6zhl - Revision history

OCA at 13:49, 24 January 2024

OCA — Wed, 24 Jan 2024 13:49:51 GMT

←Older revision		Revision as of 13:49, 24 January 2024
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	<StructureSection load='6zhl' size='340' side='right'caption='[[6zhl]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='6zhl' size='340' side='right'caption='[[6zhl]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zhl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Staa3 Staa3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zhl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_USA300 Staphylococcus aureus subsp. aureus USA300]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.94Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6zhm\|6zhm]], [[6zjo\|6zjo]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsgA, SAUSA300_1114 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=367830 STAA3])</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=6zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhl OCA], [https://pdbe.org/6zhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhl RCSB], [https://www.ebi.ac.uk/pdbsum/6zhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhl 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=6zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhl OCA], [https://pdbe.org/6zhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhl RCSB], [https://www.ebi.ac.uk/pdbsum/6zhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~A0A0H2XJQ2_STAA3 A0A0H2XJQ2_STAA3]~~] One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit.[HAMAP-Rule:MF_01820]	+	[https://www.uniprot.org/uniprot/RSGA_STAAC RSGA_STAAC] One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit.[HAMAP-Rule:MF_01820]
	<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: ~~Staa3~~]]	+	[[Category: Staphylococcus aureus subsp. aureus USA300]]
-	[[Category: Bennison~~, D J~~]]	+	[[Category: Bennison DJ]]
-	[[Category: Corrigan~~, R M~~]]	+	[[Category: Corrigan RM]]
-	[[Category: Rafferty~~, J B]]~~	+	[[Category: Rafferty JB]]
-	~~[[Category: Gtpase]]~~	+
-	~~[[Category: Ppgpp-binding]]~~	+
-	~~[[Category: Ribosome assembly]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Trafac~~]]	+

OCA at 10:02, 12 January 2022

OCA — Wed, 12 Jan 2022 10:02:15 GMT

←Older revision		Revision as of 10:02, 12 January 2022
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	==Crystal Structure of Staphylococcus aureus RsgA bound to ppGpp.==		==Crystal Structure of Staphylococcus aureus RsgA bound to ppGpp.==
-	<StructureSection load='6zhl' size='340' side='right'caption='[[6zhl]]' scene=''>	+	<StructureSection load='6zhl' size='340' side='right'caption='[[6zhl]], [[Resolution\|resolution]] 1.94Å' 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=6ZHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zhl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staa3 Staa3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHL FirstGlance]. <br>
-	</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=6zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhl OCA], [https://pdbe.org/6zhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhl RCSB], [https://www.ebi.ac.uk/pdbsum/6zhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhl 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6zhm\|6zhm]], [[6zjo\|6zjo]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rsgA, SAUSA300_1114 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=367830 STAA3])</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=6zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhl OCA], [https://pdbe.org/6zhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhl RCSB], [https://www.ebi.ac.uk/pdbsum/6zhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A0H2XJQ2_STAA3 A0A0H2XJQ2_STAA3]] One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit.[HAMAP-Rule:MF_01820]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During nutrient limitation, bacteria produce the alarmones (p)ppGpp as effectors of a stress signaling network termed the stringent response. RsgA, RbgA, Era, and HflX are four ribosome-associated GTPases (RA-GTPases) that bind to (p)ppGpp in Staphylococcus aureus. These enzymes are cofactors in ribosome assembly, where they cycle between the ON (GTP-bound) and OFF (GDP-bound) ribosome-associated states. Entry into the OFF state occurs upon hydrolysis of GTP, with GTPase activity increasing substantially upon ribosome association. When bound to (p)ppGpp, GTPase activity is inhibited, reducing 70S ribosome assembly and growth. Here, we determine how (p)ppGpp impacts RA-GTPase-ribosome interactions. We show that RA-GTPases preferentially bind to 5'-diphosphate-containing nucleotides GDP and ppGpp over GTP, which is likely exploited as a regulatory mechanism within the cell to shut down ribosome biogenesis during stress. Stopped-flow fluorescence and association assays reveal that when bound to (p)ppGpp, the association of RA-GTPases to ribosomal subunits is destabilized, both in vitro and within bacterial cells. Consistently, structural analysis of the ppGpp-bound RA-GTPase RsgA reveals an OFF-state conformation similar to the GDP-bound state, with the G2/switch I loop adopting a conformation incompatible with ribosome association. Altogether, we highlight (p)ppGpp-mediated inhibition of RA-GTPases as a major mechanism of stringent response-mediated ribosome assembly and growth control. IMPORTANCE The stringent response is a bacterial signaling network that utilizes the nucleotides pppGpp and ppGpp to reprogram cells in order to survive nutritional stresses. However, much about how these important nucleotides control cellular reprogramming is unknown. Our previous work revealed that (p)ppGpp can bind to and inhibit the enzymatic activity of four ribosome-associated GTPases (RA-GTPases), enzymes that facilitate maturation of the 50S and 30S ribosomal subunits. Here, we examine how this occurs mechanistically and demonstrate that this interaction prevents the accommodation of RA-GTPases on ribosomal subunits both in vitro and within bacterial cells, with the ppGpp-bound state structurally mimicking the inactive GDP-bound conformation of the enzyme. We additionally reveal that these GTPase enzymes have a greater affinity for OFF-state-inducing nucleotides, which is a mechanism likely to control ribosome assembly during growth. With this, we further our understanding of how ribosome function is controlled by (p)ppGpp, enabling bacterial survival during stress.
		+
		+	The Stringent Response Inhibits 70S Ribosome Formation in Staphylococcus aureus by Impeding GTPase-Ribosome Interactions.,Bennison DJ, Nakamoto JA, Craggs TD, Milon P, Rafferty JB, Corrigan RM mBio. 2021 Dec 21;12(6):e0267921. doi: 10.1128/mBio.02679-21. Epub 2021 Nov 9. PMID:34749534<ref>PMID:34749534</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zhl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bennison DJ]]	+	[[Category: Staa3]]
-	[[Category: Corrigan RM]]	+	[[Category: Bennison, D J]]
-	[[Category: Rafferty JB]]	+	[[Category: Corrigan, R M]]
		+	[[Category: Rafferty, J B]]
		+	[[Category: Gtpase]]
		+	[[Category: Ppgpp-binding]]
		+	[[Category: Ribosome assembly]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Trafac]]

OCA at 03:31, 2 July 2021

OCA — Fri, 02 Jul 2021 03:31:32 GMT

←Older revision		Revision as of 03:31, 2 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6zhl is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of Staphylococcus aureus RsgA bound to ppGpp.==
-		+	<StructureSection load='6zhl' size='340' side='right'caption='[[6zhl]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZHL FirstGlance]. <br>
-	~~Description~~:	+	</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=6zhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zhl OCA], [https://pdbe.org/6zhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zhl RCSB], [https://www.ebi.ac.uk/pdbsum/6zhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zhl ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bennison DJ]]
		+	[[Category: Corrigan RM]]
		+	[[Category: Rafferty JB]]

OCA at 08:10, 12 August 2020

OCA — Wed, 12 Aug 2020 08:10:22 GMT

←Older revision		Revision as of 08:10, 12 August 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 08 Jul 2020 11:09:11 GMT

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

←Older revision

Revision as of 11:09, 8 July 2020

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

OCA — Wed, 08 Jul 2020 11:09:10 GMT

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

New page

'''Unreleased structure'''

The entry 6zhl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]