User:Alice Harmon/Sandbox 5 - Revision history

Alice Harmon at 16:23, 5 October 2013

Alice Harmon — Sat, 05 Oct 2013 16:23:00 GMT

←Older revision		Revision as of 16:23, 5 October 2013
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	Structures in the figure are: R, apo PYL2, [[3kdh]]; R<sup>.</sup>ABA, PYL2<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, PYL2<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].		Structures in the figure are: R, apo PYL2, [[3kdh]]; R<sup>.</sup>ABA, PYL2<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, PYL2<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].

-	~~==Pyr~~/~~Pyl~~/RCAR family of ABA receptors==	+	For further information about proteins involved in this pathway see [[PYR/PYL/RCAR family of ABA receptors]], [[ABA-regulated Protein Phosphatase 2C]], [[ABA-regulated SNRK2 Protein Kinase]].


		+	==PYR/PYL/RCAR family of ABA receptors==

Alice Harmon at 16:11, 5 October 2013

Alice Harmon — Sat, 05 Oct 2013 16:11:54 GMT

←Older revision		Revision as of 16:11, 5 October 2013
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	==ABA signaling pathway==		==ABA signaling pathway==
-	Abscisic acid (ABA,)[[Image:Abscisic acid.svg.png\|thumb\| Abscisic Acid]] is a plant hormone that regulates seed dormancy and germination, stomatal closure, and responses to drought stress, and its core signaling pathway has recently been identified.<ref>PMID:15012233</ref><ref>PMID:12045268</ref><ref>PMID:20192755</ref> In Arabidopsis, this pathway involves ~~at least four~~ ABA receptors (PYR1/RCAR11, PYL1/RCAR12, PYL2/RCAR14, PYL9/RCAR1)<ref>PMID:19407143</ref><ref>PMID:19407142</ref>, a protein phosphatase ~~2C in Clade C~~ (ABI1, ABI2, ~~and~~ HAB1)<ref>PMID:19407143</ref><ref>PMID:19407142</ref>, ~~and a~~ protein ~~kinase in subclass III of SnRK2s~~ ([[SnRK2.6/OST1/SRK2E]], SNRK2.2/SRK2D and SnRK2.3/SRK2IA).<ref name = "Mustilli2002">PMID:12468729</ref><ref>PMID:12514244</ref><ref name = "Nakashima2009">PMID:19541597</ref><ref name = "Fujii2007">PMID:17307925</ref>	+	Abscisic acid (ABA,)[[Image:Abscisic acid.svg.png\|thumb\| Abscisic Acid]] is a plant hormone that regulates seed development, dormancy and germination, stomatal closure, and responses to drought stress, and its core signaling pathway has recently been identified.<ref>PMID:15012233</ref><ref>PMID:12045268</ref><ref>PMID:20192755</ref> In Arabidopsis, this pathway involves families of ABA receptors (PYR1/RCAR11, PYL1/RCAR12, PYL2/RCAR14, PYL3/RCAR13, PYL8/RCAR3, PYL9/RCAR1)<ref>PMID:19407143</ref><ref>PMID:19407142</ref><ref>"PMID:22579247</ref><ref>PMID:23370718</ref>, protein phosphatase 2Cs (ABI1, ABI2, HAB1, HAB2, PP2CA/AHG3)<ref>PMID:19407143</ref><ref>PMID:19407142</ref><ref>PMID:16339800</ref>, SNRK2 protein kinases ([[SnRK2.6/OST1/SRK2E]], SNRK2.2/SRK2D and SnRK2.3/SRK2IA).<ref name = "Mustilli2002">PMID:12468729</ref><ref>PMID:12514244</ref><ref name = "Nakashima2009">PMID:19541597</ref><ref name = "Fujii2007">PMID:17307925</ref>

-	The core ABA signaling pathway is shown in the figure to the left. In unstimulated cells, the ABA receptor (R) is an unliganded dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref> (monomer shown) in the cytosol and nucleus , and the SNRK2 protein kinase (K) is bound to a protein phosphatase 2C (P) in a complex (K-P) in which the kinase is dephosphorylated and inactivated by the phosphatase. When the ABA level rises ABA binds to the ABA receptor<ref>PMID:19893533</ref><ref>PMID:19407143</ref><ref>PMID:19407142</ref>. The activated receptor (R<sup>.</sup>ABA) binds to a protein phosphatase 2C<ref>PMID:19624469</ref> (R<sup>.</sup>ABA-P), and frees the protein kinase to be activated by autophosphorylation or phosphorylation by another protein kinase. Activation of SnRK2.6/OST1/SRK2E leads to phosphorylation of: 1) ion channels SLAC1<ref>PMID: 19955405</ref> and KAT1<ref>PMID:19785574</ref> in guard cells and stomatal closure; 2) transcription factor ABI5<ref name = "Nakashima2009"/> in seeds/seedlings and dormancy/growth arrest; or 3) phosphorylation of transcription factor AREB/ABF <ref>PMID: 16446457</ref><ref name = "Fujii2007"/> in vegetative tissue and stress tolerance and growth regulation.	+	The core ABA signaling pathway is shown in the figure to the left. In unstimulated cells, the ABA receptor (R) is an unliganded dimer<ref>PMID:19898420</ref><ref>PMID:19933100</ref><ref>PMID:23265948</ref><ref>"PMID:22579247</ref> (monomer shown) in the cytosol and nucleus, and the SNRK2 protein kinase (K) is bound to a protein phosphatase 2C (P) in a complex (K-P) in which the kinase is dephosphorylated and inactivated by the phosphatase. When the ABA level rises ABA binds to the ABA receptor<ref>PMID:19893533</ref><ref>PMID:19407143</ref><ref>PMID:19407142</ref>. The activated receptor (R<sup>.</sup>ABA) binds to a protein phosphatase 2C<ref>PMID:19624469</ref> (R<sup>.</sup>ABA-P), and this sequestration of the phosphatase frees the protein kinase to be activated by autophosphorylation or phosphorylation by another protein kinase. Activation of SnRK2.6/OST1/SRK2E leads to phosphorylation of: 1) ion channels SLAC1<ref>PMID: 19955405</ref> and KAT1<ref>PMID:19785574</ref> in guard cells and stomatal closure; 2) transcription factor ABI5<ref name = "Nakashima2009"/> in seeds/seedlings and dormancy/growth arrest; or 3) phosphorylation of transcription factor AREB/ABF <ref>PMID: 16446457</ref><ref name = "Fujii2007"/> in vegetative tissue and stress tolerance and growth regulation.

