5nqa - Revision history

OCA at 13:22, 15 November 2023

OCA — Wed, 15 Nov 2023 13:22:23 GMT

←Older revision		Revision as of 13:22, 15 November 2023
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	<StructureSection load='5nqa' size='340' side='right'caption='[[5nqa]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5nqa' size='340' side='right'caption='[[5nqa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nqa]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NQA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5NQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nqa]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NQA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</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]] 1.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GALNT4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Polypeptide_N-acetylgalactosaminyltransferase Polypeptide~~ N-~~acetylgalactosaminyltransferase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.4.1.41 2.4.1.41]~~ </~~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=5nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nqa OCA], [https://pdbe.org/5nqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nqa RCSB], [https://www.ebi.ac.uk/pdbsum/5nqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nqa 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=5nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nqa OCA], [~~http~~://pdbe.org/5nqa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nqa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nqa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nqa ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GALT4_HUMAN GALT4_HUMAN]] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a highest activity toward Muc7, EA2 and Muc2, with a lowest activity than GALNT2. Glycosylates 'Thr-57' of SELPLG.	+	[https://www.uniprot.org/uniprot/GALT4_HUMAN GALT4_HUMAN] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a highest activity toward Muc7, EA2 and Muc2, with a lowest activity than GALNT2. Glycosylates 'Thr-57' of SELPLG.
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Polypeptide N-acetylgalactosaminyltransferase]]~~	+	[[Category: Clausen H]]
-	[[Category: Clausen, H]]	+	[[Category: Coelho H]]
-	[[Category: Coelho, H]]	+	[[Category: Companon I]]
-	[[Category: Companon, I]]	+	[[Category: Corzana F]]
-	[[Category: Corzana, F]]	+	[[Category: Daniel EJP]]
-	[[Category: Daniel~~, E J.P~~]]	+	[[Category: Diniz A]]
-	[[Category: Diniz, A]]	+	[[Category: Gerken TA]]
-	[[Category: Gerken~~, T A~~]]	+	[[Category: Hurtado-Guerrero R]]
-	[[Category: Hurtado-Guerrero, R]]	+	[[Category: Jimenez-Barbero J]]
-	[[Category: Jimenez-Barbero, J]]	+	[[Category: Jimenez-Oses G]]
-	[[Category: Jimenez-Oses, G]]	+	[[Category: Lira-Navarrete E]]
-	[[Category: Lira-Navarrete, E]]	+	[[Category: Marcelo F]]
-	[[Category: Marcelo, F]]	+	[[Category: Peregrina JM]]
-	[[Category: Peregrina~~, J M~~]]	+	[[Category: De las Rivas M]]
-	[[Category: Rivas, M ~~de las]]~~	+
-	~~[[Category: Chimera]]~~	+
-	~~[[Category: Flexible linker]]~~	+
-	~~[[Category: Galnac-t2]]~~	+
-	~~[[Category: Galnac-t4]]~~	+
-	~~[[Category: Glycosylation preference]]~~	+
-	~~[[Category: Std-nmr]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:10, 26 August 2020

OCA — Wed, 26 Aug 2020 12:10:19 GMT

←Older revision		Revision as of 12:10, 26 August 2020
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	==Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3==		==Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3==
-	<StructureSection load='5nqa' size='340' side='right' caption='[[5nqa]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5nqa' size='340' side='right'caption='[[5nqa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nqa]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NQA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NQA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nqa]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NQA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NQA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GALNT4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polypeptide_N-acetylgalactosaminyltransferase Polypeptide N-acetylgalactosaminyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.41 2.4.1.41] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polypeptide_N-acetylgalactosaminyltransferase Polypeptide N-acetylgalactosaminyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.41 2.4.1.41] </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=5nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nqa OCA], [http://pdbe.org/5nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nqa RCSB], [http://www.ebi.ac.uk/pdbsum/5nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nqa 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=5nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nqa OCA], [http://pdbe.org/5nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nqa RCSB], [http://www.ebi.ac.uk/pdbsum/5nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nqa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Polypeptide N-acetylgalactosaminyltransferase]]		[[Category: Polypeptide N-acetylgalactosaminyltransferase]]
	[[Category: Clausen, H]]		[[Category: Clausen, H]]

