5gmy - Revision history

OCA at 11:36, 2 August 2023

OCA — Wed, 02 Aug 2023 11:36:48 GMT

←Older revision		Revision as of 11:36, 2 August 2023
Line 3:		Line 3:
	<StructureSection load='5gmy' size='340' side='right'caption='[[5gmy]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5gmy' size='340' side='right'caption='[[5gmy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gmy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arcfu Arcfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GMY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gmy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304] 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=5GMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GMY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AF_0380 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~224325 ARCFU])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Dolichyl-diphosphooligosaccharide--protein_glycotransferase Dolichyl-diphosphooligosaccharide--protein glycotransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.18 2.4.99.18] </~~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=5gmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmy OCA], [https://pdbe.org/5gmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gmy RCSB], [https://www.ebi.ac.uk/pdbsum/5gmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmy 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=5gmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmy OCA], [https://pdbe.org/5gmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gmy RCSB], [https://www.ebi.ac.uk/pdbsum/5gmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AGLB3_ARCFU AGLB3_ARCFU] Oligosaccharyl transferase (OST) that catalyzes the initial transfer of a defined glycan (a glucose-linked heptasaccharide composed of 3 Glc, 2 Man, 2 Gal and a sulfate for A.fulgidus AglB-L) from the lipid carrier dolichol-monophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation.<ref>PMID:24127570</ref> <ref>PMID:27015803</ref> <ref>PMID:27997792</ref>
	<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: ~~Arcfu]]~~	+	[[Category: Archaeoglobus fulgidus DSM 4304]]
-	~~[[Category: Dolichyl-diphosphooligosaccharide--protein glycotransferase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kohda, D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Matsumoto, S~~]]	+	[[Category: Kohda D]]
-	[[Category: ~~Aglb]]~~	+	[[Category: Matsumoto S]]
-	~~[[Category: Archaeoglobus fulgidus]]~~	+
-	~~[[Category: N-lineked glycosylation]]~~	+
-	~~[[Category: Oligosaccharyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:38, 31 March 2021

OCA — Wed, 31 Mar 2021 10:38:49 GMT

←Older revision		Revision as of 10:38, 31 March 2021
Line 3:		Line 3:
	<StructureSection load='5gmy' size='340' side='right'caption='[[5gmy]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5gmy' size='340' side='right'caption='[[5gmy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gmy]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GMY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gmy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GMY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_0380 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_0380 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Dolichyl-diphosphooligosaccharide--protein_glycotransferase Dolichyl-diphosphooligosaccharide--protein glycotransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.18 2.4.99.18] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dolichyl-diphosphooligosaccharide--protein_glycotransferase Dolichyl-diphosphooligosaccharide--protein glycotransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.18 2.4.99.18] </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=5gmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmy OCA], [~~http~~://pdbe.org/5gmy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gmy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gmy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmy 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=5gmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmy OCA], [https://pdbe.org/5gmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gmy RCSB], [https://www.ebi.ac.uk/pdbsum/5gmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:08, 26 February 2020

OCA — Wed, 26 Feb 2020 10:08:49 GMT

←Older revision		Revision as of 10:08, 26 February 2020
Line 1:		Line 1:

	==Crystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) tethered with an acceptor peptide containing the NVT sequon via a disulfide bond==		==Crystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) tethered with an acceptor peptide containing the NVT sequon via a disulfide bond==
-	<StructureSection load='5gmy' size='340' side='right' caption='[[5gmy]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5gmy' size='340' side='right'caption='[[5gmy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gmy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gmy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_0380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dolichyl-diphosphooligosaccharide--protein_glycotransferase Dolichyl-diphosphooligosaccharide--protein glycotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.18 2.4.99.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dolichyl-diphosphooligosaccharide--protein_glycotransferase Dolichyl-diphosphooligosaccharide--protein glycotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.18 2.4.99.18] </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=5gmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmy OCA], [http://pdbe.org/5gmy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmy RCSB], [http://www.ebi.ac.uk/pdbsum/5gmy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmy 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=5gmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmy OCA], [http://pdbe.org/5gmy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmy RCSB], [http://www.ebi.ac.uk/pdbsum/5gmy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmy ProSAT]</span></td></tr>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arcfu]]
	[[Category: Dolichyl-diphosphooligosaccharide--protein glycotransferase]]		[[Category: Dolichyl-diphosphooligosaccharide--protein glycotransferase]]
		+	[[Category: Large Structures]]
	[[Category: Kohda, D]]		[[Category: Kohda, D]]
	[[Category: Matsumoto, S]]		[[Category: Matsumoto, S]]

