5a6k - Revision history

OCA at 11:04, 10 January 2024

OCA — Wed, 10 Jan 2024 11:04:29 GMT

←Older revision		Revision as of 11:04, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5a6k]] is a 2 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=5A6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A6K FirstGlance]. <br>		<table><tr><td colspan='2'>[[5a6k]] is a 2 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=5A6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A6K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NSG:(2S,3AR,5R,6R,7R,7AR)-5-(HYDROXYMETHYL)-2-METHYL-2,3A,5,6,7,7A-HEXAHYDRO-1H-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL'>NSG</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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NSG:(2S,3AR,5R,6R,7R,7AR)-5-(HYDROXYMETHYL)-2-METHYL-2,3A,5,6,7,7A-HEXAHYDRO-1H-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL'>NSG</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=5a6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6k OCA], [https://pdbe.org/5a6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a6k RCSB], [https://www.ebi.ac.uk/pdbsum/5a6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6k 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=5a6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6k OCA], [https://pdbe.org/5a6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a6k RCSB], [https://www.ebi.ac.uk/pdbsum/5a6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6k ProSAT]</span></td></tr>
	</table>		</table>

OCA at 04:41, 25 May 2023

OCA — Thu, 25 May 2023 04:41:43 GMT

←Older revision		Revision as of 04:41, 25 May 2023
Line 3:		Line 3:
	<StructureSection load='5a6k' size='340' side='right'caption='[[5a6k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5a6k' size='340' side='right'caption='[[5a6k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5a6k]] is a 2 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=5A6K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5A6K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5a6k]] is a 2 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=5A6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A6K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NSG:(2S,3AR,5R,6R,7R,7AR)-5-(HYDROXYMETHYL)-2-METHYL-2,3A,5,6,7,7A-HEXAHYDRO-1H-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL'>NSG</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NSG:(2S,3AR,5R,6R,7R,7AR)-5-(HYDROXYMETHYL)-2-METHYL-2,3A,5,6,7,7A-HEXAHYDRO-1H-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL'>NSG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a69\|5a69]], [[5a6a\|5a6a]], [[5a6b\|5a6b]], [[5a6j\|5a6j]]</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=5a6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6k OCA], [https://pdbe.org/5a6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a6k RCSB], [https://www.ebi.ac.uk/pdbsum/5a6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6k ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </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=5a6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6k OCA], [~~http~~://pdbe.org/5a6k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5a6k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5a6k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6k ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H2US73_STRPN A0A0H2US73_STRPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5a6k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5a6k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-N-acetylhexosaminidase 3D structures\|Beta-N-acetylhexosaminidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-N-acetylhexosaminidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Strpn~~]]	+	[[Category: Streptococcus pneumoniae TIGR4]]
-	[[Category: Boraston~~, A B~~]]	+	[[Category: Boraston AB]]
-	[[Category: Cid, M]]	+	[[Category: Cid M]]
-	[[Category: Higgins~~, M A~~]]	+	[[Category: Higgins MA]]
-	[[Category: Robb~~, C S]]~~	+	[[Category: Robb CS]]
-	~~[[Category: Bacterial protein]]~~	+
-	~~[[Category: Beta-hexosaminidase]]~~	+
-	~~[[Category: Carbohydrate conformation]]~~	+
-	~~[[Category: Catalytic domain]]~~	+
-	~~[[Category: Enzyme inhibitor]]~~	+
-	~~[[Category: Host-pathogen interaction]]~~	+
-	~~[[Category: Hydrogen bonding]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolysis]]~~	+
-	~~[[Category: Model]]~~	+
-	~~[[Category: Polysaccharide]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Streptococcus pneumoniae]]~~	+
-	~~[[Category: Virulence factor~~]]	+

OCA at 07:38, 4 March 2020

OCA — Wed, 04 Mar 2020 07:38:35 GMT

←Older revision		Revision as of 07:38, 4 March 2020
Line 1:		Line 1:

	==GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT==		==GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT==
-	<StructureSection load='5a6k' size='340' side='right' caption='[[5a6k]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5a6k' size='340' side='right'caption='[[5a6k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5a6k]] is a 2 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=5A6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A6K FirstGlance]. <br>		<table><tr><td colspan='2'>[[5a6k]] is a 2 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=5A6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A6K FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
		+	[[Category: Large Structures]]
	[[Category: Strpn]]		[[Category: Strpn]]
	[[Category: Boraston, A B]]		[[Category: Boraston, A B]]

OCA at 15:34, 16 November 2017

OCA — Thu, 16 Nov 2017 15:34:20 GMT

←Older revision		Revision as of 15:34, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='5a6k' size='340' side='right' caption='[[5a6k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5a6k' size='340' side='right' caption='[[5a6k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5a6k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A6K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5a6k]] is a 2 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=5A6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A6K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NSG:(2S,3AR,5R,6R,7R,7AR)-5-(HYDROXYMETHYL)-2-METHYL-2,3A,5,6,7,7A-HEXAHYDRO-1H-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL'>NSG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NSG:(2S,3AR,5R,6R,7R,7AR)-5-(HYDROXYMETHYL)-2-METHYL-2,3A,5,6,7,7A-HEXAHYDRO-1H-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL'>NSG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a69\|5a69]], [[5a6a\|5a6a]], [[5a6b\|5a6b]], [[5a6j\|5a6j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a69\|5a69]], [[5a6a\|5a6a]], [[5a6b\|5a6b]], [[5a6j\|5a6j]]</td></tr>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Beta-N-acetylhexosaminidase]]		[[Category: Beta-N-acetylhexosaminidase]]
		+	[[Category: Strpn]]
	[[Category: Boraston, A B]]		[[Category: Boraston, A B]]
	[[Category: Cid, M]]		[[Category: Cid, M]]

