6upd - Revision history

OCA at 07:55, 11 October 2023

OCA — Wed, 11 Oct 2023 07:55:54 GMT

←Older revision		Revision as of 07:55, 11 October 2023
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	<StructureSection load='6upd' size='340' side='right'caption='[[6upd]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6upd' size='340' side='right'caption='[[6upd]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6upd]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salts Salts~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UPD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6UPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6upd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._SL1344 Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UPD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA~~-~~D-GLUCOSE'>GLC</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.052Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~otsB, SL1344_1863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=216597 SALTS])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRD_900006:trehalose'>PRD_900006</scene></td></tr>
-	<~~tr id~~='~~activity~~'><~~td class="sblockLbl"~~><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Trehalose-phosphatase Trehalose-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.12 3.1.3.12]~~ </~~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=6upd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6upd OCA], [https://pdbe.org/6upd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6upd RCSB], [https://www.ebi.ac.uk/pdbsum/6upd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6upd ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6upd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6upd OCA], [~~http~~://pdbe.org/6upd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6upd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6upd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6upd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/OTSB_SALTS OTSB_SALTS]] Removes the phosphate from trehalose 6-phosphate to produce free trehalose.	+	[https://www.uniprot.org/uniprot/OTSB_SALTS OTSB_SALTS] Removes the phosphate from trehalose 6-phosphate to produce free trehalose.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Salts]]~~	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344]]
-	~~[[Category: Trehalose-phosphatase~~]]	+	[[Category: Allen KN]]
-	[[Category: Allen~~, K N~~]]	+	[[Category: Harvey CM]]
-	[[Category: Harvey~~, C M~~]]	+	[[Category: O'Toole KH]]
-	[[Category: Toole~~, K H.O]]~~	+
-	~~[[Category: Had superfamily]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Sugar binding~~]]	+

OCA at 11:26, 23 September 2020

OCA — Wed, 23 Sep 2020 11:26:56 GMT

←Older revision		Revision as of 11:26, 23 September 2020
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	==Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose==		==Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose==
-	<StructureSection load='6upd' size='340' side='right'caption='[[6upd]]' scene=''>	+	<StructureSection load='6upd' size='340' side='right'caption='[[6upd]], [[Resolution\|resolution]] 2.05Å' 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=6UPD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6upd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salts Salts]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UPD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UPD FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6upd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6upd OCA], [http://pdbe.org/6upd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6upd RCSB], [http://www.ebi.ac.uk/pdbsum/6upd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6upd ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">otsB, SL1344_1863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216597 SALTS])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trehalose-phosphatase Trehalose-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.12 3.1.3.12] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6upd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6upd OCA], [http://pdbe.org/6upd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6upd RCSB], [http://www.ebi.ac.uk/pdbsum/6upd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6upd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OTSB_SALTS OTSB_SALTS]] Removes the phosphate from trehalose 6-phosphate to produce free trehalose.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trehalose-6-phosphate phosphatase (T6PP) catalyzes the dephosphorylation of trehalose 6-phosphate (T6P) to the disaccharide trehalose. The enzyme is not present in mammals but is essential to the viability of multiple lower organisms as trehalose is a critical metabolite, and T6P accumulation is toxic. Hence, T6PP is a target for therapeutics of human pathologies caused by bacteria, fungi, and parasitic nematodes. Here, we report the X-ray crystal structures of Salmonella typhimurium T6PP (StT6PP) in its apo form and in complex with the cofactor Mg(2+) and the substrate analogue trehalose 6-sulfate (T6S), the product trehalose, or the competitive inhibitor 4-n-octylphenyl alpha-d-glucopyranoside 6-sulfate (OGS). OGS replaces the substrate phosphoryl group with a sulfate group and the glucosyl ring distal to the sulfate group with an octylphenyl moiety. The structures of these substrate-analogue and product complexes with T6PP show that specificity is conferred via hydrogen bonds to the glucosyl group proximal to the phosphoryl moiety through Glu123, Lys125, and Glu167, conserved in T6PPs from multiple species. The structure of the first-generation inhibitor OGS shows that it retains the substrate-binding interactions observed for the sulfate group and the proximal glucosyl ring. The OGS octylphenyl moiety binds in a unique manner, indicating that this subsite can tolerate various chemotypes. Together, these findings show that these conserved interactions at the proximal glucosyl ring binding site could provide the basis for the development of broad-spectrum therapeutics, whereas variable interactions at the divergent distal subsite could present an opportunity for the design of potent organism-specific therapeutics.
		+
		+	Structural Analysis of Binding Determinants of Salmonella typhimurium Trehalose-6-phosphate Phosphatase Using Ground-State Complexes.,Harvey CM, O'Toole KH, Liu C, Mariano P, Dunaway-Mariano D, Allen KN Biochemistry. 2020 Aug 17. doi: 10.1021/acs.biochem.0c00317. PMID:32786412<ref>PMID:32786412</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6upd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Allen KN]]	+	[[Category: Salts]]
-	[[Category: Harvey CM]]	+	[[Category: Trehalose-phosphatase]]
-	[[Category: O'Toole KH]]	+	[[Category: Allen, K N]]
		+	[[Category: Harvey, C M]]
		+	[[Category: Toole, K H.O]]
		+	[[Category: Had superfamily]]
		+	[[Category: Hydrolase]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Sugar binding]]

OCA at 11:15, 26 August 2020

OCA — Wed, 26 Aug 2020 11:15:25 GMT

←Older revision		Revision as of 11:15, 26 August 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6upd is ~~ON HOLD until Paper Publication~~	+	==Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose==
-		+	<StructureSection load='6upd' size='340' side='right'caption='[[6upd]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UPD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6UPD FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6upd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6upd OCA], [http://pdbe.org/6upd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6upd RCSB], [http://www.ebi.ac.uk/pdbsum/6upd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6upd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Allen KN]]
		+	[[Category: Harvey CM]]
		+	[[Category: O'Toole KH]]

OCA at 13:52, 20 November 2019

OCA — Wed, 20 Nov 2019 13:52:07 GMT

←Older revision		Revision as of 13:52, 20 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6upd is ON HOLD	+	The entry 6upd is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 23 Oct 2019 05:19:13 GMT

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

←Older revision

Revision as of 05:19, 23 October 2019

OCA: New page: '''Unreleased structure''' The entry 6upd is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 23 Oct 2019 05:19:11 GMT

New page: '''Unreleased structure''' The entry 6upd is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6upd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]