OCA at 17:55, 1 February 2017

OCA — Wed, 01 Feb 2017 17:55:04 GMT

←Older revision		Revision as of 17:55, 1 February 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gmy is ~~ON HOLD until Jul~~ 18 ~~2018~~	+	==Crystal structure of the Archaeoglobus fulgidus oligosaccharyltransferase (O29867_ARCFU) tethered with an acceptor peptide containing the NVT sequon via a disulfide bond==
		+	<StructureSection load='5gmy' size='340' side='right' caption='[[5gmy]], [[Resolution\|resolution]] 3.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gmy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dolichyl-diphosphooligosaccharide--protein_glycotransferase Dolichyl-diphosphooligosaccharide--protein glycotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.18 2.4.99.18] </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=5gmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmy OCA], [http://pdbe.org/5gmy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmy RCSB], [http://www.ebi.ac.uk/pdbsum/5gmy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmy ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Oligosaccharyltransferase (OST) transfers an oligosaccharide chain to the Asn residue in the Asn-X-Ser/Thr sequon in proteins, where X is not proline. A sequon was tethered to an archaeal OST enzyme via a disulfide bond. The positions of the cysteine residues in the OST protein and the sequon-containing acceptor peptide were selected by reference to the eubacterial OST structure in a noncovalent complex with an acceptor peptide. We determined the crystal structure of the cross-linked OST-sequon complex. The Ser/Thr-binding pocket recognizes the Thr residue in the sequon, and the catalytic structure termed the "carboxylate dyad" interacted with the Asn residue. Thus, the recognition and the catalytic mechanism of the sequon are conserved between the archaeal and eubacterial OSTs. We found that the tethered peptides in the complex were efficiently glycosylated in the presence of the oligosaccharide donor. The stringent requirements are greatly relaxed in the cross-linked state. The two conserved acidic residues in the catalytic structure were each dispensable, although the double mutation abolished the activity. A Gln residue at the Asn position in the sequon functioned as an acceptor, and the hydroxy group at position +2 was not required. In the standard assay using short free peptides, strong amino acid preferences were observed at the X position, but the preferences, except for Pro, completely disappeared in the cross-linked state. By skipping the initial binding process and stabilizing the complex state, the catalytically competent cross-linked complex offers a unique system for studying the oligosaccharyl transfer reaction.

-	~~Authors~~:	+	Tethering an N-Glycosylation Sequon-Containing Peptide Creates a Catalytically Competent Oligosaccharyltransferase Complex.,Matsumoto S, Taguchi Y, Shimada A, Igura M, Kohda D Biochemistry. 2017 Jan 31;56(4):602-611. doi: 10.1021/acs.biochem.6b01089. Epub, 2017 Jan 17. PMID:27997792<ref>PMID:27997792</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5gmy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dolichyl-diphosphooligosaccharide--protein glycotransferase]]
		+	[[Category: Kohda, D]]
		+	[[Category: Matsumoto, S]]
		+	[[Category: Aglb]]
		+	[[Category: Archaeoglobus fulgidus]]
		+	[[Category: N-lineked glycosylation]]
		+	[[Category: Oligosaccharyltransferase]]
		+	[[Category: Transferase]]

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

OCA — Wed, 27 Jul 2016 10:38:11 GMT

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

←Older revision

Revision as of 10:38, 27 July 2016

OCA: New page: '''Unreleased structure''' The entry 5gmy is ON HOLD until Jul 18 2018 Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Jul 2016 10:38:10 GMT

New page: '''Unreleased structure''' The entry 5gmy is ON HOLD until Jul 18 2018 Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5gmy is ON HOLD until Jul 18 2018

Authors:

Description:
[[Category: Unreleased Structures]]