	Structures in the figure are: R, apo PYL2, [[3kdh]]; R<sup>.</sup>ABA, PYL2<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, PYL2<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].		Structures in the figure are: R, apo PYL2, [[3kdh]]; R<sup>.</sup>ABA, PYL2<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, PYL2<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].
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	==Pyr/Pyl/RCAR family of ABA receptors==		==Pyr/Pyl/RCAR family of ABA receptors==

-	The following Proteopedia pages

-	crystal structures of
-	PYR1/RCAR11 and PYL9/RCAR1
-	PYR1, PYL1, PYL2, and PYL3 show ABA-dependent inhibition of PP2Cs such as ABI1, HYPERSENSITIVE TO ABA 1 (HAB1), HAB2, and ABA-HYPERSENSITIVE GERMINATION 3 (AHG3, also named PP2CA)<ref>PMID:23265948</ref>
-
-	"Upon binding to ABA or pyrabactin, the gate
-	(Melcher et al., 2009) of PYL undergoes a pronounced conformational
-	change, and the PYL protomers in the cis-homodimer
-	separate slightly, decreasing the area of interface and creating
-	a binding surface for protein phosphatase 2C (PP2C)." "Upon ligand binding, the apo-PYL3 cis-homodimer is
-	converted to a trans-homodimer, in which two ligand-bound
-	PYLs bind to each other in a reverse direction"<ref>"PMID:22579247</ref>

Alice Harmon at 15:23, 5 October 2013

Alice Harmon — Sat, 05 Oct 2013 15:23:27 GMT

←Older revision		Revision as of 15:23, 5 October 2013
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	\|-		\|-
	\|<applet load='3k3k' size='300' frame='true' align='left' caption='3k3k - PYR1 dimer' scene = '56/564059/Pyr1dimer/2'/><br clear='both'>'''3k3k scene'''<Br><scene name='56/564059/Pyr1dimer/2'>3. PYR1 dimer</scene> in which one monomer is bound to ABA. The native form of the receptor is a dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref>.		\|<applet load='3k3k' size='300' frame='true' align='left' caption='3k3k - PYR1 dimer' scene = '56/564059/Pyr1dimer/2'/><br clear='both'>'''3k3k scene'''<Br><scene name='56/564059/Pyr1dimer/2'>3. PYR1 dimer</scene> in which one monomer is bound to ABA. The native form of the receptor is a dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref>.
-	\|<applet load='3klx' size='300' frame='true' align='left' caption='3klx - PYL3 ''cis'' dimer' scene = '56/564059/Apopyl3cisdimer/1'/><br clear='both'>'''3klx scene'''<Br><scene name='56/564059/Apopyl3cisdimer/1'>Apo PYL3 ''cis'' dimer </scene>	+	\|<applet load='3klx' size='300' frame='true' align='left' caption='3klx - PYL3 ''cis'' dimer' scene = '56/564059/Apopyl3cisdimer/2'/><br clear='both'>'''3klx scene'''<Br><scene name='56/564059/Apopyl3cisdimer/2'>Apo PYL3 ''cis'' dimer </scene>
-	\|<applet load='4dsc' size='300' frame='true' align='left' caption='4dsc - PYL3.ABA ''trans'' dimer' scene = '56/564059/Pylabatransdimer/1'/><br clear='both'>'''4dsc scene'''<Br><scene name='56/564059/Pylabatransdimer/1'>PYL3.ABA ''trans'' dimer'</scene>	+	\|<applet load='4dsc' size='300' frame='true' align='left' caption='4dsc - PYL3.ABA ''trans'' dimer' scene = '56/564059/Pylabatransdimer/2'/><br clear='both'>'''4dsc scene'''<Br><scene name='56/564059/Pylabatransdimer/2'>PYL3.ABA ''trans'' dimer'</scene>
	\|}		\|}

