OCA at 10:48, 28 July 2021

OCA — Wed, 28 Jul 2021 10:48:09 GMT

←Older revision		Revision as of 10:48, 28 July 2021
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	==Crystal Structure of POMGNT2 in complex with UDP==		==Crystal Structure of POMGNT2 in complex with UDP==
-	<StructureSection load='7e9j' size='340' side='right'caption='[[7e9j]]' scene=''>	+	<StructureSection load='7e9j' size='340' side='right'caption='[[7e9j]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7e9j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E9J FirstGlance]. <br>
-	</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=7e9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e9j OCA], [https://pdbe.org/7e9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e9j RCSB], [https://www.ebi.ac.uk/pdbsum/7e9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e9j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POMGNT2, AGO61, GTDC2 ([https://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'>[https://en.wikipedia.org/wiki/Protein_O-mannose_beta-1,4-N-acetylglucosaminyltransferase Protein O-mannose beta-1,4-N-acetylglucosaminyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.312 2.4.1.312] </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=7e9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e9j OCA], [https://pdbe.org/7e9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e9j RCSB], [https://www.ebi.ac.uk/pdbsum/7e9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e9j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PMGT2_BOVIN PMGT2_BOVIN]] O-linked mannose beta-1,4-N-acetylglucosaminyltransferase that transfers UDP-N-acetyl-D-glucosamine to the 4-position of the mannose to generate N-acetyl-D-glucosamine-beta-1,4-O-D-mannosylprotein. Involved in the biosynthesis of the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity (By similarity).[UniProtKB:Q8NAT1]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Defects in the O-mannosyl glycan of alpha-dystroglycan (alpha-DG) are associated with alpha-dystroglycanopathy, a group of congenital muscular dystrophies. While alpha-DG has many O-mannosylation sites, only the specific positions can be modified with the functional O-mannosyl glycan, namely, core M3-type glycan. POMGNT2 is a glycosyltransferase which adds beta1,4-linked GlcNAc to the O-mannose (Man) residue to acquire core M3-type glycan. Although it is assumed that POMGNT2 extends the specific O-Man residues around particular amino acid sequences, the details are not well understood. Here, we determined a series of crystal structures of POMGNT2 with and without the acceptor O-mannosyl peptides and identified the critical interactions between POMGNT2 and the acceptor peptide. POMGNT2 has an N-terminal catalytic domain and a C-terminal fibronectin type III (FnIII) domain, and forms a dimer. The acceptor peptide is sandwiched between the two protomers. The catalytic domain of one protomer recognizes the O-mannosylation site (TPT motif), and the FnIII domain of the other protomer recognizes the C-terminal region of the peptide. Structure-based mutational studies confirmed that amino acid residues of the catalytic domain interacting with mannose or the TPT motif are essential for POMGNT2 enzymatic activity. In addition, the FnIII domain is also essential for the activity and it interacts with the peptide mainly by hydrophobic interaction. Our study provides the first atomic-resolution insights into specific acceptor recognition by the FnIII domain of POMGNT2. The catalytic mechanism of POMGNT2 is proposed based on the structure.
		+
		+	The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan.,Imae R, Kuwabara N, Manya H, Tanaka T, Tsuyuguchi M, Mizuno M, Endo T, Kato R Genes Cells. 2021 Apr 23. doi: 10.1111/gtc.12853. PMID:33893702<ref>PMID:33893702</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7e9j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovin]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kuwabara N]]	+	[[Category: Protein O-mannose beta-1,4-N-acetylglucosaminyltransferase]]
		+	[[Category: Kuwabara, N]]
		+	[[Category: Glycosyltransferase]]
		+	[[Category: O-mannose type glycosylation]]
		+	[[Category: Transferase]]

OCA at 08:53, 5 May 2021

OCA — Wed, 05 May 2021 08:53:19 GMT

←Older revision		Revision as of 08:53, 5 May 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7e9j ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of POMGNT2 in complex with UDP==
-		+	<StructureSection load='7e9j' size='340' side='right'caption='[[7e9j]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E9J FirstGlance]. <br>
-	~~Description~~:	+	</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=7e9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e9j OCA], [https://pdbe.org/7e9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e9j RCSB], [https://www.ebi.ac.uk/pdbsum/7e9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e9j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kuwabara N]]

OCA at 05:16, 17 March 2021

OCA — Wed, 17 Mar 2021 05:16:28 GMT

←Older revision		Revision as of 05:16, 17 March 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7e9j is ON HOLD	+	The entry 7e9j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7e9j" [edit=sysop:move=sysop]

OCA — Wed, 10 Mar 2021 14:36:35 GMT

Protected "7e9j" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:36, 10 March 2021

OCA: New page: '''Unreleased structure''' The entry 7e9j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Mar 2021 14:36:33 GMT

New page: '''Unreleased structure''' The entry 7e9j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7e9j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7e9j - Revision history

OCA at 10:48, 28 July 2021

OCA at 08:53, 5 May 2021

OCA at 05:16, 17 March 2021

OCA: Protected "7e9j" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7e9j is ON HOLD Authors: Description: Category: Unreleased Structures