2nye - Revision history

OCA at 10:26, 30 August 2023

OCA — Wed, 30 Aug 2023 10:26:31 GMT

←Older revision		Revision as of 10:26, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2nye' size='340' side='right'caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2nye' size='340' side='right'caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nye]] is a 2 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=2NYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nye]] is a 2 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=2NYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NYE FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 2.5Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2nyc\|2nyc]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SNF4, CAT3 ([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=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [https://pdbe.org/2nye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [https://www.ebi.ac.uk/pdbsum/2nye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nye 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=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [https://pdbe.org/2nye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [https://www.ebi.ac.uk/pdbsum/2nye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nye ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AAKG_YEAST AAKG_YEAST]] Adenine nucleotides-binding subunit gamma of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (SNF1) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits.<ref>PMID:10099331</ref> <ref>PMID:10224244</ref> <ref>PMID:11486005</ref> <ref>PMID:12393914</ref> <ref>PMID:12960168</ref> <ref>PMID:1468623</ref> <ref>PMID:18474591</ref> <ref>PMID:2169717</ref> <ref>PMID:22019086</ref> <ref>PMID:2557546</ref> <ref>PMID:3049551</ref> <ref>PMID:3939253</ref> <ref>PMID:6392017</ref> <ref>PMID:7050076</ref> <ref>PMID:8224185</ref> <ref>PMID:8544831</ref> <ref>PMID:8985180</ref> <ref>PMID:9600950</ref>	+	[https://www.uniprot.org/uniprot/AAKG_YEAST AAKG_YEAST] Adenine nucleotides-binding subunit gamma of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (SNF1) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits.<ref>PMID:10099331</ref> <ref>PMID:10224244</ref> <ref>PMID:11486005</ref> <ref>PMID:12393914</ref> <ref>PMID:12960168</ref> <ref>PMID:1468623</ref> <ref>PMID:18474591</ref> <ref>PMID:2169717</ref> <ref>PMID:22019086</ref> <ref>PMID:2557546</ref> <ref>PMID:3049551</ref> <ref>PMID:3939253</ref> <ref>PMID:6392017</ref> <ref>PMID:7050076</ref> <ref>PMID:8224185</ref> <ref>PMID:8544831</ref> <ref>PMID:8985180</ref> <ref>PMID:9600950</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Amodeo~~, G A~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Carlson, M]]	+	[[Category: Amodeo GA]]
-	[[Category: Hong, S]]	+	[[Category: Carlson M]]
-	[[Category: Iram, S]]	+	[[Category: Hong S]]
-	[[Category: Pirino, G]]	+	[[Category: Iram S]]
-	[[Category: Rudolph~~, M J~~]]	+	[[Category: Pirino G]]
-	[[Category: Tong, L]]	+	[[Category: Rudolph MJ]]
-	~~[[Category: Amp kinase]]~~	+	[[Category: Tong L]]
-	~~[[Category: Bateman2 domain]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Snf4~~]]	+

OCA at 15:54, 8 June 2021

OCA — Tue, 08 Jun 2021 15:54:59 GMT

←Older revision		Revision as of 15:54, 8 June 2021
Line 1:		Line 1:

	==Crystal structure of the Bateman2 domain of yeast Snf4==		==Crystal structure of the Bateman2 domain of yeast Snf4==
-	<StructureSection load='2nye' size='340' side='right' caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2nye' size='340' side='right'caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nye]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2NYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nye]] is a 2 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=2NYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NYE FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nyc\|2nyc]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [~~http~~://pdbe.org/2nye PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2nye PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2nye 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=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [https://pdbe.org/2nye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [https://www.ebi.ac.uk/pdbsum/2nye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nye ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AAKG_YEAST AAKG_YEAST]] Adenine nucleotides-binding subunit gamma of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (SNF1) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits.<ref>PMID:10099331</ref> <ref>PMID:10224244</ref> <ref>PMID:11486005</ref> <ref>PMID:12393914</ref> <ref>PMID:12960168</ref> <ref>PMID:1468623</ref> <ref>PMID:18474591</ref> <ref>PMID:2169717</ref> <ref>PMID:22019086</ref> <ref>PMID:2557546</ref> <ref>PMID:3049551</ref> <ref>PMID:3939253</ref> <ref>PMID:6392017</ref> <ref>PMID:7050076</ref> <ref>PMID:8224185</ref> <ref>PMID:8544831</ref> <ref>PMID:8985180</ref> <ref>PMID:9600950</ref>	+	[[https://www.uniprot.org/uniprot/AAKG_YEAST AAKG_YEAST]] Adenine nucleotides-binding subunit gamma of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (SNF1) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits.<ref>PMID:10099331</ref> <ref>PMID:10224244</ref> <ref>PMID:11486005</ref> <ref>PMID:12393914</ref> <ref>PMID:12960168</ref> <ref>PMID:1468623</ref> <ref>PMID:18474591</ref> <ref>PMID:2169717</ref> <ref>PMID:22019086</ref> <ref>PMID:2557546</ref> <ref>PMID:3049551</ref> <ref>PMID:3939253</ref> <ref>PMID:6392017</ref> <ref>PMID:7050076</ref> <ref>PMID:8224185</ref> <ref>PMID:8544831</ref> <ref>PMID:8985180</ref> <ref>PMID:9600950</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Amodeo, G A]]		[[Category: Amodeo, G A]]
	[[Category: Carlson, M]]		[[Category: Carlson, M]]