OCA at 06:11, 20 December 2017

OCA — Wed, 20 Dec 2017 06:11:27 GMT

←Older revision		Revision as of 06:11, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nqa is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3==
		+	<StructureSection load='5nqa' size='340' side='right' caption='[[5nqa]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5nqa]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NQA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polypeptide_N-acetylgalactosaminyltransferase Polypeptide N-acetylgalactosaminyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.41 2.4.1.41] </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=5nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nqa OCA], [http://pdbe.org/5nqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nqa RCSB], [http://www.ebi.ac.uk/pdbsum/5nqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nqa ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GALT4_HUMAN GALT4_HUMAN]] Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a highest activity toward Muc7, EA2 and Muc2, with a lowest activity than GALNT2. Glycosylates 'Thr-57' of SELPLG.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The polypeptide GalNAc-transferases (GalNAc-Ts), that initiate mucin-type O-glycosylation, consist of a catalytic and a lectin domain connected by a flexible linker. In addition to recognizing polypeptide sequence, the GalNAc-Ts exhibit unique long-range N- and/or C-terminal prior glycosylation (GalNAc-O-Ser/Thr) preferences modulated by the lectin domain. Here we report studies on GalNAc-T4 that reveal the origins of its unique N-terminal long-range glycopeptide specificity, which is the opposite of GalNAc-T2. The GalNAc-T4 structure bound to a monoglycopeptide shows that the GalNAc-binding site of its lectin domain is rotated relative to the homologous GalNAc-T2 structure, explaining their different long-range preferences. Kinetics and molecular dynamics simulations on several GalNAc-T2 flexible linker constructs show altered remote prior glycosylation preferences, confirming that the flexible linker dictates the rotation of the lectin domain, thus modulating the GalNAc-Ts' long-range preferences. This work for the first time provides the structural basis for the different remote prior glycosylation preferences of the GalNAc-Ts.

-	~~Authors~~:	+	The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences.,Rivas ML, Lira-Navarrete E, Daniel EJP, Companon I, Coelho H, Diniz A, Jimenez-Barbero J, Peregrina JM, Clausen H, Corzana F, Marcelo F, Jimenez-Oses G, Gerken TA, Hurtado-Guerrero R Nat Commun. 2017 Dec 5;8(1):1959. doi: 10.1038/s41467-017-02006-0. PMID:29208955<ref>PMID:29208955</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5nqa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Polypeptide N-acetylgalactosaminyltransferase]]
		+	[[Category: Clausen, H]]
		+	[[Category: Coelho, H]]
		+	[[Category: Companon, I]]
		+	[[Category: Corzana, F]]
		+	[[Category: Daniel, E J.P]]
		+	[[Category: Diniz, A]]
		+	[[Category: Gerken, T A]]
		+	[[Category: Hurtado-Guerrero, R]]
		+	[[Category: Jimenez-Barbero, J]]
		+	[[Category: Jimenez-Oses, G]]
		+	[[Category: Lira-Navarrete, E]]
		+	[[Category: Marcelo, F]]
		+	[[Category: Peregrina, J M]]
		+	[[Category: Rivas, M de las]]
		+	[[Category: Chimera]]
		+	[[Category: Flexible linker]]
		+	[[Category: Galnac-t2]]
		+	[[Category: Galnac-t4]]
		+	[[Category: Glycosylation preference]]
		+	[[Category: Std-nmr]]
		+	[[Category: Transferase]]

OCA at 11:39, 27 September 2017

OCA — Wed, 27 Sep 2017 11:39:42 GMT

←Older revision		Revision as of 11:39, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Thu, 27 Apr 2017 10:47:09 GMT

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

←Older revision

Revision as of 10:47, 27 April 2017

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

OCA — Thu, 27 Apr 2017 10:47:08 GMT

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

New page

'''Unreleased structure'''

The entry 5nqa is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]