6xqk - Revision history

OCA at 14:51, 6 March 2024

OCA — Wed, 06 Mar 2024 14:51:13 GMT

←Older revision		Revision as of 14:51, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6xqk' size='340' side='right'caption='[[6xqk]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='6xqk' size='340' side='right'caption='[[6xqk]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xqk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xqk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQK 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=GOL:GLYCEROL'>GOL</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]] 2.56Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~BCY1, REG1, SRA1, YIL033C ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=4932 ATCC 18824])~~</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=GOL:GLYCEROL'>GOL</scene></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=6xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqk OCA], [https://pdbe.org/6xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqk RCSB], [https://www.ebi.ac.uk/pdbsum/6xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqk 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=6xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqk OCA], [https://pdbe.org/6xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqk RCSB], [https://www.ebi.ac.uk/pdbsum/6xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KAPR_YEAST KAPR_YEAST]] Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA), an effector of the Ras/cAMP pathway. Inhibits PKA activity in the absence of cAMP. cAMP activates PKA and promotes growth and proliferation in response to good nutrient conditions. Together with ZDS1, provides a negative feedback control on the cell wall integrity-signaling pathway by acting as a negative regulator of MAP kinase SLT2/MPK1.<ref>PMID:3037314</ref> <ref>PMID:2823100</ref> <ref>PMID:6243658</ref> <ref>PMID:12704202</ref>	+	[https://www.uniprot.org/uniprot/KAPR_YEAST KAPR_YEAST] Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA), an effector of the Ras/cAMP pathway. Inhibits PKA activity in the absence of cAMP. cAMP activates PKA and promotes growth and proliferation in response to good nutrient conditions. Together with ZDS1, provides a negative feedback control on the cell wall integrity-signaling pathway by acting as a negative regulator of MAP kinase SLT2/MPK1.<ref>PMID:3037314</ref> <ref>PMID:2823100</ref> <ref>PMID:6243658</ref> <ref>PMID:12704202</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Protein kinase A (PKA) is a widespread enzyme that plays a key role in many signaling pathways from lower eukaryotes to metazoans. In mammals, the regulatory (R) subunits sequester and target the catalytic (C) subunits to proper subcellular locations. This targeting is accomplished by the dimerization and docking (D/D) domain of the R subunits. The activation of the holoenzyme depends on the binding of the second messenger cAMP. The only available structures of the D/D domain proceed from mammalian sources. Unlike dimeric mammalian counterparts, the R subunit from Saccharomyces cerevisiae (Bcy1) forms tetramers in solution. Here we describe the first high-resolution structure of a non-mammalian D/D domain. The tetramer in the crystals of the Bcy1 D/D domain is a dimer of dimers that retain the classical D/D domain fold. By using phylogenetic and structural analyses combined with site-directed mutagenesis, we found that fungal R subunits present an insertion of a single amino acid at the D/D domain that shifts the position of a downstream, conserved arginine. This residue participates in intra-dimer interactions in mammalian D/D domains, while due to this insertion it is involved in inter-dimer contacts in Bcy1, which are crucial for the stability of the tetramer. This surprising finding challenges well-established concepts regarding the oligomeric state within the PKAR protein family and provides important insights into the yet unexplored structural diversity of the D/D domains and the molecular determinants of R subunit oligomerization.	+

-	The crystal structure of yeast regulatory subunit reveals key evolutionary insights into Protein Kinase A oligomerization.,Bardeci NG, Tofolon E, Trajtenberg F, Caramelo J, Larrieux N, Rossi S, Buschiazzo A, Moreno S J Struct Biol. 2021 Apr 2:107732. doi: 10.1016/j.jsb.2021.107732. PMID:33819633<ref>PMID:33819633</ref>	+	==See Also==
-		+	*[[CAMP-dependent protein kinase 3D structures\|CAMP-dependent protein kinase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe~~-~~citations 6xqk" style="background~~-~~color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bardeci, N Gonzalez~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Buschiazzo, A]]	+	[[Category: Buschiazzo A]]
-	[[Category: ~~Larrieux,~~ N]]	+	[[Category: Gonzalez Bardeci N]]
-	[[Category: ~~Trajtenberg, F~~]]	+	[[Category: Larrieux N]]
-	[[Category: ~~Protein kinase some]]~~	+	[[Category: Trajtenberg F]]
-	~~[[Category: Signaling protein~~]]	+

