6s2u - Revision history

OCA at 12:33, 24 January 2024

2024-01-24T12:33:56Z

←Older revision		Revision as of 12:33, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6s2u' size='340' side='right'caption='[[6s2u]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='6s2u' size='340' side='right'caption='[[6s2u]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s2u]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6S2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s2u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S2U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GN3:[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic+acid'>GN3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</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]] 2.95Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ththe16_1734 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GN3:[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic+acid'>GN3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/GTP_diphosphokinase GTP diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.5 2.7.6.5] </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=6s2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2u OCA], [https://pdbe.org/6s2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s2u RCSB], [https://www.ebi.ac.uk/pdbsum/6s2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2u 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=6s2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2u OCA], [~~http~~://pdbe.org/6s2u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6s2u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6s2u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2u ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~F6DES6_THETG F6DES6_THETG]~~] In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance.[RuleBase:RU003847]	+	[https://www.uniprot.org/uniprot/Q5SHL3_THET8 Q5SHL3_THET8] In eubacteria ppGpp (guanosine 3'-diphosphate 5'-diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance.[RuleBase:RU003847]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: GTP diphosphokinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Garcia-Pino, A~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: ~~Ppgpp]]~~	+	[[Category: Garcia-Pino A]]
-	~~[[Category: Ppgpp hydrolase]]~~	+
-	~~[[Category: Ppgpp synthetase]]~~	+
-	~~[[Category: Stringent response]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 11:33, 29 July 2020

2020-07-29T11:33:58Z

←Older revision		Revision as of 11:33, 29 July 2020
Line 1:		Line 1:

	==Structure of the catalytic domain of T. thermophilus Rel in complex with AMP and ppGpp==		==Structure of the catalytic domain of T. thermophilus Rel in complex with AMP and ppGpp==
-	<StructureSection load='6s2u' size='340' side='right'caption='[[6s2u]]' scene=''>	+	<StructureSection load='6s2u' size='340' side='right'caption='[[6s2u]], [[Resolution\|resolution]] 2.95Å' 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=6S2U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6S2U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s2u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6S2U 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=6s2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2u OCA], [http://pdbe.org/6s2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s2u RCSB], [http://www.ebi.ac.uk/pdbsum/6s2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2u 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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GN3:[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic+acid'>GN3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Ththe16_1734 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/GTP_diphosphokinase GTP diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.5 2.7.6.5] </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=6s2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2u OCA], [http://pdbe.org/6s2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s2u RCSB], [http://www.ebi.ac.uk/pdbsum/6s2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/F6DES6_THETG F6DES6_THETG]] In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance.[RuleBase:RU003847]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bifunctional Rel stringent factors, the most abundant class of RelA/SpoT homologs, are ribosome-associated enzymes that transfer a pyrophosphate from ATP onto the 3' of guanosine tri-/diphosphate (GTP/GDP) to synthesize the bacterial alarmone (p)ppGpp, and also catalyze the 3' pyrophosphate hydrolysis to degrade it. The regulation of the opposing activities of Rel enzymes is a complex allosteric mechanism that remains an active research topic despite decades of research. We show that a guanine-nucleotide-switch mechanism controls catalysis by Thermus thermophilus Rel (RelTt). The binding of GDP/ATP opens the N-terminal catalytic domains (NTD) of RelTt (RelTt(NTD)) by stretching apart the two catalytic domains. This activates the synthetase domain and allosterically blocks hydrolysis. Conversely, binding of ppGpp to the hydrolase domain closes the NTD, burying the synthetase active site and precluding the binding of synthesis precursors. This allosteric mechanism is an activity switch that safeguards against futile cycles of alarmone synthesis and degradation.
		+
		+	A nucleotide-switch mechanism mediates opposing catalytic activities of Rel enzymes.,Tamman H, Van Nerom K, Takada H, Vandenberk N, Scholl D, Polikanov Y, Hofkens J, Talavera A, Hauryliuk V, Hendrix J, Garcia-Pino A Nat Chem Biol. 2020 Aug;16(8):834-840. doi: 10.1038/s41589-020-0520-2. Epub 2020 , May 11. PMID:32393900<ref>PMID:32393900</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6s2u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: GTP diphosphokinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Garcia-Pino A]]	+	[[Category: Garcia-Pino, A]]
		+	[[Category: Ppgpp]]
		+	[[Category: Ppgpp hydrolase]]
		+	[[Category: Ppgpp synthetase]]
		+	[[Category: Stringent response]]
		+	[[Category: Transferase]]
		+	[[Category: Translation]]

OCA at 14:04, 8 July 2020

2020-07-08T14:04:05Z

←Older revision		Revision as of 14:04, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6s2u ~~is ON HOLD until Paper Publication~~	+	==Structure of the catalytic domain of T. thermophilus Rel in complex with AMP and ppGpp==
-		+	<StructureSection load='6s2u' size='340' side='right'caption='[[6s2u]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S2U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6S2U 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=6s2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s2u OCA], [http://pdbe.org/6s2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s2u RCSB], [http://www.ebi.ac.uk/pdbsum/6s2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s2u ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Garcia-Pino A]]

OCA: Protected "6s2u" [edit=sysop:move=sysop]

2019-07-03T04:29:52Z

Protected "6s2u" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:29, 3 July 2019

OCA: New page: '''Unreleased structure''' The entry 6s2u is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2019-07-03T04:29:50Z

New page: '''Unreleased structure''' The entry 6s2u is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6s2u is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]