OCA at 19:29, 9 December 2016

OCA — Fri, 09 Dec 2016 19:29:04 GMT

←Older revision		Revision as of 19:29, 9 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5a6k is ~~ON HOLD~~	+	==GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT==
		+	<StructureSection load='5a6k' size='340' side='right' caption='[[5a6k]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5a6k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A6K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NSG:(2S,3AR,5R,6R,7R,7AR)-5-(HYDROXYMETHYL)-2-METHYL-2,3A,5,6,7,7A-HEXAHYDRO-1H-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL'>NSG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a69\|5a69]], [[5a6a\|5a6a]], [[5a6b\|5a6b]], [[5a6j\|5a6j]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </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=5a6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6k OCA], [http://pdbe.org/5a6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a6k RCSB], [http://www.ebi.ac.uk/pdbsum/5a6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6k ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	An important facet of the interaction between the pathogen Streptococcus pneumoniae (pneumococcus) and its human host is the ability of this bacterium to process host glycans. To achieve cleavage of the glycosidic bonds in host glycans, S. pneumoniae deploys a wide array of glycoside hydrolases. Here, we identify and characterize a new family 20 glycoside hydrolase, GH20C, from S. pneumoniae. Recombinant GH20C possessed the ability to hydrolyze the beta-linkages joining either N-acetylglucosamine or N-acetylgalactosamine to a wide variety of aglycon residues, thus revealing this enzyme to be a generalist N-acetylhexosaminidase in vitro. X-ray crystal structures were determined for GH20C in a ligand-free form, in complex with the N-acetylglucosamine and N-acetylgalactosamine products of catalysis and in complex with both gluco- and galacto-configured inhibitors O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino N-phenyl carbamate (PUGNAc), O-(2-acetamido-2-deoxy-D-galactopyranosylidene)amino N-phenyl carbamate (GalPUGNAc), N-acetyl-D-glucosamine-thiazoline (NGT), and N-acetyl-D-galactosamine-thiazoline (GalNGT) at resolutions from 1.84 to 2.7 A. These structures showed N-acetylglucosamine and N-acetylgalactosamine to be recognized via identical sets of molecular interactions. Although the same sets of interaction were maintained with the gluco- and galacto-configured inhibitors, the inhibition constants suggested preferred recognition of the axial O4 when an aglycon moiety was present (Ki for PUGNAc > GalPUGNAc) but preferred recognition of an equatorial O4 when the aglycon was absent (Ki for GalNGT > NGT). Overall, this study reveals GH20C to be another tool that is unique in the arsenal of S. pneumoniae and that it may implement the effort of the bacterium to utilize and/or destroy the wide array of host glycans that it may encounter.

-	~~Authors: Cid~~, M., Robb~~, C.S.~~, Higgins, ~~M.A.~~, ~~Boraston~~, A.B.	+	A Second beta-Hexosaminidase Encoded in the Streptococcus pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans.,Robb M, Robb CS, Higgins MA, Hobbs JK, Paton JC, Boraston AB J Biol Chem. 2015 Dec 25;290(52):30888-900. doi: 10.1074/jbc.M115.688630. Epub, 2015 Oct 21. PMID:26491009<ref>PMID:26491009</ref>

-	~~Description: GH20C~~, ~~Beta~~-~~hexosaminidase from Streptococcus pneumoniae in complex with Gal~~-~~NGT~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Robb~~, ~~C.S~~]]	+	<div class="pdbe-citations 5a6k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-N-acetylhexosaminidase]]
		+	[[Category: Boraston, A B]]
	[[Category: Cid, M]]		[[Category: Cid, M]]
-	[[Category: ~~Boraston~~, A.B]]	+	[[Category: Higgins, M A]]
-	[[Category: ~~Higgins~~, ~~M.A~~]]	+	[[Category: Robb, C S]]
		+	[[Category: Bacterial protein]]
		+	[[Category: Beta-hexosaminidase]]
		+	[[Category: Carbohydrate conformation]]
		+	[[Category: Catalytic domain]]
		+	[[Category: Enzyme inhibitor]]
		+	[[Category: Host-pathogen interaction]]
		+	[[Category: Hydrogen bonding]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolysis]]
		+	[[Category: Model]]
		+	[[Category: Polysaccharide]]
		+	[[Category: Protein binding]]
		+	[[Category: Streptococcus pneumoniae]]
		+	[[Category: Virulence factor]]

OCA: Protected "5a6k" [edit=sysop:move=sysop]

OCA — Wed, 08 Jul 2015 13:04:48 GMT

Protected "5a6k" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:04, 8 July 2015

OCA: New page: '''Unreleased structure''' The entry 5a6k is ON HOLD Authors: Cid, M., Robb, C.S., Higgins, M.A., Boraston, A.B. Description: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae i...

OCA — Wed, 08 Jul 2015 13:04:47 GMT

New page: '''Unreleased structure''' The entry 5a6k is ON HOLD Authors: Cid, M., Robb, C.S., Higgins, M.A., Boraston, A.B. Description: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae i...

New page

'''Unreleased structure'''

The entry 5a6k is ON HOLD

Authors: Cid, M., Robb, C.S., Higgins, M.A., Boraston, A.B.

Description: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT
[[Category: Unreleased Structures]]
[[Category: Robb, C.S]]
[[Category: Cid, M]]
[[Category: Boraston, A.B]]
[[Category: Higgins, M.A]]