ratio of AnbetaGal. Thus, we generated mutants with improved transgalactosylation activity. In particular, the variant Y304F/Y355H/N357G/W806F displays a higher level of galacto-oligosaccharides (GOS) production than the Aspergillus oryzae beta-galactosidase, which is the preferred enzyme in the industry owing to its high transferase activity. Our results provide new knowledge on the determinants modulating specificity and the catalytic performance of fungal GH35 beta-galactosidases. In turn, this fundamental background gives novel tools for the future improvement of these enzymes, which represent an interesting target for rational design. This article is protected by copyright. All rights reserved.

-	~~Authors:~~ Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan~~, M.E.~~, Becerra, M., Sanz-Aparicio, J.	+	Structural features of Aspergillus niger beta-galactosidase define its activity against glycoside linkages.,Rico-Diaz A, Ramirez-Escudero M, Vizoso-Vazquez A, Cerdan ME, Becerra M, Sanz-Aparicio J FEBS J. 2017 Apr 8. doi: 10.1111/febs.14083. PMID:28391618<ref>PMID:28391618</ref>

-	~~Description: STRUCTURE OF BETA~~-~~GALACTOSIDASE FROM ASPERGILLUS NIGER~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ifp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-galactosidase]]
	[[Category: Becerra, M]]		[[Category: Becerra, M]]
		+	[[Category: Cerdan, M E]]
	[[Category: Ramirez-Escudero, M]]		[[Category: Ramirez-Escudero, M]]
-	[[Category: Vizoso Vazquez, A]]
-	[[Category: Cerdan, M.E]]
-	[[Category: Sanz-Aparicio, J]]
	[[Category: Rico-Diaz, A]]		[[Category: Rico-Diaz, A]]
		+	[[Category: Sanz-Aparicio, J]]
		+	[[Category: Vazquez, A Vizoso]]
		+	[[Category: Aspergillus niger]]
		+	[[Category: B-galactosidase]]
		+	[[Category: Carbohydrate metabolism]]
		+	[[Category: Fungal protein]]
		+	[[Category: Galactooligosaccharide]]
		+	[[Category: Gh35]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Go]]
		+	[[Category: Hydrolase]]
		+	[[Category: Kinetic]]
		+	[[Category: Native]]
		+	[[Category: Prebiotic]]
		+	[[Category: Protein conformation]]
		+	[[Category: Substrate specificity]]
		+	[[Category: Tim barrel]]
		+	[[Category: Wildtype]]

OCA at 00:28, 11 May 2016

OCA — Wed, 11 May 2016 00:28:06 GMT

←Older revision		Revision as of 00:28, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.		Authors: Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.

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

OCA — Thu, 10 Mar 2016 02:14:36 GMT

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

←Older revision

Revision as of 02:14, 10 March 2016

OCA: New page: '''Unreleased structure''' The entry 5ifp is ON HOLD Authors: Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J. Description: STRUCTU...

OCA — Thu, 10 Mar 2016 02:14:34 GMT

New page: '''Unreleased structure''' The entry 5ifp is ON HOLD Authors: Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J. Description: STRUCTU...

New page

'''Unreleased structure'''

The entry 5ifp is ON HOLD

Authors: Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.

Description: STRUCTURE OF BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER
[[Category: Unreleased Structures]]
[[Category: Becerra, M]]
[[Category: Ramirez-Escudero, M]]
[[Category: Vizoso Vazquez, A]]
[[Category: Cerdan, M.E]]
[[Category: Sanz-Aparicio, J]]
[[Category: Rico-Diaz, A]]