4d0t - Revision history

OCA at 12:18, 20 December 2023

2023-12-20T12:18:57Z

←Older revision		Revision as of 12:18, 20 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D0T FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D0T 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 2.45Å</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [https://pdbe.org/4d0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [https://www.ebi.ac.uk/pdbsum/4d0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d0t 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=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [https://pdbe.org/4d0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [https://www.ebi.ac.uk/pdbsum/4d0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d0t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_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 broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>	+	[https://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_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 broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:41, 14 September 2022

2022-09-14T07:41:44Z

←Older revision		Revision as of 07:41, 14 September 2022
Line 3:		Line 3:
	<StructureSection load='4d0t' size='340' side='right'caption='[[4d0t]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='4d0t' size='340' side='right'caption='[[4d0t]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D0T 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</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=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [https://pdbe.org/4d0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [https://www.ebi.ac.uk/pdbsum/4d0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d0t ProSAT]</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=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [~~http~~://pdbe.org/4d0t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d0t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d0t ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_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 broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>	+	[[https://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_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 broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Polypeptide N-acetylgalactosaminyltransferase]]
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
-	[[Category: Clausen, H]]	+	[[Category: Clausen H]]
-	[[Category: Companon, I]]	+	[[Category: Companon I]]
-	[[Category: Corzana, F]]	+	[[Category: Corzana F]]
-	[[Category: Hurtado-Guerrero, R]]	+	[[Category: Hurtado-Guerrero R]]
-	[[Category: Iglesias-Fernandez, J]]	+	[[Category: Iglesias-Fernandez J]]
-	[[Category: Kong, Y]]	+	[[Category: Kong Y]]
-	[[Category: Lira-Navarrete, E]]	+	[[Category: Lira-Navarrete E]]
-	[[Category: Peregrina~~, J M~~]]	+	[[Category: Peregrina JM]]
-	[[Category: Pinto~~, B M~~]]	+	[[Category: Pinto BM]]
-	[[Category: Rovira, C]]	+	[[Category: Rovira C]]
-	[[Category: Vocadlo, D]]	+	[[Category: Vocadlo D]]
-	[[Category: Zandberg~~, W F]]~~	+	[[Category: Zandberg WF]]
-	~~[[Category: Acetamido group]]~~	+
-	~~[[Category: Bi-bi kinetic mechanism]]~~	+
-	~~[[Category: Protein x-ray crystallography]]~~	+
-	~~[[Category: Qm/mm metadynamic]]~~	+
-	~~[[Category: Retaining galnac-t2]]~~	+
-	~~[[Category: Substrate specificity]]~~	+
-	~~[[Category: Substrate-guided sni-type reaction]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:45, 20 March 2019

2019-03-20T09:45:57Z

←Older revision		Revision as of 09:45, 20 March 2019
Line 1:		Line 1:

	==GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese==		==GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese==
-	<StructureSection load='4d0t' size='340' side='right' caption='[[4d0t]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='4d0t' size='340' side='right'caption='[[4d0t]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D0T 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</td></tr>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Polypeptide N-acetylgalactosaminyltransferase]]		[[Category: Polypeptide N-acetylgalactosaminyltransferase]]
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]

OCA at 10:39, 4 August 2016

2016-08-04T10:39:21Z

←Older revision		Revision as of 10:39, 4 August 2016
Line 1:		Line 1:
		+
	==GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese==		==GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese==
	<StructureSection load='4d0t' size='340' side='right' caption='[[4d0t]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='4d0t' size='340' side='right' caption='[[4d0t]], [[Resolution\|resolution]] 2.45Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</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=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [http://www.ebi.ac.uk/pdbsum/4d0t PDBsum]</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=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [http://pdbe.org/4d0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [http://www.ebi.ac.uk/pdbsum/4d0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d0t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4d0t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:26, 25 December 2014

2014-12-25T08:26:25Z

←Older revision		Revision as of 08:26, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D0T FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D0T FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [http://www.ebi.ac.uk/pdbsum/4d0t PDBsum]</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=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [http://www.ebi.ac.uk/pdbsum/4d0t PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GALT2_HUMAN GALT2_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 broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region.<ref>PMID:9295285</ref> <ref>PMID:12438318</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	[[Category: Polypeptide N-acetylgalactosaminyltransferase]]		[[Category: Polypeptide N-acetylgalactosaminyltransferase]]
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
-	[[Category: Clausen, H.]]	+	[[Category: Clausen, H]]
-	[[Category: Companon, I.]]	+	[[Category: Companon, I]]
-	[[Category: Corzana, F.]]	+	[[Category: Corzana, F]]
-	[[Category: Hurtado-Guerrero, R.]]	+	[[Category: Hurtado-Guerrero, R]]
-	[[Category: Iglesias-Fernandez, J.]]	+	[[Category: Iglesias-Fernandez, J]]
-	[[Category: Kong, Y.]]	+	[[Category: Kong, Y]]
-	[[Category: Lira-Navarrete, E.]]	+	[[Category: Lira-Navarrete, E]]
-	[[Category: Peregrina, J M.]]	+	[[Category: Peregrina, J M]]
-	[[Category: Pinto, B M.]]	+	[[Category: Pinto, B M]]
-	[[Category: Rovira, C.]]	+	[[Category: Rovira, C]]
-	[[Category: Vocadlo, D.]]	+	[[Category: Vocadlo, D]]
-	[[Category: Zandberg, W F.]]	+	[[Category: Zandberg, W F]]
	[[Category: Acetamido group]]		[[Category: Acetamido group]]
	[[Category: Bi-bi kinetic mechanism]]		[[Category: Bi-bi kinetic mechanism]]

