7pmo - Revision history

OCA at 13:06, 1 February 2024

OCA — Thu, 01 Feb 2024 13:06:27 GMT

←Older revision		Revision as of 13:06, 1 February 2024
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	==Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)==		==Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)==
-	<StructureSection load='7pmo' size='340' side='right'caption='[[7pmo]]' scene=''>	+	<StructureSection load='7pmo' size='340' side='right'caption='[[7pmo]], [[Resolution\|resolution]] 2.10Å' 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=7PMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PMO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pmo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruminococcus_gnavus_ATCC_29149 Ruminococcus gnavus ATCC 29149]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PMO 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=7pmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pmo OCA], [https://pdbe.org/7pmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pmo RCSB], [https://www.ebi.ac.uk/pdbsum/7pmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pmo ProSAT]</span></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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7pmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pmo OCA], [https://pdbe.org/7pmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pmo RCSB], [https://www.ebi.ac.uk/pdbsum/7pmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pmo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A7B6A6_RUMGV A7B6A6_RUMGV]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human gut symbiont Ruminococcus gnavus displays strain-specific repertoires of glycoside hydrolases (GHs) contributing to its spatial location in the gut. Sequence similarity network analysis identified strain-specific differences in blood-group endo-beta-1,4-galactosidase belonging to the GH98 family. We determined the substrate and linkage specificities of GH98 from R. gnavus ATCC 29149, RgGH98, against a range of defined oligosaccharides and glycoconjugates including mucin. We showed by HPAEC-PAD and LC-FD-MS/MS that RgGH98 is specific for blood group A tetrasaccharide type II (BgA II). Isothermal titration calorimetry (ITC) and saturation transfer difference (STD) NMR confirmed RgGH98 affinity for blood group A over blood group B and H antigens. The molecular basis of RgGH98 strict specificity was further investigated using a combination of glycan microarrays, site-directed mutagenesis, and X-ray crystallography. The crystal structures of RgGH98 in complex with BgA trisaccharide (BgAtri) and of RgGH98 E411A with BgA II revealed a dedicated hydrogen network of residues, which were shown by site-directed mutagenesis to be critical to the recognition of the BgA epitope. We demonstrated experimentally that RgGH98 is part of an operon of 10 genes that is overexpresssed in vitro when R. gnavus ATCC 29149 is grown on mucin as sole carbon source as shown by RNAseq analysis and RT-qPCR confirmed RgGH98 expression on BgA II growth. Using MALDI-ToF MS, we showed that RgGH98 releases BgAtri from mucin and that pretreatment of mucin with RgGH98 confered R. gnavus E1 the ability to grow, by enabling the E1 strain to metabolise BgAtri and access the underlying mucin glycan chain. These data further support that the GH repertoire of R. gnavus strains enable them to colonise different nutritional niches in the human gut and has potential applications in diagnostic and therapeutics against infection.
		+
		+	The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract.,Wu H, Crost EH, Owen CD, van Bakel W, Martinez Gascuena A, Latousakis D, Hicks T, Walpole S, Urbanowicz PA, Ndeh D, Monaco S, Sanchez Salom L, Griffiths R, Reynolds RS, Colvile A, Spencer DIR, Walsh M, Angulo J, Juge N PLoS Biol. 2021 Dec 22;19(12):e3001498. doi: 10.1371/journal.pbio.3001498., eCollection 2021 Dec. PMID:34936658<ref>PMID:34936658</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7pmo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:01, 2 February 2022