Alice Harmon at 15:11, 5 October 2013

Alice Harmon — Sat, 05 Oct 2013 15:11:08 GMT

←Older revision		Revision as of 15:11, 5 October 2013
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	The core ABA signaling pathway is shown in the figure to the left. In unstimulated cells, the ABA receptor (R) is an unliganded dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref> (monomer shown) in the cytosol and nucleus , and the SNRK2 protein kinase (K) is bound to a protein phosphatase 2C (P) in a complex (K-P) in which the kinase is dephosphorylated and inactivated by the phosphatase. When the ABA level rises ABA binds to the ABA receptor<ref>PMID:19893533</ref><ref>PMID:19407143</ref><ref>PMID:19407142</ref>. The activated receptor (R<sup>.</sup>ABA) binds to a protein phosphatase 2C<ref>PMID:19624469</ref> (R<sup>.</sup>ABA-P), and frees the protein kinase to be activated by autophosphorylation or phosphorylation by another protein kinase. Activation of SnRK2.6/OST1/SRK2E leads to phosphorylation of: 1) ion channels SLAC1<ref>PMID: 19955405</ref> and KAT1<ref>PMID:19785574</ref> in guard cells and stomatal closure; 2) transcription factor ABI5<ref name = "Nakashima2009"/> in seeds/seedlings and dormancy/growth arrest; or 3) phosphorylation of transcription factor AREB/ABF <ref>PMID: 16446457</ref><ref name = "Fujii2007"/> in vegetative tissue and stress tolerance and growth regulation.		The core ABA signaling pathway is shown in the figure to the left. In unstimulated cells, the ABA receptor (R) is an unliganded dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref> (monomer shown) in the cytosol and nucleus , and the SNRK2 protein kinase (K) is bound to a protein phosphatase 2C (P) in a complex (K-P) in which the kinase is dephosphorylated and inactivated by the phosphatase. When the ABA level rises ABA binds to the ABA receptor<ref>PMID:19893533</ref><ref>PMID:19407143</ref><ref>PMID:19407142</ref>. The activated receptor (R<sup>.</sup>ABA) binds to a protein phosphatase 2C<ref>PMID:19624469</ref> (R<sup>.</sup>ABA-P), and frees the protein kinase to be activated by autophosphorylation or phosphorylation by another protein kinase. Activation of SnRK2.6/OST1/SRK2E leads to phosphorylation of: 1) ion channels SLAC1<ref>PMID: 19955405</ref> and KAT1<ref>PMID:19785574</ref> in guard cells and stomatal closure; 2) transcription factor ABI5<ref name = "Nakashima2009"/> in seeds/seedlings and dormancy/growth arrest; or 3) phosphorylation of transcription factor AREB/ABF <ref>PMID: 16446457</ref><ref name = "Fujii2007"/> in vegetative tissue and stress tolerance and growth regulation.

-	Structures in the figure are: R, apo ~~PYR2~~, [[3kdh]]; R<sup>.</sup>ABA, ~~PYR2~~<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, ~~PYR2~~<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].	+	Structures in the figure are: R, apo PYL2, [[3kdh]]; R<sup>.</sup>ABA, PYL2<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, PYL2<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].

	==Pyr/Pyl/RCAR family of ABA receptors==		==Pyr/Pyl/RCAR family of ABA receptors==
Line 15:		Line 15:
	PYR1/RCAR11 and PYL9/RCAR1		PYR1/RCAR11 and PYL9/RCAR1
	PYR1, PYL1, PYL2, and PYL3 show ABA-dependent inhibition of PP2Cs such as ABI1, HYPERSENSITIVE TO ABA 1 (HAB1), HAB2, and ABA-HYPERSENSITIVE GERMINATION 3 (AHG3, also named PP2CA)<ref>PMID:23265948</ref>		PYR1, PYL1, PYL2, and PYL3 show ABA-dependent inhibition of PP2Cs such as ABI1, HYPERSENSITIVE TO ABA 1 (HAB1), HAB2, and ABA-HYPERSENSITIVE GERMINATION 3 (AHG3, also named PP2CA)<ref>PMID:23265948</ref>
		+
		+	"Upon binding to ABA or pyrabactin, the gate
		+	(Melcher et al., 2009) of PYL undergoes a pronounced conformational
		+	change, and the PYL protomers in the cis-homodimer
		+	separate slightly, decreasing the area of interface and creating
		+	a binding surface for protein phosphatase 2C (PP2C)." "Upon ligand binding, the apo-PYL3 cis-homodimer is
		+	converted to a trans-homodimer, in which two ligand-bound
		+	PYLs bind to each other in a reverse direction"<ref>"PMID:22579247</ref>


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	\|-		\|-
	\|<applet load='3k3k' size='300' frame='true' align='left' caption='3k3k - PYR1 dimer' scene = '56/564059/Pyr1dimer/2'/><br clear='both'>'''3k3k scene'''<Br><scene name='56/564059/Pyr1dimer/2'>3. PYR1 dimer</scene> in which one monomer is bound to ABA. The native form of the receptor is a dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref>.		\|<applet load='3k3k' size='300' frame='true' align='left' caption='3k3k - PYR1 dimer' scene = '56/564059/Pyr1dimer/2'/><br clear='both'>'''3k3k scene'''<Br><scene name='56/564059/Pyr1dimer/2'>3. PYR1 dimer</scene> in which one monomer is bound to ABA. The native form of the receptor is a dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref>.
		+	\|<applet load='3klx' size='300' frame='true' align='left' caption='3klx - PYL3 ''cis'' dimer' scene = '56/564059/Apopyl3cisdimer/1'/><br clear='both'>'''3klx scene'''<Br><scene name='56/564059/Apopyl3cisdimer/1'>Apo PYL3 ''cis'' dimer </scene>
		+	\|<applet load='4dsc' size='300' frame='true' align='left' caption='4dsc - PYL3.ABA ''trans'' dimer' scene = '56/564059/Pylabatransdimer/1'/><br clear='both'>'''4dsc scene'''<Br><scene name='56/564059/Pylabatransdimer/1'>PYL3.ABA ''trans'' dimer'</scene>
	\|}		\|}

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	[[3kay]], apo AtPYL1 <br>		[[3kay]], apo AtPYL1 <br>
	[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>		[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>
-	[[3klx]], ~~apo~~ AtPYL3<br>	+	[[3klx]], Apo AtPYL3<br>
	[[4jdl]], Apo AtPYL5<br>		[[4jdl]], Apo AtPYL5<br>
	[[3rt2]], [[3uqh]] apo AtPYL10<br>		[[3rt2]], [[3uqh]] apo AtPYL10<br>