OCA at 10:16, 19 May 2021

OCA — Wed, 19 May 2021 10:16:11 GMT

←Older revision		Revision as of 10:16, 19 May 2021
Line 3:		Line 3:
	<StructureSection load='6xqk' size='340' side='right'caption='[[6xqk]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='6xqk' size='340' side='right'caption='[[6xqk]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xqk]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xqk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQK 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=GOL:GLYCEROL'>GOL</scene></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=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCY1, REG1, SRA1, YIL033C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=6xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqk OCA], [https://pdbe.org/6xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqk RCSB], [https://www.ebi.ac.uk/pdbsum/6xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqk 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=6xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqk OCA], [https://pdbe.org/6xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqk RCSB], [https://www.ebi.ac.uk/pdbsum/6xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqk ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bardeci, N Gonzalez]]		[[Category: Bardeci, N Gonzalez]]

OCA at 08:29, 21 April 2021

OCA — Wed, 21 Apr 2021 08:29:20 GMT

←Older revision		Revision as of 08:29, 21 April 2021
Line 1:		Line 1:

	==Crystal structure of the D/D domain of PKA from S. cerevisiae==		==Crystal structure of the D/D domain of PKA from S. cerevisiae==
-	<StructureSection load='6xqk' size='340' side='right'caption='[[6xqk]]' scene=''>	+	<StructureSection load='6xqk' size='340' side='right'caption='[[6xqk]], [[Resolution\|resolution]] 2.56Å' 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=6XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xqk]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQK 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=6xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqk OCA], [https://pdbe.org/6xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqk RCSB], [https://www.ebi.ac.uk/pdbsum/6xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqk 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=GOL:GLYCEROL'>GOL</scene></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=6xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqk OCA], [https://pdbe.org/6xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqk RCSB], [https://www.ebi.ac.uk/pdbsum/6xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/KAPR_YEAST KAPR_YEAST]] Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA), an effector of the Ras/cAMP pathway. Inhibits PKA activity in the absence of cAMP. cAMP activates PKA and promotes growth and proliferation in response to good nutrient conditions. Together with ZDS1, provides a negative feedback control on the cell wall integrity-signaling pathway by acting as a negative regulator of MAP kinase SLT2/MPK1.<ref>PMID:3037314</ref> <ref>PMID:2823100</ref> <ref>PMID:6243658</ref> <ref>PMID:12704202</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein kinase A (PKA) is a widespread enzyme that plays a key role in many signaling pathways from lower eukaryotes to metazoans. In mammals, the regulatory (R) subunits sequester and target the catalytic (C) subunits to proper subcellular locations. This targeting is accomplished by the dimerization and docking (D/D) domain of the R subunits. The activation of the holoenzyme depends on the binding of the second messenger cAMP. The only available structures of the D/D domain proceed from mammalian sources. Unlike dimeric mammalian counterparts, the R subunit from Saccharomyces cerevisiae (Bcy1) forms tetramers in solution. Here we describe the first high-resolution structure of a non-mammalian D/D domain. The tetramer in the crystals of the Bcy1 D/D domain is a dimer of dimers that retain the classical D/D domain fold. By using phylogenetic and structural analyses combined with site-directed mutagenesis, we found that fungal R subunits present an insertion of a single amino acid at the D/D domain that shifts the position of a downstream, conserved arginine. This residue participates in intra-dimer interactions in mammalian D/D domains, while due to this insertion it is involved in inter-dimer contacts in Bcy1, which are crucial for the stability of the tetramer. This surprising finding challenges well-established concepts regarding the oligomeric state within the PKAR protein family and provides important insights into the yet unexplored structural diversity of the D/D domains and the molecular determinants of R subunit oligomerization.
		+
		+	The crystal structure of yeast regulatory subunit reveals key evolutionary insights into Protein Kinase A oligomerization.,Bardeci NG, Tofolon E, Trajtenberg F, Caramelo J, Larrieux N, Rossi S, Buschiazzo A, Moreno S J Struct Biol. 2021 Apr 2:107732. doi: 10.1016/j.jsb.2021.107732. PMID:33819633<ref>PMID:33819633</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xqk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Buschiazzo A~~]]	+	[[Category: Bardeci, N Gonzalez]]
-	[[Category: ~~Gonzalez Bardeci N~~]]	+	[[Category: Buschiazzo, A]]
-	[[Category: Larrieux N]]	+	[[Category: Larrieux, N]]
-	[[Category: Trajtenberg F]]	+	[[Category: Trajtenberg, F]]
		+	[[Category: Protein kinase some]]
		+	[[Category: Signaling protein]]

