6nz6 - Revision history

OCA at 14:49, 13 March 2024

OCA — Wed, 13 Mar 2024 14:49:38 GMT

←Older revision		Revision as of 14:49, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6nz6' size='340' side='right'caption='[[6nz6]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6nz6' size='340' side='right'caption='[[6nz6]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nz6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sheon Sheon~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NZ6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NZ6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nz6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NZ6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=GDP:GUANOSINE~~-~~5-DIPHOSPHATE'>GDP</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]] 1.95Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ycjX, SO_1810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=211586 SHEON])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></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=6nz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nz6 OCA], [~~http~~://pdbe.org/6nz6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nz6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nz6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nz6 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=6nz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nz6 OCA], [https://pdbe.org/6nz6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nz6 RCSB], [https://www.ebi.ac.uk/pdbsum/6nz6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nz6 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q8EG04_SHEON Q8EG04_SHEON]
-	Stress proteins promote cell survival by monitoring protein homeostasis in cells and organelles. YcjX is a conserved protein of unknown function, which is highly upregulated in response to acute and chronic stress. Notably, heat shock induction of ycjX exceeded even levels observed for major stress-induced chaperones, including GroEL, ClpB, and HtpG, which use ATP as energy source. YcjX features a Walker-type nucleotide-binding domain indicating that YcjX might function as a molecular chaperone. Here, we present the first crystal structure of YcjX from Shewanella oneidensis solved at 1.9-A resolution by SAD phasing. We show that YcjX is a GTP-binding protein that shares at its core the canonical alpha-beta domain of p21(ras) (Ras). However, unlike Ras, YcjX features several unique insertions, including an entirely alpha-helical domain not previously observed in Ras-like GTPases. We note that this helical domain is reminiscent of a similar domain in the Galpha subunit of heterotrimeric G proteins, supporting a potential role for YcjX as a signal transducer of stress responses. To elucidate the mechanism of GTP hydrolysis, we determined crystal structures of YcjX bound to GDP and GDPCP, respectively, which crystallized in three different nucleotide switch conformations. Supported by targeted mutagenesis experiments, we show that YcjX utilizes a non-canonical switch 2' motif not previously observed in Ras-like GTPases. Together, our structures provide atomic snapshots of YcjX in different functional states, illustrating the structural determinants for stress signaling.	+
-		+
-	~~Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.,Tsai JT, Sung N, Lee J, Chang C, Lee S, Tsai FTF J Mol Biol. 2019 Aug 9;431(17)~~:~~3179-3190. doi: 10.1016~~/~~j.jmb.2019.06.006. Epub, 2019 Jun 14. PMID:31202886<ref>PMID:31202886<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6nz6" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sheon~~]]	+	[[Category: Shewanella oneidensis MR-1]]
-	[[Category: Chang, C]]	+	[[Category: Chang C]]
-	[[Category: Lee, J]]	+	[[Category: Lee J]]
-	[[Category: Lee, S]]	+	[[Category: Lee S]]
-	[[Category: Sung, N]]	+	[[Category: Sung N]]
-	[[Category: Tsai~~, F T~~]]	+	[[Category: Tsai FT]]
-	[[Category: Tsai, J]]	+	[[Category: Tsai J]]
-	~~[[Category: G-protein]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 11:44, 1 January 2020

OCA — Wed, 01 Jan 2020 11:44:39 GMT

←Older revision		Revision as of 11:44, 1 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nz6 is ~~ON HOLD until Paper~~ Publication	+	==YcjX-GDP (type II)==
		+	<StructureSection load='6nz6' size='340' side='right'caption='[[6nz6]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6nz6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NZ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NZ6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ycjX, SO_1810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</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=6nz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nz6 OCA], [http://pdbe.org/6nz6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nz6 RCSB], [http://www.ebi.ac.uk/pdbsum/6nz6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nz6 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Stress proteins promote cell survival by monitoring protein homeostasis in cells and organelles. YcjX is a conserved protein of unknown function, which is highly upregulated in response to acute and chronic stress. Notably, heat shock induction of ycjX exceeded even levels observed for major stress-induced chaperones, including GroEL, ClpB, and HtpG, which use ATP as energy source. YcjX features a Walker-type nucleotide-binding domain indicating that YcjX might function as a molecular chaperone. Here, we present the first crystal structure of YcjX from Shewanella oneidensis solved at 1.9-A resolution by SAD phasing. We show that YcjX is a GTP-binding protein that shares at its core the canonical alpha-beta domain of p21(ras) (Ras). However, unlike Ras, YcjX features several unique insertions, including an entirely alpha-helical domain not previously observed in Ras-like GTPases. We note that this helical domain is reminiscent of a similar domain in the Galpha subunit of heterotrimeric G proteins, supporting a potential role for YcjX as a signal transducer of stress responses. To elucidate the mechanism of GTP hydrolysis, we determined crystal structures of YcjX bound to GDP and GDPCP, respectively, which crystallized in three different nucleotide switch conformations. Supported by targeted mutagenesis experiments, we show that YcjX utilizes a non-canonical switch 2' motif not previously observed in Ras-like GTPases. Together, our structures provide atomic snapshots of YcjX in different functional states, illustrating the structural determinants for stress signaling.

-	~~Authors~~:	+	Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.,Tsai JT, Sung N, Lee J, Chang C, Lee S, Tsai FTF J Mol Biol. 2019 Aug 9;431(17):3179-3190. doi: 10.1016/j.jmb.2019.06.006. Epub, 2019 Jun 14. PMID:31202886<ref>PMID:31202886</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6nz6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sheon]]
		+	[[Category: Chang, C]]
		+	[[Category: Lee, J]]
		+	[[Category: Lee, S]]
		+	[[Category: Sung, N]]
		+	[[Category: Tsai, F T]]
		+	[[Category: Tsai, J]]
		+	[[Category: G-protein]]
		+	[[Category: Signaling protein]]

OCA at 04:56, 27 March 2019

OCA — Wed, 27 Mar 2019 04:56:34 GMT

←Older revision		Revision as of 04:56, 27 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6nz6 is ON HOLD	+	The entry 6nz6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6nz6" [edit=sysop:move=sysop]

OCA — Thu, 21 Feb 2019 05:15:21 GMT

Protected "6nz6" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:15, 21 February 2019

OCA: New page: '''Unreleased structure''' The entry 6nz6 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 21 Feb 2019 05:15:20 GMT

New page: '''Unreleased structure''' The entry 6nz6 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6nz6 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]