Alice Harmon at 14:20, 5 October 2013

Alice Harmon — Sat, 05 Oct 2013 14:20:39 GMT

←Older revision		Revision as of 14:20, 5 October 2013
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	Santiago J, Dupeux F, Betz K, Antoni R, Gonzalez-Guzman M, Rodriguez L, Márquez JA, Rodriguez PL.Plant Sci. 2012 182:3-11<ref>PMID:22118610</ref>		Santiago J, Dupeux F, Betz K, Antoni R, Gonzalez-Guzman M, Rodriguez L, Márquez JA, Rodriguez PL.Plant Sci. 2012 182:3-11<ref>PMID:22118610</ref>

-	===~~Pyr~~/PYL/RCAR structures===	+	===PYR/PYL/RCAR structures===
		+	At is ''Arabidopsis thaliana''

	'''Apo structures'''<br>		'''Apo structures'''<br>

-	[[3k3k]], ~~AtPyr1~~ dimer, one monomer is bound to ABA and the other unliganded<br>	+	[[3k3k]], AtPYR1 dimer, one monomer is bound to ABA and the other unliganded<br>
	[[3kay]], apo AtPYL1 <br>		[[3kay]], apo AtPYL1 <br>
	[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>		[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>
-	[[3klx]], apo ~~ATPYL3~~<br>	+	[[3klx]], apo AtPYL3<br>
-	[[4jdl]], Apo ~~PYL5~~<br>	+	[[4jdl]], Apo AtPYL5<br>
-	[[3rt2]], [[3uqh]] apo ~~PYL10~~<br>	+	[[3rt2]], [[3uqh]] apo AtPYL10<br>


	'''Structures with (+)-ABA'''<br>		'''Structures with (+)-ABA'''<br>
-	[[3k90]], ~~PYR1~~.ABA<br>	+	[[3k90]], AtPYR1.ABA<br>
	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>		[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
	[[3jrs]], AtPYL1.ABA<br>		[[3jrs]], AtPYL1.ABA<br>
	[[3kdi]], [[3kb0]] AtPYL2.ABA<br>		[[3kdi]], [[3kb0]] AtPYL2.ABA<br>
	[[4dsb]], [[4dsc]] AtPYL3 with ABA<br>		[[4dsb]], [[4dsc]] AtPYL3 with ABA<br>
-	[[3oqu]], ~~PYL9~~.ABA<br>	+	[[3oqu]], AtPYL9.ABA<br>
-	[[3r6p]], ~~PYL10~~.ABA<br>	+	[[3r6p]], AtPYL10.ABA<br>


	'''Structures with (-)-ABA'''<br>		'''Structures with (-)-ABA'''<br>
-	[[4jda]], ~~PYL3~~ with (-)-ABA<br>	+	[[4jda]], AtPYL3 with (-)-ABA<br>


	'''Structures with pyrabactin'''<br>		'''Structures with pyrabactin'''<br>
-	[[3njo]], ~~PYR1~~.Pyrabactin<br>	+	[[3njo]], AtPYR1.Pyrabactin<br>
-	[[3nef]], [[3neg]], [[3nr4]] ~~PYL1~~.pyrabactin<br>	+	[[3nef]], [[3neg]], [[3nr4]] AtPYL1.pyrabactin<br>
-	[[3nj0]], [[3ns2]] ~~PYL2~~.Pyrabactin<br>	+	[[3nj0]], [[3ns2]] AtPYL2.Pyrabactin<br>
-	[[3nj1]], ~~PYL2~~ V114I mutant.Pyrabactin <br>	+	[[3nj1]], AtPYL2 V114I mutant.Pyrabactin <br>
	[[3nmh]], AtPYL2 in complex with pyrabactin<br>		[[3nmh]], AtPYL2 in complex with pyrabactin<br>
	[[3nmp]], AtPYL2 mutant A93F in complex with pyrabactin<br>		[[3nmp]], AtPYL2 mutant A93F in complex with pyrabactin<br>
-	[[3oji]], ~~PYL3~~ with pyrabactin(?)<br>	+	[[3oji]], AtPYL3 with pyrabactin(?)<br>


	'''Structures with (+)-ABA or homolog and a PP2C'''<br>		'''Structures with (+)-ABA or homolog and a PP2C'''<br>
-	[[3qn1]], ~~PYR1~~.ABA - ~~HAB1~~<br>	+	[[3qn1]], AtPYR1.ABA - AtHAB1<br>
-	[[3zvu]], ~~PYR1~~ H60P mutant .ABA - ~~HAB1~~<br>	+	[[3zvu]], AtPYR1 H60P mutant .ABA - AtHAB1<br>
	[[3kb3]], AtPYL1.ABA - HAB1<br>		[[3kb3]], AtPYL1.ABA - HAB1<br>
	[[3jrq]], [[3kdj]] AtPYL1.ABA - ABI1<br>		[[3jrq]], [[3kdj]] AtPYL1.ABA - ABI1<br>
-	[[3ujl]], ~~PYL2~~.ABA - ~~ABI2~~<br>	+	[[3ujl]], AtPYL2.ABA - AtABI2<br>
-	[[4lga]], [[4lgb]] ~~PYL2~~.ABA mimic - ~~HAB1~~<br>	+	[[4lga]], [[4lgb]] AtPYL2.ABA mimic - AtHAB1<br>
-	[[4ds8]], AtPYL3.ABA complex with ~~HAB1~~	+	[[4ds8]], AtPYL3.ABA complex with AtHAB1
-	[[3rt0]], ~~PYL10~~.ABA - ~~HAB1~~<br>	+	[[3rt0]], AtPYL10.ABA - AtHAB1<br>


