User:Alice Harmon/Sandbox 5: Difference between revisions

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>  

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^.ABA) binds to a protein phosphatase 2C<ref>PMID:19624469</ref> (R^.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^.ABA, PYR2^.ABA, [[3kdi]]; K-P; SnRK2.6-HAB1, [[3ujg]]; R^.ABA-P, PYR2^.ABA-ABI2, [[3ujl]]; K, SnRK2.6,[[3uc4]].

PYR1/RCAR11 and PYL9/RCAR1

| <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> 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'>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).