OCA at 06:43, 14 April 2021

OCA — Wed, 14 Apr 2021 06:43:00 GMT

←Older revision		Revision as of 06:43, 14 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6xqk ~~is ON HOLD~~	+	==Crystal structure of the D/D domain of PKA from S. cerevisiae==
-		+	<StructureSection load='6xqk' size='340' side='right'caption='[[6xqk]]' scene=''>
-	~~Authors~~: ~~Larrieux~~, N., ~~Gonzalez Bardeci, N~~., ~~Trajtenberg, F~~., ~~Buschiazzo~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQK FirstGlance]. <br>
-	~~Description: Crystal structure of the D~~/~~D domain of PKA from S. cerevisiae~~	+	</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=6xqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqk OCA], [https://pdbe.org/6xqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqk RCSB], [https://www.ebi.ac.uk/pdbsum/6xqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqk ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Buschiazzo, A]]	+	__TOC__
-	[[Category: Gonzalez Bardeci, N]]	+	</StructureSection>
-	[[Category: Larrieux, N]]	+	[[Category: Large Structures]]
-	[[Category: Trajtenberg, F]]	+	[[Category: Buschiazzo A]]
		+	[[Category: Gonzalez Bardeci N]]
		+	[[Category: Larrieux N]]
		+	[[Category: Trajtenberg F]]

OCA at 04:54, 2 September 2020

OCA — Wed, 02 Sep 2020 04:54:26 GMT

←Older revision		Revision as of 04:54, 2 September 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xqk is ON HOLD ~~until Paper Publication~~	+	The entry 6xqk is ON HOLD

	Authors: Larrieux, N., Gonzalez Bardeci, N., Trajtenberg, F., Buschiazzo, A.		Authors: Larrieux, N., Gonzalez Bardeci, N., Trajtenberg, F., Buschiazzo, A.

OCA at 09:06, 26 August 2020

OCA — Wed, 26 Aug 2020 09:06:18 GMT

←Older revision		Revision as of 09:06, 26 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Larrieux, N., Gonzalez Bardeci, N., Trajtenberg, F., Buschiazzo, A.		Authors: Larrieux, N., Gonzalez Bardeci, N., Trajtenberg, F., Buschiazzo, A.
Line 7:		Line 7:
	Description: Crystal structure of the D/D domain of PKA from S. cerevisiae		Description: Crystal structure of the D/D domain of PKA from S. cerevisiae
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Buschiazzo, A]]
	[[Category: Gonzalez Bardeci, N]]		[[Category: Gonzalez Bardeci, N]]
	[[Category: Larrieux, N]]		[[Category: Larrieux, N]]
-	[[Category: Buschiazzo, A]]
	[[Category: Trajtenberg, F]]		[[Category: Trajtenberg, F]]

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

OCA — Wed, 22 Jul 2020 06:53:55 GMT

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

←Older revision

Revision as of 06:53, 22 July 2020

OCA: New page: '''Unreleased structure''' The entry 6xqk is ON HOLD Authors: Larrieux, N., Gonzalez Bardeci, N., Trajtenberg, F., Buschiazzo, A. Description: Crystal structure of the D/D domain of PK...

OCA — Wed, 22 Jul 2020 06:53:53 GMT

New page: '''Unreleased structure''' The entry 6xqk is ON HOLD Authors: Larrieux, N., Gonzalez Bardeci, N., Trajtenberg, F., Buschiazzo, A. Description: Crystal structure of the D/D domain of PK...

New page

'''Unreleased structure'''

The entry 6xqk is ON HOLD

Authors: Larrieux, N., Gonzalez Bardeci, N., Trajtenberg, F., Buschiazzo, A.

Description: Crystal structure of the D/D domain of PKA from S. cerevisiae
[[Category: Unreleased Structures]]
[[Category: Gonzalez Bardeci, N]]
[[Category: Larrieux, N]]
[[Category: Buschiazzo, A]]
[[Category: Trajtenberg, F]]