	'''Structures with pyrabactin or homolog and a PP2C'''<br>		'''Structures with pyrabactin or homolog and a PP2C'''<br>
-	[[4la7]], [[4lg5]] ~~PYL2~~.Quinabactin - ~~HAB1~~<br>	+	[[4la7]], [[4lg5]] AtPYL2.Quinabactin - AtHAB1<br>
-	[[3nmn]], AtPYL1.pyrabactin in complex with ~~ABI1~~<br>	+	[[3nmn]], AtPYL1.pyrabactin in complex with AtABI1<br>
-	[[3nmt]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ~~HAB1~~<br>	+	[[3nmt]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase AtHAB1<br>
-	[[3nmv]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ~~ABI1~~<br>	+	[[3nmv]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase AtABI1<br>

Alice Harmon at 14:15, 5 October 2013

Alice Harmon — Sat, 05 Oct 2013 14:15:44 GMT

←Older revision		Revision as of 14:15, 5 October 2013
Line 44:		Line 44:
	Santiago J, Dupeux F, Betz K, Antoni R, Gonzalez-Guzman M, Rodriguez L, Márquez JA, Rodriguez PL.Plant Sci. 2012 182:3-11<ref>PMID:22118610</ref>		Santiago J, Dupeux F, Betz K, Antoni R, Gonzalez-Guzman M, Rodriguez L, Márquez JA, Rodriguez PL.Plant Sci. 2012 182:3-11<ref>PMID:22118610</ref>

		+	===Pyr/PYL/RCAR structures===
		+
		+	'''Apo structures'''<br>
		+
		+	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
		+	[[3kay]], apo AtPYL1 <br>
		+	[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>
		+	[[3klx]], apo ATPYL3<br>
		+	[[4jdl]], Apo PYL5<br>
		+	[[3rt2]], [[3uqh]] apo PYL10<br>
		+
		+
		+	'''Structures with (+)-ABA'''<br>
		+	[[3k90]], PYR1.ABA<br>
		+	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
		+	[[3jrs]], AtPYL1.ABA<br>
		+	[[3kdi]], [[3kb0]] AtPYL2.ABA<br>
		+	[[4dsb]], [[4dsc]] AtPYL3 with ABA<br>
		+	[[3oqu]], PYL9.ABA<br>
		+	[[3r6p]], PYL10.ABA<br>
		+
		+
		+	'''Structures with (-)-ABA'''<br>
		+	[[4jda]], PYL3 with (-)-ABA<br>
		+
		+
		+	'''Structures with pyrabactin'''<br>
		+	[[3njo]], PYR1.Pyrabactin<br>
		+	[[3nef]], [[3neg]], [[3nr4]] PYL1.pyrabactin<br>
		+	[[3nj0]], [[3ns2]] PYL2.Pyrabactin<br>
		+	[[3nj1]], PYL2 V114I mutant.Pyrabactin <br>
		+	[[3nmh]], AtPYL2 in complex with pyrabactin<br>
		+	[[3nmp]], AtPYL2 mutant A93F in complex with pyrabactin<br>
		+	[[3oji]], PYL3 with pyrabactin(?)<br>
		+
		+
		+	'''Structures with (+)-ABA or homolog and a PP2C'''<br>
		+	[[3qn1]], PYR1.ABA - HAB1<br>
		+	[[3zvu]], PYR1 H60P mutant .ABA - HAB1<br>
		+	[[3kb3]], AtPYL1.ABA - HAB1<br>
		+	[[3jrq]], [[3kdj]] AtPYL1.ABA - ABI1<br>
		+	[[3ujl]], PYL2.ABA - ABI2<br>
		+	[[4lga]], [[4lgb]] PYL2.ABA mimic - HAB1<br>
		+	[[4ds8]], AtPYL3.ABA complex with HAB1
		+	[[3rt0]], PYL10.ABA - HAB1<br>
		+
		+
		+	'''Structures with pyrabactin or homolog and a PP2C'''<br>
		+	[[4la7]], [[4lg5]] PYL2.Quinabactin - HAB1<br>
		+	[[3nmn]], AtPYL1.pyrabactin in complex with ABI1<br>
		+	[[3nmt]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>
		+	[[3nmv]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ABI1<br>