OCA at 06:14, 2 July 2014

2014-07-02T06:14:33Z

←Older revision		Revision as of 06:14, 2 July 2014
Line 8:		Line 8:
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [http://www.ebi.ac.uk/pdbsum/4d0t PDBsum]</span></td></tr>		<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [http://www.ebi.ac.uk/pdbsum/4d0t PDBsum]</span></td></tr>
	<table>		<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The retaining glycosyltransferase GalNAc-T2 is a member of a large family of human polypeptide GalNAc-transferases that is responsible for the post-translational modification of many cell-surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum-mechanics/molecular-mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic-electronic level of detail. Our study provides a detailed structural rationale for an ordered bi-bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front-face SN i-type reaction in which the substrate N-acetyl sugar substituent coordinates efficient glycosyl transfer.
		+
		+	Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N-Acetylgalactosaminyltransferase 2.,Lira-Navarrete E, Iglesias-Fernandez J, Zandberg WF, Companon I, Kong Y, Corzana F, Pinto BM, Clausen H, Peregrina JM, Vocadlo DJ, Rovira C, Hurtado-Guerrero R Angew Chem Int Ed Engl. 2014 Jun 20. doi: 10.1002/anie.201402781. PMID:24954443<ref>PMID:24954443</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:00, 28 May 2014

2014-05-28T10:00:18Z

←Older revision		Revision as of 10:00, 28 May 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese==
-		+	<StructureSection load='4d0t' size='340' side='right' caption='[[4d0t]], [[Resolution\|resolution]] 2.45Å' scene=''>
-	~~The entry~~ 4d0t is ~~ON HOLD until Apr 30 2016~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4d0t]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D0T FirstGlance]. <br>
-	~~Authors~~: ~~Lira~~-~~Navarrete~~, E., ~~Iglesias~~-~~Fernandez~~, J., ~~Zandberg~~, W.F., ~~Companon~~, I., ~~Kong~~, Y., Corzana, F., ~~Pinto~~, ~~B.M~~., ~~Clausen, H~~., Peregrina, J.M., ~~Vocadlo, D~~., Rovira, C., ~~Hurtado-Guerrero~~, R.	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d0z\|4d0z]], [[4d11\|4d11]]</td></tr>
-	~~Description~~: ~~GalNAc~~-~~T2 crystal soaked with UDP~~-~~GalNAc, EA2 peptide and manganese~~	+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d0t RCSB], [http://www.ebi.ac.uk/pdbsum/4d0t PDBsum]</span></td></tr>
		+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Polypeptide N-acetylgalactosaminyltransferase]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Clausen, H.]]
		+	[[Category: Companon, I.]]
		+	[[Category: Corzana, F.]]
		+	[[Category: Hurtado-Guerrero, R.]]
		+	[[Category: Iglesias-Fernandez, J.]]
		+	[[Category: Kong, Y.]]
		+	[[Category: Lira-Navarrete, E.]]
		+	[[Category: Peregrina, J M.]]
		+	[[Category: Pinto, B M.]]
		+	[[Category: Rovira, C.]]
		+	[[Category: Vocadlo, D.]]
		+	[[Category: Zandberg, W F.]]
		+	[[Category: Acetamido group]]
		+	[[Category: Bi-bi kinetic mechanism]]
		+	[[Category: Protein x-ray crystallography]]
		+	[[Category: Qm/mm metadynamic]]
		+	[[Category: Retaining galnac-t2]]
		+	[[Category: Substrate specificity]]
		+	[[Category: Substrate-guided sni-type reaction]]
		+	[[Category: Transferase]]

OCA: Protected "4d0t" [edit=sysop:move=sysop]

2014-05-07T07:24:25Z

Protected "4d0t" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:24, 7 May 2014

OCA: New page: '''Unreleased structure''' The entry 4d0t is ON HOLD until Apr 30 2016 Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F., Pinto, B...

2014-05-07T07:24:24Z

New page: '''Unreleased structure''' The entry 4d0t is ON HOLD until Apr 30 2016 Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F., Pinto, B...

New page

'''Unreleased structure'''

The entry 4d0t is ON HOLD until Apr 30 2016

Authors: Lira-Navarrete, E., Iglesias-Fernandez, J., Zandberg, W.F., Companon, I., Kong, Y., Corzana, F., Pinto, B.M., Clausen, H., Peregrina, J.M., Vocadlo, D., Rovira, C., Hurtado-Guerrero, R.

Description: GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese