5nrd - Revision history

OCA at 12:04, 22 November 2023

OCA — Wed, 22 Nov 2023 12:04:04 GMT

←Older revision		Revision as of 12:04, 22 November 2023
Line 1:		Line 1:

	==A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - alpha-3GalT in complex with Co2+, UDP-Gal and lactose - a3GalT-Co2+-UDP-Gal-LAT-2==		==A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - alpha-3GalT in complex with Co2+, UDP-Gal and lactose - a3GalT-Co2+-UDP-Gal-LAT-2==
-	<StructureSection load='5nrd' size='340' side='right' caption='[[5nrd]], [[Resolution\|resolution]] 2.12Å' scene=''>	+	<StructureSection load='5nrd' size='340' side='right'caption='[[5nrd]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nrd]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NRD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nrd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NRD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CO:COBALT+(II)+ION'~~>~~CO</scene>, <scene name='pdbligand=GDU:GALACTOSE~~-~~URIDINE-5-DIPHOSPHATE'>GDU</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LAT:BETA-LACTOSE'>LAT</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]] 2.12Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GGTA1 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9913 BOVIN]~~)~~</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900004:beta-lactose'>PRD_900004</scene></td></tr>
-	<~~tr id~~='~~activity~~'><~~td class="sblockLbl"~~><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/N-acetyllactosaminide_3-alpha-galactosyltransferase N-acetyllactosaminide 3-alpha-galactosyltransferase]~~, ~~with EC number [http~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.4.1.87 2.4.1.87]~~ </~~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=5nrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nrd OCA], [https://pdbe.org/5nrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nrd RCSB], [https://www.ebi.ac.uk/pdbsum/5nrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nrd ProSAT]</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=5nrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nrd OCA], [~~http~~://pdbe.org/5nrd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nrd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nrd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nrd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GGTA1_BOVIN GGTA1_BOVIN]] Transfer of galactose from UDP-galactose to an acceptor molecule (R).	+	[https://www.uniprot.org/uniprot/GGTA1_BOVIN GGTA1_BOVIN] Transfer of galactose from UDP-galactose to an acceptor molecule (R).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin~~]]	+	[[Category: Bos taurus]]
-	[[Category: ~~N-acetyllactosaminide 3-alpha-galactosyltransferase~~]]	+	[[Category: Large Structures]]
-	[[Category: Albesa-Jove, D]]	+	[[Category: Albesa-Jove D]]
-	[[Category: Guerin~~, M E~~]]	+	[[Category: Guerin ME]]
-	[[Category: Marina, A]]	+	[[Category: Marina A]]
-	[[Category: Sainz-Polo~~, M A]]~~	+	[[Category: Sainz-Polo MA]]
-	~~[[Category: Glycosyltransferase]]~~	+
-	~~[[Category: Gta]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:09, 22 November 2017

OCA — Wed, 22 Nov 2017 10:09:02 GMT

←Older revision		Revision as of 10:09, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='5nrd' size='340' side='right' caption='[[5nrd]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='5nrd' size='340' side='right' caption='[[5nrd]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nrd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nrd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NRD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LAT:BETA-LACTOSE'>LAT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LAT:BETA-LACTOSE'>LAT</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGTA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetyllactosaminide_3-alpha-galactosyltransferase N-acetyllactosaminide 3-alpha-galactosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.87 2.4.1.87] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetyllactosaminide_3-alpha-galactosyltransferase N-acetyllactosaminide 3-alpha-galactosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.87 2.4.1.87] </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=5nrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nrd OCA], [http://pdbe.org/5nrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nrd RCSB], [http://www.ebi.ac.uk/pdbsum/5nrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nrd ProSAT]</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=5nrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nrd OCA], [http://pdbe.org/5nrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nrd RCSB], [http://www.ebi.ac.uk/pdbsum/5nrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nrd ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovin]]
	[[Category: N-acetyllactosaminide 3-alpha-galactosyltransferase]]		[[Category: N-acetyllactosaminide 3-alpha-galactosyltransferase]]
	[[Category: Albesa-Jove, D]]		[[Category: Albesa-Jove, D]]

OCA at 06:54, 11 October 2017

OCA — Wed, 11 Oct 2017 06:54:01 GMT

←Older revision		Revision as of 06:54, 11 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nrd is ~~ON HOLD until Paper~~ Publication	+	==A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - alpha-3GalT in complex with Co2+, UDP-Gal and lactose - a3GalT-Co2+-UDP-Gal-LAT-2==
		+	<StructureSection load='5nrd' size='340' side='right' caption='[[5nrd]], [[Resolution\|resolution]] 2.12Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5nrd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NRD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GDU:GALACTOSE-URIDINE-5-DIPHOSPHATE'>GDU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LAT:BETA-LACTOSE'>LAT</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetyllactosaminide_3-alpha-galactosyltransferase N-acetyllactosaminide 3-alpha-galactosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.87 2.4.1.87] </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=5nrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nrd OCA], [http://pdbe.org/5nrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nrd RCSB], [http://www.ebi.ac.uk/pdbsum/5nrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nrd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GGTA1_BOVIN GGTA1_BOVIN]] Transfer of galactose from UDP-galactose to an acceptor molecule (R).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycosyltransferases (GTs) are a key family of enzymes that catalyses the synthesis of glycosidic bonds in all living organisms. The reaction involves the transfer of a glycosyl moiety and can proceed with retention or inversion of the anomeric configuration. To date, the elucidation of the catalytic mechanism of retaining GTs is of great controversy, particularly for those enzymes containing a putative nucleophilic residue in the active site, for which a double-displacement mechanism has been suggested. Here, we report native ternary complexes of the retaining alpha1,3-Galactosyltransferase (alpha3GalT) from Bos taurus - containing such a nucleophile in the active site - in a productive mode for catalysis, in the presence of its sugar donor UDP-Gal, the acceptor substrate lactose, and the divalent cation cofactor. This new experimental evidence supports a front-side substrate-assisted SNi-type reaction for alpha3GalT, and suggests a conserved common catalytic mechanism among retaining GTs.

-	~~Authors~~:	+	Structural Snapshots of the Reaction Center of Family GT6 alpha1,3-Galactosyltransferase with Native Substrates. Insights into the Catalytic Mechanism of Retaining Glycosyltransferases.,Guerin ME, Albesa-Jove D, Sainz-Polo MA, Marina A Angew Chem Int Ed Engl. 2017 Sep 28. doi: 10.1002/anie.201707922. PMID:28960760<ref>PMID:28960760</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5nrd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: N-acetyllactosaminide 3-alpha-galactosyltransferase]]
		+	[[Category: Albesa-Jove, D]]
		+	[[Category: Guerin, M E]]
		+	[[Category: Marina, A]]
		+	[[Category: Sainz-Polo, M A]]
		+	[[Category: Glycosyltransferase]]
		+	[[Category: Gta]]
		+	[[Category: Transferase]]

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

OCA — Thu, 04 May 2017 09:36:54 GMT

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

←Older revision

Revision as of 09:36, 4 May 2017

OCA: New page: '''Unreleased structure''' The entry 5nrd is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 04 May 2017 09:36:53 GMT

New page: '''Unreleased structure''' The entry 5nrd is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5nrd is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]