OCA — Wed, 02 Feb 2022 07:01:48 GMT

←Older revision		Revision as of 07:01, 2 February 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7pmo ~~is ON HOLD until Paper Publication~~	+	==Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)==
-		+	<StructureSection load='7pmo' size='340' side='right'caption='[[7pmo]]' scene=''>
-	~~Authors~~: ~~Owen, C~~.D.~~, Wu, H~~.~~, Crost, E~~.H.~~, van Bakel, W~~.~~, Gascuena, A~~.M.~~, Latousakis, D~~., ~~Hicks, T~~.~~, Walpole, S~~.~~, Urbanowicz, P.A~~., ~~Ndeh, D~~., ~~Monaco, S~~.~~, Salom, L~~.S., ~~Griffiths, R~~.~~, Colvile, A~~.~~, Spencer, D.I.R~~., ~~Walsh, M~~.~~A., Angulo, J., Juge, N~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PMO FirstGlance]. <br>
-	~~Description: Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)~~	+	</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=7pmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pmo OCA], [https://pdbe.org/7pmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pmo RCSB], [https://www.ebi.ac.uk/pdbsum/7pmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pmo ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Spencer, D.I.R~~]]	+	__TOC__
-	[[Category: ~~Walpole, S~~]]	+	</StructureSection>
-	[[Category: ~~Angulo, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Griffiths, R~~]]	+	[[Category: Angulo J]]
-	[[Category: ~~Urbanowicz, P.A~~]]	+	[[Category: Colvile A]]
-	[[Category: ~~Walsh, M.A~~]]	+	[[Category: Crost EH]]
-	[[Category: ~~Crost, E.H~~]]	+	[[Category: Gascuena AM]]
-	[[Category: ~~Juge, N~~]]	+	[[Category: Griffiths R]]
-	[[Category: ~~Salom, L.~~S]]	+	[[Category: Hicks T]]
-	[[Category: ~~Monaco, S~~]]	+	[[Category: Juge N]]
-	[[Category: ~~Ndeh, D~~]]	+	[[Category: Latousakis D]]
-	[[Category: ~~Hicks, T~~]]	+	[[Category: Monaco S]]
-	[[Category: ~~Van Bakel, W~~]]	+	[[Category: Ndeh D]]
-	[[Category: ~~Gascuena, A.M~~]]	+	[[Category: Owen CD]]
-	[[Category: ~~Latousakis, D~~]]	+	[[Category: Salom LS]]
-	[[Category: ~~Colvile, A~~]]	+	[[Category: Spencer DIR]]
-	[[Category: ~~Owen, C.D~~]]	+	[[Category: Urbanowicz PA]]
-	[[Category: ~~Wu, H~~]]	+	[[Category: Walpole S]]
		+	[[Category: Walsh MA]]
		+	[[Category: Wu H]]
		+	[[Category: Van Bakel W]]

OCA at 04:04, 6 October 2021

OCA — Wed, 06 Oct 2021 04:04:25 GMT

←Older revision		Revision as of 04:04, 6 October 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Owen, C.D., Wu, H., Crost, E.H., van Bakel, W., Gascuena, A.M., Latousakis, D., Hicks, T., Walpole, S., Urbanowicz, P.A., Ndeh, D., Monaco, S., Salom, L.S., Griffiths, R., Colvile, A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.		Authors: Owen, C.D., Wu, H., Crost, E.H., van Bakel, W., Gascuena, A.M., Latousakis, D., Hicks, T., Walpole, S., Urbanowicz, P.A., Ndeh, D., Monaco, S., Salom, L.S., Griffiths, R., Colvile, A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.

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

OCA — Wed, 08 Sep 2021 07:38:24 GMT

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

←Older revision

Revision as of 07:38, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7pmo is ON HOLD Authors: Owen, C.D., Wu, H., Crost, E.H., van Bakel, W., Gascuena, A.M., Latousakis, D., Hicks, T., Walpole, S., Urbanowicz, P.A., N...

OCA — Wed, 08 Sep 2021 07:38:23 GMT

New page: '''Unreleased structure''' The entry 7pmo is ON HOLD Authors: Owen, C.D., Wu, H., Crost, E.H., van Bakel, W., Gascuena, A.M., Latousakis, D., Hicks, T., Walpole, S., Urbanowicz, P.A., N...

New page

'''Unreleased structure'''

The entry 7pmo is ON HOLD

Authors: Owen, C.D., Wu, H., Crost, E.H., van Bakel, W., Gascuena, A.M., Latousakis, D., Hicks, T., Walpole, S., Urbanowicz, P.A., Ndeh, D., Monaco, S., Salom, L.S., Griffiths, R., Colvile, A., Spencer, D.I.R., Walsh, M.A., Angulo, J., Juge, N.

Description: Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)
[[Category: Unreleased Structures]]
[[Category: Spencer, D.I.R]]
[[Category: Walpole, S]]
[[Category: Angulo, J]]
[[Category: Griffiths, R]]
[[Category: Urbanowicz, P.A]]
[[Category: Walsh, M.A]]
[[Category: Crost, E.H]]
[[Category: Juge, N]]
[[Category: Salom, L.S]]
[[Category: Monaco, S]]
[[Category: Ndeh, D]]
[[Category: Hicks, T]]
[[Category: Van Bakel, W]]
[[Category: Gascuena, A.M]]
[[Category: Latousakis, D]]
[[Category: Colvile, A]]
[[Category: Owen, C.D]]
[[Category: Wu, H]]