Alice Harmon at 14:05, 5 October 2013

Alice Harmon — Sat, 05 Oct 2013 14:05:43 GMT

←Older revision		Revision as of 14:05, 5 October 2013
Line 23:		Line 23:
	\|'''Right panel''' - PYL<sup>'''.'''</sup>ABA bound to HAB1[[3ujl]]		\|'''Right panel''' - PYL<sup>'''.'''</sup>ABA bound to HAB1[[3ujl]]
	\|-		\|-
-	\| <applet load='3kdh' size='300' frame='true' align='left' caption='~~3kaz~~ - apo-Pyl2' scene = '56/564059/Apopyl2/1'/><br clear='both'>'''3kdh scenes''' <Br><scene name='56/564059/Apopyl2/1'>1. Default scene </scene> PYL2 is shown as a monomer. See also Scene 3 of the middle panel, which shows the receptor dimer. <br><scene name='56/564059/Apopyl2/3'>2. Open gate</scene> The entrance to binding pocket for ABA is regulated by a "latch" shown in orchid and a "gate" shown in blue. Proline 92 is shown in ball and stick. Here the gate and entrance to the binding site are open.	+	\| <applet load='3kdh' size='300' frame='true' align='left' caption='3kdh - apo-Pyl2' scene = '56/564059/Apopyl2/1'/><br clear='both'>'''3kdh scenes''' <Br><scene name='56/564059/Apopyl2/1'>1. Default scene </scene> PYL2 is shown as a monomer. See also Scene 3 of the middle panel, which shows the receptor dimer. <br><scene name='56/564059/Apopyl2/3'>2. Open gate</scene> The entrance to binding pocket for ABA is regulated by a "latch" shown in orchid and a "gate" shown in blue. Proline 92 is shown in ball and stick. Here the gate and entrance to the binding site are open.
-	\| <applet load='3kdi' size='300' frame='true' align='left' caption='3kdi - ABA bound to PYL2' scene = '56/564059/Abapyl2/1' /><Br clear='both'>'''~~3ujg~~ scenes'''<Br><scene name='56/564059/Abapyl2/1'>1. Default scene </scene> ABA (CPK spheres) binds to a water-filled (not shown) pocket of PYL2. <br><scene name='56/564059/Abapyl2/2'>2. Closed gate </scene> The gate folds over ABA and interacts with the latch. <br>~~<scene name='56/564059/Pyr1dimer/2'>3. PYR1 dimer</scene> in which one monomer is bound to ABA. The native form of the receptor is a dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref>.~~	+	\| <applet load='3kdi' size='300' frame='true' align='left' caption='3kdi - ABA bound to PYL2' scene = '56/564059/Abapyl2/1' /><Br clear='both'>'''3kdi scenes'''<Br><scene name='56/564059/Abapyl2/1'>1. Default scene </scene> ABA (CPK spheres) binds to a water-filled (not shown) pocket of PYL2. <br><scene name='56/564059/Abapyl2/2'>2. Closed gate </scene> The gate folds over ABA and interacts with the latch. <br>
-	\|<applet load='3ujl' size='300' frame='true' align='left' caption='3ujl - PYR2-HAB1' scene = '56/564059/Pyl2hab1/2' /><Br clear='both'>'''~~3ujg~~ scenes'''<Br><scene name='56/564059/Pyl2hab1/1'>1. Default scene</scene> Complex between PYL2 (blue) with bound ABA (CPK spheres)and HAB1 (gold), a protein phosphatase 2C. Magnesium ions in the active site of HAB1 are shown as green spheres. <br><scene name='56/564059/Pyl2hab1/5'>2. Closed gate locked by interaction with HAB1</scene> Gate residue proline 92 (blue ball and stick) interacts with typtophan 290 (gold ball and stick and residues in a hydrophobic loop (dark gold ball and stick) of HAB1. The gate also interacts with residues surrounding the phosphatase's active site, which is marked by magnesium ions (small green spheres).	+	\|<applet load='3ujl' size='300' frame='true' align='left' caption='3ujl - PYR2-HAB1' scene = '56/564059/Pyl2hab1/2' /><Br clear='both'>'''3ujl scenes'''<Br><scene name='56/564059/Pyl2hab1/1'>1. Default scene</scene> Complex between PYL2 (blue) with bound ABA (CPK spheres)and HAB1 (gold), a protein phosphatase 2C. Magnesium ions in the active site of HAB1 are shown as green spheres. <br><scene name='56/564059/Pyl2hab1/5'>2. Closed gate locked by interaction with HAB1</scene> Gate residue proline 92 (blue ball and stick) interacts with typtophan 290 (gold ball and stick and residues in a hydrophobic loop (dark gold ball and stick) of HAB1. The gate also interacts with residues surrounding the phosphatase's active site, which is marked by magnesium ions (small green spheres).
		+	\|-
		+	\|<applet load='3k3k' size='300' frame='true' align='left' caption='3k3k - PYR1 dimer' scene = '56/564059/Pyr1dimer/2'/><br clear='both'>'''3k3k scene'''<Br><scene name='56/564059/Pyr1dimer/2'>3. PYR1 dimer</scene> in which one monomer is bound to ABA. The native form of the receptor is a dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref>.
	\|}		\|}

Alice Harmon at 19:47, 4 October 2013

Alice Harmon — Fri, 04 Oct 2013 19:47:18 GMT

←Older revision		Revision as of 19:47, 4 October 2013
Line 1:		Line 1:
-	==Pyr/Pyl/RCAR family of ABA receptors==
-
	[[Image:ABA model 2 med.jpg\|left]]		[[Image:ABA model 2 med.jpg\|left]]

	==ABA signaling pathway==		==ABA signaling pathway==
-	Abscisic acid (ABA,)[[Image:Abscisic acid.svg.png\|thumb\| Abscisic Acid]] is a plant hormone that regulates seed dormancy and germination, stomatal closure, and responses to drought stress, and its core signaling pathway has recently been identified.<ref>PMID:15012233</ref><ref>PMID:12045268</ref><ref>PMID:20192755</ref> In Arabidopsis, this pathway involves an ABA ~~receptor~~ (PYR1~~, PYR2~~, PYL1, PYL2, ~~and RCAR~~), a protein phosphatase 2C in Clade C (ABI1, ABI2, and HAB1), and a protein kinase in subclass III of SnRK2s ([[SnRK2.6/OST1/SRK2E]], SNRK2.2/SRK2D and SnRK2.3/SRK2IA).<ref name = "Mustilli2002">PMID:12468729</ref><ref>PMID:12514244</ref><ref name = "Nakashima2009">PMID:19541597</ref><ref name = "Fujii2007">PMID:17307925</ref>	+	Abscisic acid (ABA,)[[Image:Abscisic acid.svg.png\|thumb\| Abscisic Acid]] is a plant hormone that regulates seed dormancy and germination, stomatal closure, and responses to drought stress, and its core signaling pathway has recently been identified.<ref>PMID:15012233</ref><ref>PMID:12045268</ref><ref>PMID:20192755</ref> In Arabidopsis, this pathway involves at least four ABA receptors (PYR1/RCAR11, PYL1/RCAR12, PYL2/RCAR14, PYL9/RCAR1)<ref>PMID:19407143</ref><ref>PMID:19407142</ref>, a protein phosphatase 2C in Clade C (ABI1, ABI2, and HAB1)<ref>PMID:19407143</ref><ref>PMID:19407142</ref>, and a protein kinase in subclass III of SnRK2s ([[SnRK2.6/OST1/SRK2E]], SNRK2.2/SRK2D and SnRK2.3/SRK2IA).<ref name = "Mustilli2002">PMID:12468729</ref><ref>PMID:12514244</ref><ref name = "Nakashima2009">PMID:19541597</ref><ref name = "Fujii2007">PMID:17307925</ref>

