6yxa - Revision history

OCA at 13:37, 24 January 2024

OCA — Wed, 24 Jan 2024 13:37:43 GMT

←Older revision		Revision as of 13:37, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6yxa' size='340' side='right'caption='[[6yxa]], [[Resolution\|resolution]] 3.95Å' scene=''>		<StructureSection load='6yxa' size='340' side='right'caption='[[6yxa]], [[Resolution\|resolution]] 3.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yxa]] 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=6YXA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YXA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yxa]] 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=6YXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.95Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>relA, BSU27600 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~224308 BACSU])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6yxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxa OCA], [https://pdbe.org/6yxa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxa RCSB], [https://www.ebi.ac.uk/pdbsum/6yxa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxa 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=6yxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxa OCA], [~~http~~://pdbe.org/6yxa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yxa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yxa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxa ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RELA_BACSU RELA_BACSU]] 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. This enzyme catalyzes the formation of pppGpp which is then hydrolyzed to form ppGpp, it is probably the hydrolysis activity that is required for optimal growth (Probable).<ref>PMID:18067544</ref>	+	[https://www.uniprot.org/uniprot/RELA_BACSU RELA_BACSU] 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. This enzyme catalyzes the formation of pppGpp which is then hydrolyzed to form ppGpp, it is probably the hydrolysis activity that is required for optimal growth (Probable).<ref>PMID:18067544</ref>
	<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: ~~Bacsu]]~~	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-	~~[[Category: GTP diphosphokinase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bange, G]]	+	[[Category: Bange G]]
-	[[Category: Pausch, P]]	+	[[Category: Pausch P]]
-	~~[[Category: Ribosome interacting]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Stringent response~~]]	+

OCA at 07:52, 30 September 2020

OCA — Wed, 30 Sep 2020 07:52:40 GMT

←Older revision		Revision as of 07:52, 30 September 2020
Line 1:		Line 1:

	==Structure of the bifunctional Rel enzyme from B. subtilis==		==Structure of the bifunctional Rel enzyme from B. subtilis==
-	<StructureSection load='6yxa' size='340' side='right'caption='[[6yxa]]' scene=''>	+	<StructureSection load='6yxa' size='340' side='right'caption='[[6yxa]], [[Resolution\|resolution]] 3.95Å' 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=6YXA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YXA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yxa]] 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=6YXA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YXA 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=6yxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxa OCA], [http://pdbe.org/6yxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yxa RCSB], [http://www.ebi.ac.uk/pdbsum/6yxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxa 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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">relA, BSU27600 ([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/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=6yxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxa OCA], [http://pdbe.org/6yxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yxa RCSB], [http://www.ebi.ac.uk/pdbsum/6yxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RELA_BACSU RELA_BACSU]] 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. This enzyme catalyzes the formation of pppGpp which is then hydrolyzed to form ppGpp, it is probably the hydrolysis activity that is required for optimal growth (Probable).<ref>PMID:18067544</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase and synthetase activity and a stress-perceiving and regulatory C-terminal domain (CTD). CTD-mediated binding of Rel to stalled ribosomes boosts (p)ppGpp synthesis. However, how the opposing activities of the NTD are controlled in the absence of stress was poorly understood. Here, we demonstrate on the RSH-type protein Rel that the critical regulative elements reside within the TGS (ThrRS, GTPase, and SpoT) subdomain of the CTD, which associates to and represses the synthetase to concomitantly allow for activation of the hydrolase. Furthermore, we show that Rel forms homodimers, which appear to control the interaction with deacylated-tRNA, but not the enzymatic activity of Rel. Collectively, our study provides a detailed molecular view into the mechanism of stringent response repression in the absence of stress.
		+
		+	Structural Basis for Regulation of the Opposing (p)ppGpp Synthetase and Hydrolase within the Stringent Response Orchestrator Rel.,Pausch P, Abdelshahid M, Steinchen W, Schafer H, Gratani FL, Freibert SA, Wolz C, Turgay K, Wilson DN, Bange G Cell Rep. 2020 Sep 15;32(11):108157. doi: 10.1016/j.celrep.2020.108157. PMID:32937119<ref>PMID:32937119</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yxa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
		+	[[Category: GTP diphosphokinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bange G]]	+	[[Category: Bange, G]]
-	[[Category: Pausch P]]	+	[[Category: Pausch, P]]
		+	[[Category: Ribosome interacting]]
		+	[[Category: Signaling protein]]
		+	[[Category: Stringent response]]

OCA at 11:14, 23 September 2020

OCA — Wed, 23 Sep 2020 11:14:27 GMT

←Older revision		Revision as of 11:14, 23 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yxa ~~is ON HOLD until Paper Publication~~	+	==Structure of the bifunctional Rel enzyme from B. subtilis==
-		+	<StructureSection load='6yxa' size='340' side='right'caption='[[6yxa]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YXA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YXA 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=6yxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxa OCA], [http://pdbe.org/6yxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yxa RCSB], [http://www.ebi.ac.uk/pdbsum/6yxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxa ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bange G]]
		+	[[Category: Pausch P]]

OCA at 04:14, 13 May 2020

OCA — Wed, 13 May 2020 04:14:07 GMT

←Older revision		Revision as of 04:14, 13 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 06 May 2020 04:50:05 GMT

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

←Older revision

Revision as of 04:50, 6 May 2020

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

OCA — Wed, 06 May 2020 04:50:04 GMT

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

New page

'''Unreleased structure'''

The entry 6yxa is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]