OCA at 08:19, 14 November 2018

2018-11-14T08:19:44Z

←Older revision		Revision as of 08:19, 14 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6gxc is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Bacterial oligosaccharyltransferase PglB in complex with an inhibitory peptide and a reactive lipid-linked oligosaccharide analog==
		+	<StructureSection load='6gxc' size='340' side='right' caption='[[6gxc]], [[Resolution\|resolution]] 3.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6gxc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GXC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GXC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FFK:[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]+[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]+hydrogen+phosphate'>FFK</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAB:2,4-DIAMINOBUTYRIC+ACID'>DAB</scene>, <scene name='pdbligand=PPN:PARA-NITROPHENYLALANINE'>PPN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.19 2.4.99.19] </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=6gxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gxc OCA], [http://pdbe.org/6gxc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gxc RCSB], [http://www.ebi.ac.uk/pdbsum/6gxc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gxc ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PGLB_CAMLR PGLB_CAMLR]] Oligosaccharyltransferase that catalyzes the transfer of a preassembled heptasaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains, affording a beta-linked glycan to the asparagine side chain of target proteins.<ref>PMID:21677752</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Oligosaccharyltransferase (OST) is a key enzyme of the N-glycosylation pathway, where it catalyzes the transfer of a glycan from a lipid-linked oligosaccharide (LLO) to an acceptor asparagine within the conserved sequon N-X-T/S. A previous structure of a ternary complex of bacterial single subunit OST, PglB, bound to a non-hydrolyzable LLO analog and a wild type acceptor peptide showed how both substrates bind and how an external loop (EL5) of the enzyme provided specific substrate-binding contacts. However, there was a relatively large separation of the substrates at the active site. Here we present the X-ray structure of PglB bound to a reactive LLO analog and an inhibitory peptide, revealing previously unobserved interactions in the active site. We found that the atoms forming the N-glycosidic bond (C-1 of the GlcNAc moiety of LLO and the -NH2 group of the peptide) are closer than in the previous structure, suggesting that we have captured a conformation closer to the transition state of the reaction. We find that the distance between the divalent metal ion and the glycosidic oxygen of LLO is now 4 A, suggesting that the metal stabilizes the leaving group of the nucleophilic substitution reaction. Further, the carboxylate group of a conserved aspartate of PglB mediates an interaction network between the reducing-end sugar of the LLO, the asparagine side chain of the acceptor peptide, and a bound divalent metal ion. The interactions identified in this novel state are likely to be relevant in the catalytic mechanisms of all OSTs.

-	~~Authors~~:	+	Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide.,Napiorkowska M, Boilevin J, Darbre T, Reymond JL, Locher KP Sci Rep. 2018 Nov 2;8(1):16297. doi: 10.1038/s41598-018-34534-0. PMID:30389987<ref>PMID:30389987</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6gxc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Transferase]]
		+	[[Category: Boilevin, J]]
		+	[[Category: Darbre, T]]
		+	[[Category: Locher, K P]]
		+	[[Category: Napiorkowska, M]]
		+	[[Category: Reymond, J L]]
		+	[[Category: Glycosyltransferase]]
		+	[[Category: Lipid-linked oligosaccharide]]
		+	[[Category: Membrane protein]]
		+	[[Category: Ternary complex]]

OCA: Protected "6gxc" [edit=sysop:move=sysop]

2018-07-04T05:56:32Z

Protected "6gxc" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:56, 4 July 2018

OCA: New page: '''Unreleased structure''' The entry 6gxc is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2018-07-04T05:56:31Z

New page: '''Unreleased structure''' The entry 6gxc is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6gxc is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]

6gxc - Revision history

OCA at 08:19, 14 November 2018

OCA: Protected "6gxc" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6gxc is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures