6phy - Revision history

OCA at 07:29, 11 October 2023

2023-10-11T07:29:50Z

← Older revision		Revision as of 07:29, 11 October 2023
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	<StructureSection load='6phy' size='340' side='right'caption='[[6phy]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6phy' size='340' side='right'caption='[[6phy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6phy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strpn Strpn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PHY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6phy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PHY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2Å</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aga, SP_1898 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=6phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6phy OCA], [https://pdbe.org/6phy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6phy RCSB], [https://www.ebi.ac.uk/pdbsum/6phy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6phy 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=6phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6phy OCA], [~~http~~://pdbe.org/6phy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6phy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6phy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6phy ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A0A0H2URQ6_STRPN A0A0H2URQ6_STRPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6phy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6phy" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Alpha-galactosidase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Strpn~~]]		[[Category: Streptococcus pneumoniae TIGR4]]
	[[Category: Boraston~~, A B~~]]		[[Category: Boraston AB]]
	[[Category: Pluvinage, B]]		[[Category: Pluvinage B]]
	~~[[Category: Glycoside hydrolase]]~~
	~~[[Category: Hydrolase~~]]

OCA at 08:03, 23 October 2019

2019-10-23T08:03:54Z

← Older revision		Revision as of 08:03, 23 October 2019
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	<StructureSection load='6phy' size='340' side='right'caption='[[6phy]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6phy' size='340' side='right'caption='[[6phy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6phy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6phy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PHY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aga, SP_1898 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </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=6phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6phy OCA], [http://pdbe.org/6phy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6phy RCSB], [http://www.ebi.ac.uk/pdbsum/6phy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6phy 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=6phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6phy OCA], [http://pdbe.org/6phy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6phy RCSB], [http://www.ebi.ac.uk/pdbsum/6phy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6phy ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Streptococcus pneumoniae is an opportunistic respiratory pathogen that can spread to other body sites, including the ears, brain and blood. The ability of this bacterium to breakdown, import and metabolize a wide range of glycans is key to its virulence. Intriguingly, S. pneumoniae can utilize several plant oligosaccharides for growth in vitro, including raffinose-family oligosaccharides (RFOs, which are alpha-(1-->6)-galactosyl extensions of sucrose). An RFO utilization locus has been identified in the pneumococcal genome; however, none of the proteins encoded by this locus have been biochemically characterized. The enigmatic ability of S. pneumoniae to utilize RFOs has recently received attention as mutations in two of the RFO locus genes have been linked to the tissue tropism of clinical pneumococcal isolates. Here, we use functional studies combined with X-ray crystallography to show that, while the pneumococcal RFO locus encodes for all the machinery required for uptake and degradation of RFOs, the individual pathway components are biochemically inefficient. We also demonstrate that the initiating enzyme in this pathway, the alpha-galactosidase Aga (a family 36 glycoside hydrolase), can cleave alpha-(1-->3)-linked galactose units from a linear blood group antigen. We propose that the pneumococcal RFO pathway is an evolutionary relic that is not utilized in this streptococcal species and, as such, is under no selection pressure to maintain binding affinity and/or catalytic efficiency. We speculate that the apparent contribution of RFO utilization to pneumococcal tissue tropism may, in fact, be due to the essential role the ATPase RafK plays in the transport of other carbohydrates.

			Molecular analysis of an enigmatic Streptococcus pneumoniae virulence factor: the raffinose-family oligosaccharide utilization system.,Hobbs JK, Meier EPW, Pluvinage B, Mey MA, Boraston AB J Biol Chem. 2019 Oct 7. pii: RA119.010280. doi: 10.1074/jbc.RA119.010280. PMID:31591266<ref>PMID:31591266</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6phy" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Alpha-galactosidase]]		[[Category: Alpha-galactosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
			[[Category: Strpn]]
	[[Category: Boraston, A B]]		[[Category: Boraston, A B]]
	[[Category: Pluvinage, B]]		[[Category: Pluvinage, B]]
	[[Category: Glycoside hydrolase]]		[[Category: Glycoside hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 10:32, 2 October 2019

2019-10-02T10:32:13Z

← Older revision		Revision as of 10:32, 2 October 2019
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6phy is ~~ON HOLD until Paper Publication~~		==SpAga D472N structure in complex alpha 1,3 galactobiose==
			<StructureSection load='6phy' size='340' side='right'caption='[[6phy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	~~Authors~~: ~~Pluvinage~~, B., ~~Boraston~~, A.B.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6phy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PHY FirstGlance]. <br>
	~~Description~~: ~~SpAga D472N structure in complex alpha 1,3 galactobiose~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </span></td></tr>
	[[Category: Boraston, A.B]]		<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=6phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6phy OCA], [http://pdbe.org/6phy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6phy RCSB], [http://www.ebi.ac.uk/pdbsum/6phy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6phy ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Alpha-galactosidase]]
			[[Category: Large Structures]]
			[[Category: Boraston, A B]]
	[[Category: Pluvinage, B]]		[[Category: Pluvinage, B]]
			[[Category: Glycoside hydrolase]]
			[[Category: Hydrolase]]

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

2019-07-03T04:22:15Z

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

← Older revision	Revision as of 04:22, 3 July 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6phy is ON HOLD until Paper Publication Authors: Pluvinage, B., Boraston, A.B. Description: SpAga D472N structure in complex alpha 1,3 galactobiose...

2019-07-03T04:22:13Z

New page: '''Unreleased structure''' The entry 6phy is ON HOLD until Paper Publication Authors: Pluvinage, B., Boraston, A.B. Description: SpAga D472N structure in complex alpha 1,3 galactobiose...

New page

'''Unreleased structure'''

The entry 6phy is ON HOLD until Paper Publication

Authors: Pluvinage, B., Boraston, A.B.

Description: SpAga D472N structure in complex alpha 1,3 galactobiose
[[Category: Unreleased Structures]]
[[Category: Boraston, A.B]]
[[Category: Pluvinage, B]]