OCA at 06:39, 31 January 2018

OCA — Wed, 31 Jan 2018 06:39:55 GMT

←Older revision		Revision as of 06:39, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Bateman2 domain of yeast Snf4==		==Crystal structure of the Bateman2 domain of yeast Snf4==
	<StructureSection load='2nye' size='340' side='right' caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2nye' size='340' side='right' caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [http://pdbe.org/2nye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [http://www.ebi.ac.uk/pdbsum/2nye PDBsum]</span></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=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [http://pdbe.org/2nye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [http://www.ebi.ac.uk/pdbsum/2nye PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2nye ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2nye_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2nye_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 01:36, 8 February 2016

OCA — Mon, 08 Feb 2016 01:36:59 GMT

←Older revision		Revision as of 01:36, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nye ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:39, 10 September 2015

OCA — Thu, 10 Sep 2015 06:39:46 GMT

←Older revision		Revision as of 06:39, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2nye' size='340' side='right' caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2nye' size='340' side='right' caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NYE FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [http://www.ebi.ac.uk/pdbsum/2nye PDBsum]</span></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=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [http://pdbe.org/2nye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [http://www.ebi.ac.uk/pdbsum/2nye PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~SNF4_YEAST SNF4_YEAST~~]] Adenine nucleotides-binding subunit gamma of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (SNF1) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits.<ref>PMID:~~7050076~~</ref> <ref>PMID:~~6392017~~</ref> <ref>PMID:~~3939253~~</ref> <ref>PMID:~~3049551~~</ref> <ref>PMID:~~2557546~~</ref> <ref>PMID:~~2169717~~</ref> <ref>PMID:~~1468623~~</ref> <ref>PMID:~~8224185~~</ref> <ref>PMID:~~8544831~~</ref> <ref>PMID:~~8985180~~</ref> <ref>PMID:~~10099331~~</ref> <ref>PMID:~~9600950~~</ref> <ref>PMID:~~10224244~~</ref> <ref>PMID:~~11486005~~</ref> <ref>PMID:~~12393914~~</ref> <ref>PMID:~~12960168~~</ref> <ref>PMID:~~18474591~~</ref> <ref>PMID:~~22019086~~</ref>	+	[[http://www.uniprot.org/uniprot/AAKG_YEAST AAKG_YEAST]] Adenine nucleotides-binding subunit gamma of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (SNF1) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits.<ref>PMID:10099331</ref> <ref>PMID:10224244</ref> <ref>PMID:11486005</ref> <ref>PMID:12393914</ref> <ref>PMID:12960168</ref> <ref>PMID:1468623</ref> <ref>PMID:18474591</ref> <ref>PMID:2169717</ref> <ref>PMID:22019086</ref> <ref>PMID:2557546</ref> <ref>PMID:3049551</ref> <ref>PMID:3939253</ref> <ref>PMID:6392017</ref> <ref>PMID:7050076</ref> <ref>PMID:8224185</ref> <ref>PMID:8544831</ref> <ref>PMID:8985180</ref> <ref>PMID:9600950</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2nye" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Amodeo, G A]]		[[Category: Amodeo, G A]]
	[[Category: Carlson, M]]		[[Category: Carlson, M]]

