8csf - Revision history

OCA at 11:59, 23 October 2024

2024-10-23T11:59:56Z

← Older revision		Revision as of 11:59, 23 October 2024
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	WbbB, a lipopolysaccharide O-antigen synthesis enzyme from Raoultella terrigena, contains an N-terminal glycosyltransferase domain with a highly modified architecture that adds a terminal beta-Kdo (3-deoxy-D-manno-oct-2-ulosonic acid) residue to the O-antigen saccharide, with retention of stereochemistry. We show, using mass spectrometry, that WbbB forms a covalent adduct between the catalytic nucleophile, Asp232, and Kdo. We also determine X-ray structures for the CMP-beta-Kdo donor complex, for Kdo-adducts with D232N and D232C WbbB variants, for a synthetic disaccharide acceptor complex, and for a ternary complex with both a Kdo-adduct and the acceptor. Together, these structures show that the enzyme-linked Asp232-Kdo adduct rotates to reposition the Kdo into a second sub-site, which then transfers Kdo to the acceptor. Retaining glycosyltransferases were thought to use only the front-side ~~SNi~~ substitution mechanism; here we show that retaining glycosyltransferases can also potentially use double-displacement mechanisms, but incorporating an additional catalytic subsite requires rearrangement of the protein's architecture.		WbbB, a lipopolysaccharide O-antigen synthesis enzyme from Raoultella terrigena, contains an N-terminal glycosyltransferase domain with a highly modified architecture that adds a terminal beta-Kdo (3-deoxy-D-manno-oct-2-ulosonic acid) residue to the O-antigen saccharide, with retention of stereochemistry. We show, using mass spectrometry, that WbbB forms a covalent adduct between the catalytic nucleophile, Asp232, and Kdo. We also determine X-ray structures for the CMP-beta-Kdo donor complex, for Kdo-adducts with D232N and D232C WbbB variants, for a synthetic disaccharide acceptor complex, and for a ternary complex with both a Kdo-adduct and the acceptor. Together, these structures show that the enzyme-linked Asp232-Kdo adduct rotates to reposition the Kdo into a second sub-site, which then transfers Kdo to the acceptor. Retaining glycosyltransferases were thought to use only the front-side S(N)i substitution mechanism; here we show that retaining glycosyltransferases can also potentially use double-displacement mechanisms, but incorporating an additional catalytic subsite requires rearrangement of the protein's architecture.

	The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.,Forrester TJB, Ovchinnikova OG, Li Z, Kitova EN, Nothof JT, Koizumi A, Klassen JS, Lowary TL, Whitfield C, Kimber MS Nat Commun. 2022 Oct 21;13(1):6277. doi: 10.1038/s41467-022-33988-1. PMID:36271007<ref>PMID:36271007</ref>		The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.,Forrester TJB, Ovchinnikova OG, Li Z, Kitova EN, Nothof JT, Koizumi A, Klassen JS, Lowary TL, Whitfield C, Kimber MS Nat Commun. 2022 Oct 21;13(1):6277. doi: 10.1038/s41467-022-33988-1. PMID:36271007<ref>PMID:36271007</ref>

OCA at 17:23, 18 October 2023

2023-10-18T17:23:51Z

← Older revision		Revision as of 17:23, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8csf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Raoultella_terrigena Raoultella terrigena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CSF FirstGlance]. <br>		<table><tr><td colspan='2'>[[8csf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Raoultella_terrigena Raoultella terrigena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CSF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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]] 2.4Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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=8csf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8csf OCA], [https://pdbe.org/8csf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8csf RCSB], [https://www.ebi.ac.uk/pdbsum/8csf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8csf 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=8csf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8csf OCA], [https://pdbe.org/8csf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8csf RCSB], [https://www.ebi.ac.uk/pdbsum/8csf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8csf ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:33, 9 November 2022

2022-11-09T07:33:09Z

← Older revision		Revision as of 07:33, 9 November 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 8csf is ~~ON HOLD until Paper~~ Publication		==WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex==
			<StructureSection load='8csf' size='340' side='right'caption='[[8csf]], [[Resolution\|resolution]] 2.40Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[8csf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Raoultella_terrigena Raoultella terrigena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CSF FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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=8csf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8csf OCA], [https://pdbe.org/8csf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8csf RCSB], [https://www.ebi.ac.uk/pdbsum/8csf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8csf ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q6U8B0_RAOTE Q6U8B0_RAOTE]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			WbbB, a lipopolysaccharide O-antigen synthesis enzyme from Raoultella terrigena, contains an N-terminal glycosyltransferase domain with a highly modified architecture that adds a terminal beta-Kdo (3-deoxy-D-manno-oct-2-ulosonic acid) residue to the O-antigen saccharide, with retention of stereochemistry. We show, using mass spectrometry, that WbbB forms a covalent adduct between the catalytic nucleophile, Asp232, and Kdo. We also determine X-ray structures for the CMP-beta-Kdo donor complex, for Kdo-adducts with D232N and D232C WbbB variants, for a synthetic disaccharide acceptor complex, and for a ternary complex with both a Kdo-adduct and the acceptor. Together, these structures show that the enzyme-linked Asp232-Kdo adduct rotates to reposition the Kdo into a second sub-site, which then transfers Kdo to the acceptor. Retaining glycosyltransferases were thought to use only the front-side SNi substitution mechanism; here we show that retaining glycosyltransferases can also potentially use double-displacement mechanisms, but incorporating an additional catalytic subsite requires rearrangement of the protein's architecture.

	~~Authors:~~ Forrester, T.J.~~B., Kimber, M~~.S.		The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.,Forrester TJB, Ovchinnikova OG, Li Z, Kitova EN, Nothof JT, Koizumi A, Klassen JS, Lowary TL, Whitfield C, Kimber MS Nat Commun. 2022 Oct 21;13(1):6277. doi: 10.1038/s41467-022-33988-1. PMID:36271007<ref>PMID:36271007</ref>

	~~Description: WbbB D232C~~-~~Kdo adduct + alpha~~-~~Rha(1,3)GlcNAc ternary complex~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: Forrester~~, T.J.B~~]]		<div class="pdbe-citations 8csf" style="background-color:#fffaf0;"></div>
	[[Category: Kimber~~, M.S~~]]		== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Raoultella terrigena]]
			[[Category: Forrester TJB]]
			[[Category: Kimber MS]]

OCA at 06:57, 25 May 2022

2022-05-25T06:57:58Z

← Older revision		Revision as of 06:57, 25 May 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8csf is ON HOLD		The entry 8csf is ON HOLD until Paper Publication

	Authors: Forrester, T.J.B., Kimber, M.S.		Authors: Forrester, T.J.B., Kimber, M.S.

OCA: Protected "8csf" [edit=sysop:move=sysop]

2022-05-18T09:23:59Z

Protected "8csf" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:23, 18 May 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8csf is ON HOLD Authors: Forrester, T.J.B., Kimber, M.S. Description: WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex [[Category: Unre...

2022-05-18T09:23:58Z

New page: '''Unreleased structure''' The entry 8csf is ON HOLD Authors: Forrester, T.J.B., Kimber, M.S. Description: WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex [[Category: Unre...

New page

'''Unreleased structure'''

The entry 8csf is ON HOLD

Authors: Forrester, T.J.B., Kimber, M.S.

Description: WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex
[[Category: Unreleased Structures]]
[[Category: Forrester, T.J.B]]
[[Category: Kimber, M.S]]