5t9c - Revision history

OCA at 12:56, 4 October 2023

OCA — Wed, 04 Oct 2023 12:56:51 GMT

←Older revision		Revision as of 12:56, 4 October 2023
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	<StructureSection load='5t9c' size='340' side='right'caption='[[5t9c]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='5t9c' size='340' side='right'caption='[[5t9c]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t9c]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T9C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T9C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t9c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T9C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T9C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.48Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t91\|5t91]], [[5t9b\|5t9b]]</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=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpQ, ybeD, BSU02130 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5t9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t9c OCA], [https://pdbe.org/5t9c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t9c RCSB], [https://www.ebi.ac.uk/pdbsum/5t9c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t9c 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/Glycerophosphodiester_phosphodiesterase Glycerophosphodiester phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.46 3.1.4.46] </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=5t9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t9c OCA], [~~http~~://pdbe.org/5t9c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t9c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t9c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t9c ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLPQ_BACSU GLPQ_BACSU]] Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols.	+	[https://www.uniprot.org/uniprot/GLPQ_BACSU GLPQ_BACSU] Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu]]~~	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-	~~[[Category: Glycerophosphodiester phosphodiesterase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li~~, F K.K~~]]	+	[[Category: Li FKK]]
-	[[Category: Strynadka~~, N C.J]]~~	+	[[Category: Strynadka NCJ]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 16:39, 20 November 2019

OCA — Wed, 20 Nov 2019 16:39:23 GMT

←Older revision		Revision as of 16:39, 20 November 2019
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	==Crystal structure of B. subtilis 168 GlpQ in complex with glycerol-3-phosphate (1 hour soak)==		==Crystal structure of B. subtilis 168 GlpQ in complex with glycerol-3-phosphate (1 hour soak)==
-	<StructureSection load='5t9c' size='340' side='right' caption='[[5t9c]], [[Resolution\|resolution]] 1.48Å' scene=''>	+	<StructureSection load='5t9c' size='340' side='right'caption='[[5t9c]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t9c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T9C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T9C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t9c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T9C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T9C FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t91\|5t91]], [[5t9b\|5t9b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t91\|5t91]], [[5t9b\|5t9b]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpQ, ybeD, BSU02130 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerophosphodiester_phosphodiesterase Glycerophosphodiester phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.46 3.1.4.46] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerophosphodiester_phosphodiesterase Glycerophosphodiester phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.46 3.1.4.46] </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=5t9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t9c OCA], [http://pdbe.org/5t9c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t9c RCSB], [http://www.ebi.ac.uk/pdbsum/5t9c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t9c 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=5t9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t9c OCA], [http://pdbe.org/5t9c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t9c RCSB], [http://www.ebi.ac.uk/pdbsum/5t9c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t9c ProSAT]</span></td></tr>
Line 22:		Line 23:

	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Glycerophosphodiester phosphodiesterase]]		[[Category: Glycerophosphodiester phosphodiesterase]]
		+	[[Category: Large Structures]]
	[[Category: Li, F K.K]]		[[Category: Li, F K.K]]
	[[Category: Strynadka, N C.J]]		[[Category: Strynadka, N C.J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]

OCA at 08:04, 6 October 2017

OCA — Fri, 06 Oct 2017 08:04:44 GMT

←Older revision		Revision as of 08:04, 6 October 2017
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	</div>		</div>
	<div class="pdbe-citations 5t9c" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5t9c" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase\|Phosphodiesterase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:10, 9 December 2016

OCA — Fri, 09 Dec 2016 20:10:01 GMT

←Older revision		Revision as of 20:10, 9 December 2016
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GLPQ_BACSU GLPQ_BACSU]] Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols.		[[http://www.uniprot.org/uniprot/GLPQ_BACSU GLPQ_BACSU]] Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cell wall of most Gram-positive bacteria contains equal amounts of peptidoglycan and the phosphate-rich glycopolymer wall teichoic acid (WTA). During phosphate-limited growth of the Gram-positive model organism Bacillus subtilis 168, WTA is lost from the cell wall in a response mediated by the PhoPR two component system, which regulates genes involved in phosphate conservation and acquisition. It has been thought that WTA provides a phosphate source to sustain growth during starvation conditions, however, WTA degradative pathways have not been described for this, or any condition of bacterial growth. Here, we uncover roles for the Bacillus subtilis PhoP regulon genes glpQ and phoD as encoding secreted phosphodiesterases that function in WTA metabolism during phosphate starvation. Unlike the parent 168 strain, DeltaglpQ or DeltaphoD mutants retained WTA and ceased growth upon phosphate limitation. Characterization of GlpQ and PhoD enzymatic activities, in addition to X-ray crystal structures of GlpQ, revealed distinct mechanisms of WTA depolymerisation for the two enzymes - GlpQ catalyzes exolytic cleavage of individual monomer units, while PhoD catalyzes endo-hydrolysis at non-specific sites throughout the polymer. The combination of these activities appears requisite for the utilization of WTA as a phosphate reserve. Phenotypic characterization of the DeltaglpQ and DeltaphoD mutants revealed altered cell morphologies, and effects on autolytic activity and antibiotic susceptibilities that, unexpectedly, also occurred in phosphate-replete conditions. Our findings offer novel insight into the B. subtilis phosphate starvation response and implicate WTA hydrolase activity as a determinant of functional properties of the Gram-positive cell envelope.
		+
		+	Identification of two phosphate starvation-induced wall teichoic acid hydrolases provides first insights into the degradative pathway of a key bacterial cell wall component.,Myers CL, Li FK, Koo BM, El-Halfawy OM, French S, Gross CA, Strynadka NC, Brown ED J Biol Chem. 2016 Oct 25. pii: jbc.M116.760447. PMID:27780866<ref>PMID:27780866</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5t9c" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:32, 2 November 2016

OCA — Wed, 02 Nov 2016 18:32:36 GMT

←Older revision		Revision as of 18:32, 2 November 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t9c is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of B. subtilis 168 GlpQ in complex with glycerol-3-phosphate (1 hour soak)==
-		+	<StructureSection load='5t9c' size='340' side='right' caption='[[5t9c]], [[Resolution\|resolution]] 1.48Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5t9c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T9C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T9C FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t91\|5t91]], [[5t9b\|5t9b]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerophosphodiester_phosphodiesterase Glycerophosphodiester phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.46 3.1.4.46] </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=5t9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t9c OCA], [http://pdbe.org/5t9c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t9c RCSB], [http://www.ebi.ac.uk/pdbsum/5t9c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t9c ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLPQ_BACSU GLPQ_BACSU]] Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glycerophosphodiester phosphodiesterase]]
		+	[[Category: Li, F K.K]]
		+	[[Category: Strynadka, N C.J]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metal binding protein]]

OCA at 19:49, 5 October 2016

OCA — Wed, 05 Oct 2016 19:49:05 GMT

←Older revision		Revision as of 19:49, 5 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5t9c is ON HOLD	+	The entry 5t9c is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5t9c" [edit=sysop:move=sysop]

OCA — Wed, 21 Sep 2016 12:22:47 GMT

Protected "5t9c" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:22, 21 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t9c is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 21 Sep 2016 12:22:45 GMT

New page: '''Unreleased structure''' The entry 5t9c is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5t9c is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]