-	The core ABA signaling pathway is shown in the figure to the left. ~~When the ABA level in the cytosol is low~~, the ABA receptor (R) is an unliganded dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref> (monomer shown), and the SNRK2 protein kinase (K) is bound to a protein phosphatase 2C (P) in a complex (K-P) in which the kinase is dephosphorylated and inactivated by the phosphatase. When the ABA level rises ABA binds to the ABA receptor ~~(R)~~<ref>PMID:19893533</ref><ref>PMID:19407143</ref><ref>PMID:19407142</ref>. The activated receptor (R<sup>.</sup>ABA) binds to a protein phosphatase 2C<ref>PMID:19624469</ref> (R<sup>.</sup>ABA-P), and frees the protein kinase to be activated by autophosphorylation or phosphorylation by another protein kinase. Activation of SnRK2.6/OST1/SRK2E leads to phosphorylation of: 1) ion channels SLAC1<ref>PMID: 19955405</ref> and KAT1<ref>PMID:19785574</ref> in guard cells and stomatal closure; 2) transcription factor ABI5<ref name = "Nakashima2009"/> in seeds/seedlings and dormancy/growth arrest; or 3) phosphorylation of transcription factor AREB/ABF <ref>PMID: 16446457</ref><ref name = "Fujii2007"/> in vegetative tissue and stress tolerance and growth regulation.	+	The core ABA signaling pathway is shown in the figure to the left. In unstimulated cells, the ABA receptor (R) is an unliganded dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref> (monomer shown) in the cytosol and nucleus , and the SNRK2 protein kinase (K) is bound to a protein phosphatase 2C (P) in a complex (K-P) in which the kinase is dephosphorylated and inactivated by the phosphatase. When the ABA level rises ABA binds to the ABA receptor<ref>PMID:19893533</ref><ref>PMID:19407143</ref><ref>PMID:19407142</ref>. The activated receptor (R<sup>.</sup>ABA) binds to a protein phosphatase 2C<ref>PMID:19624469</ref> (R<sup>.</sup>ABA-P), and frees the protein kinase to be activated by autophosphorylation or phosphorylation by another protein kinase. Activation of SnRK2.6/OST1/SRK2E leads to phosphorylation of: 1) ion channels SLAC1<ref>PMID: 19955405</ref> and KAT1<ref>PMID:19785574</ref> in guard cells and stomatal closure; 2) transcription factor ABI5<ref name = "Nakashima2009"/> in seeds/seedlings and dormancy/growth arrest; or 3) phosphorylation of transcription factor AREB/ABF <ref>PMID: 16446457</ref><ref name = "Fujii2007"/> in vegetative tissue and stress tolerance and growth regulation.

	Structures in the figure are: R, apo PYR2, [[3kdh]]; R<sup>.</sup>ABA, PYR2<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, PYR2<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].		Structures in the figure are: R, apo PYR2, [[3kdh]]; R<sup>.</sup>ABA, PYR2<sup>.</sup>ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R<sup>.</sup>ABA-P, PYR2<sup>.</sup>ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].
		+
		+	==Pyr/Pyl/RCAR family of ABA receptors==

	The following Proteopedia pages		The following Proteopedia pages
Line 14:		Line 14:
	crystal structures of		crystal structures of
	PYR1/RCAR11 and PYL9/RCAR1		PYR1/RCAR11 and PYL9/RCAR1
		+	PYR1, PYL1, PYL2, and PYL3 show ABA-dependent inhibition of PP2Cs such as ABI1, HYPERSENSITIVE TO ABA 1 (HAB1), HAB2, and ABA-HYPERSENSITIVE GERMINATION 3 (AHG3, also named PP2CA)<ref>PMID:23265948</ref>

Alice Harmon at 15:17, 4 October 2013

Alice Harmon — Fri, 04 Oct 2013 15:17:17 GMT

←Older revision		Revision as of 15:17, 4 October 2013
Line 18:		Line 18:

	{\|		{\|
-	\|'''Left ~~scene~~''' - apo PYL2 [[3kdh]]	+	\|'''Left panel''' - apo PYL2 [[3kdh]]
-	\|'''Middle ~~scene~~''' - ABA bound to PYL2 [[3kdi]]	+	\|'''Middle panel''' - ABA bound to PYL2 [[3kdi]] or PYR1 [[3k3k]]
-	\|'''Right ~~scene~~''' - PYL.ABA bound to HAB1[[3ujl]]	+	\|'''Right panel''' - PYL<sup>'''.'''</sup>ABA bound to HAB1[[3ujl]]
	\|-		\|-
-	\| <applet load='3kdh' size='300' frame='true' align='left' caption='3kaz - apo-Pyl2' scene = '56/564059/Apopyl2/1'/><br clear='both'>'''3kdh scenes''' <Br><scene name='56/564059/Apopyl2/1'>1. Default scene </scene><br><scene name='56/564059/Apopyl2/3'>2. Open gate</scene>	+	\| <applet load='3kdh' size='300' frame='true' align='left' caption='3kaz - apo-Pyl2' scene = '56/564059/Apopyl2/1'/><br clear='both'>'''3kdh scenes''' <Br><scene name='56/564059/Apopyl2/1'>1. Default scene </scene> PYL2 is shown as a monomer. See also Scene 3 of the middle panel, which shows the receptor dimer. <br><scene name='56/564059/Apopyl2/3'>2. Open gate</scene> The entrance to binding pocket for ABA is regulated by a "latch" shown in orchid and a "gate" shown in blue. Proline 92 is shown in ball and stick. Here the gate and entrance to the binding site are open.
-	\| <applet load='3kdi' size='300' frame='true' align='left' caption='3kdi - ABA bound to PYL2' scene = '56/564059/Abapyl2/1' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Abapyl2/1'>1. Default scene </scene><br><scene name='56/564059/Abapyl2/2'>2. Closed gate </scene><scene name='56/564059/Pyr1dimer/2'>PYR1 dimer</scene> in which one monomer is bound to ABA.	+	\| <applet load='3kdi' size='300' frame='true' align='left' caption='3kdi - ABA bound to PYL2' scene = '56/564059/Abapyl2/1' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Abapyl2/1'>1. Default scene </scene> ABA (CPK spheres) binds to a water-filled (not shown) pocket of PYL2. <br><scene name='56/564059/Abapyl2/2'>2. Closed gate </scene> The gate folds over ABA and interacts with the latch. <br><scene name='56/564059/Pyr1dimer/2'>3. PYR1 dimer</scene> in which one monomer is bound to ABA. The native form of the receptor is a dimer<ref>PMID:19933100</ref><ref>PMID:23265948</ref>.
-	\|<applet load='3ujl' size='300' frame='true' align='left' caption='3ujl - PYR2-HAB1' scene = '56/564059/Pyl2hab1/2' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Pyl2hab1/1'>~~TextToBeDisplayed~~</scene><br><scene name='56/564059/Pyl2hab1/4'>2. ~~Gate~~ interaction with HAB1</scene>	+	\|<applet load='3ujl' size='300' frame='true' align='left' caption='3ujl - PYR2-HAB1' scene = '56/564059/Pyl2hab1/2' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Pyl2hab1/1'>1. Default scene</scene> Complex between PYL2 (blue) with bound ABA (CPK spheres)and HAB1 (gold), a protein phosphatase 2C. Magnesium ions in the active site of HAB1 are shown as green spheres. <br><scene name='56/564059/Pyl2hab1/5'>2. Closed gate locked by interaction with HAB1</scene> Gate residue proline 92 (blue ball and stick) interacts with typtophan 290 (gold ball and stick and residues in a hydrophobic loop (dark gold ball and stick) of HAB1. The gate also interacts with residues surrounding the phosphatase's active site, which is marked by magnesium ions (small green spheres).
	\|}		\|}

Alice Harmon at 14:24, 4 October 2013

Alice Harmon — Fri, 04 Oct 2013 14:24:59 GMT

←Older revision		Revision as of 14:24, 4 October 2013
Line 23:		Line 23:
	\|-		\|-
	\| <applet load='3kdh' size='300' frame='true' align='left' caption='3kaz - apo-Pyl2' scene = '56/564059/Apopyl2/1'/><br clear='both'>'''3kdh scenes''' <Br><scene name='56/564059/Apopyl2/1'>1. Default scene </scene><br><scene name='56/564059/Apopyl2/3'>2. Open gate</scene>		\| <applet load='3kdh' size='300' frame='true' align='left' caption='3kaz - apo-Pyl2' scene = '56/564059/Apopyl2/1'/><br clear='both'>'''3kdh scenes''' <Br><scene name='56/564059/Apopyl2/1'>1. Default scene </scene><br><scene name='56/564059/Apopyl2/3'>2. Open gate</scene>
-	\| <applet load='3kdi' size='300' frame='true' align='left' caption='3kdi - ABA bound to PYL2' scene = '56/564059/Abapyl2/1' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Abapyl2/1'>1. Default scene </scene><br><scene name='56/564059/Abapyl2/2'>2. Closed gate </scene>	+	\| <applet load='3kdi' size='300' frame='true' align='left' caption='3kdi - ABA bound to PYL2' scene = '56/564059/Abapyl2/1' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Abapyl2/1'>1. Default scene </scene><br><scene name='56/564059/Abapyl2/2'>2. Closed gate </scene><scene name='56/564059/Pyr1dimer/2'>PYR1 dimer</scene> in which one monomer is bound to ABA.
-	\|<applet load='3ujl' size='300' frame='true' align='left' caption='3ujl - PYR2-HAB1' scene = '56/564059/Pyl2hab1/2' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Pyl2hab1/1'>TextToBeDisplayed</scene><br><scene name='56/564059/Pyl2hab1/4'>3. Gate interaction with HAB1</scene>	+	\|<applet load='3ujl' size='300' frame='true' align='left' caption='3ujl - PYR2-HAB1' scene = '56/564059/Pyl2hab1/2' /><Br clear='both'>'''3ujg scenes'''<Br><scene name='56/564059/Pyl2hab1/1'>TextToBeDisplayed</scene><br><scene name='56/564059/Pyl2hab1/4'>2. Gate interaction with HAB1</scene>
	\|}		\|}