OCA at 19:35, 24 December 2014

OCA — Wed, 24 Dec 2014 19:35:58 GMT

←Older revision		Revision as of 19:35, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2nye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NYE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2nye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NYE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [http://www.ebi.ac.uk/pdbsum/2nye PDBsum]</span></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=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [http://www.ebi.ac.uk/pdbsum/2nye PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SNF4_YEAST SNF4_YEAST]] Adenine nucleotides-binding subunit gamma of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Gamma non-catalytic subunit mediates binding to AMP, ADP and ATP, leading to activate or inhibit AMPK: AMP-binding results in allosteric activation of alpha catalytic subunit (SNF1) both by inducing phosphorylation and preventing dephosphorylation of catalytic subunits.<ref>PMID:7050076</ref> <ref>PMID:6392017</ref> <ref>PMID:3939253</ref> <ref>PMID:3049551</ref> <ref>PMID:2557546</ref> <ref>PMID:2169717</ref> <ref>PMID:1468623</ref> <ref>PMID:8224185</ref> <ref>PMID:8544831</ref> <ref>PMID:8985180</ref> <ref>PMID:10099331</ref> <ref>PMID:9600950</ref> <ref>PMID:10224244</ref> <ref>PMID:11486005</ref> <ref>PMID:12393914</ref> <ref>PMID:12960168</ref> <ref>PMID:18474591</ref> <ref>PMID:22019086</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Amodeo, G A.]]	+	[[Category: Amodeo, G A]]
-	[[Category: Carlson, M.]]	+	[[Category: Carlson, M]]
-	[[Category: Hong, S.]]	+	[[Category: Hong, S]]
-	[[Category: Iram, S.]]	+	[[Category: Iram, S]]
-	[[Category: Pirino, G.]]	+	[[Category: Pirino, G]]
-	[[Category: Rudolph, M J.]]	+	[[Category: Rudolph, M J]]
-	[[Category: Tong, L.]]	+	[[Category: Tong, L]]
	[[Category: Amp kinase]]		[[Category: Amp kinase]]
	[[Category: Bateman2 domain]]		[[Category: Bateman2 domain]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Snf4]]		[[Category: Snf4]]

OCA at 20:18, 30 September 2014

OCA — Tue, 30 Sep 2014 20:18:57 GMT

←Older revision		Revision as of 20:18, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2nye.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Bateman2 domain of yeast Snf4==
		+	<StructureSection load='2nye' size='340' side='right' caption='[[2nye]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2nye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NYE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyc\|2nyc]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNF4, CAT3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nye RCSB], [http://www.ebi.ac.uk/pdbsum/2nye PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2nye_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals. AMP is believed to control the activity of AMPK by binding to the gamma subunit of this heterotrimeric enzyme. This subunit contains two Bateman domains, each of which is composed of a tandem pair of cystathionine beta-synthase (CBS) motifs. No structural information is currently available on this subunit, and the molecular basis for its interactions with AMP is not well understood. We report here the crystal structure at 1.9 Angstrom resolution of the Bateman2 domain of Snf4, the gamma subunit of the yeast ortholog of AMPK. The structure revealed a dimer of the Bateman2 domain, and this dimerization is supported by our light-scattering, mutagenesis, and biochemical studies. There is a prominent pocket at the center of this dimer, and most of the disease-causing mutations are located in or near this pocket.

-	~~{{STRUCTURE_2nye\| PDB=2nye \| SCENE= }}~~	+	Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding.,Rudolph MJ, Amodeo GA, Iram SH, Hong SP, Pirino G, Carlson M, Tong L Structure. 2007 Jan;15(1):65-74. PMID:17223533<ref>PMID:17223533</ref>

-	~~===Crystal structure~~ of the ~~Bateman2 domain of yeast Snf4===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17223533}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2nye]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017223533<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Amodeo, G A.]]		[[Category: Amodeo, G A.]]

OCA: Protected "2nye" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 12:41:34 GMT

Protected "2nye" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:41, 7 January 2013

OCA at 12:41, 7 January 2013

OCA — Mon, 07 Jan 2013 12:41:31 GMT

←Older revision		Revision as of 12:41, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2nye.png\|left\|200px]]		[[Image:2nye.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2nye", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2nye\| PDB=2nye \| SCENE= }}		{{STRUCTURE_2nye\| PDB=2nye \| SCENE= }}

	===Crystal structure of the Bateman2 domain of yeast Snf4===		===Crystal structure of the Bateman2 domain of yeast Snf4===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17223533}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17223533 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17223533}}		{{ABSTRACT_PUBMED_17223533}}

	==About this Structure==		==About this Structure==
-	~~2NYE~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA].	+	[[2nye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17223533~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017223533</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Amodeo, G A.]]		[[Category: Amodeo, G A.]]
Line 34:		Line 22:
	[[Category: Amp kinase]]		[[Category: Amp kinase]]
	[[Category: Bateman2 domain]]		[[Category: Bateman2 domain]]
		+	[[Category: Protein binding]]
	[[Category: Snf4]]		[[Category: Snf4]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:52:06 2009''

OCA at 15:52, 16 February 2009

OCA — Mon, 16 Feb 2009 15:52:08 GMT

←Older revision		Revision as of 15:52, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2NYE is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA].	+	2NYE is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYE OCA].

	==Reference==		==Reference==
-	Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding., Rudolph MJ, Amodeo GA, Iram SH, Hong SP, Pirino G, Carlson M, Tong L, Structure. 2007 Jan;15(1):65-74. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17223533 17223533]~~	+	<ref group="xtra">PMID:17223533</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Single protein]]
	[[Category: Amodeo, G A.]]		[[Category: Amodeo, G A.]]
	[[Category: Carlson, M.]]		[[Category: Carlson, M.]]
Line 37:		Line 36:
	[[Category: Snf4]]		[[Category: Snf4]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 21~~:20:~~59 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:52:06 2009''