PYR/PYL/RCAR family of ABA receptors

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Structural Basis of ABA-binding by ABA Receptors and of Receptor Binding to Target PP2Cs

The ABA signaling pathway is initiated by the binding of ABA to a receptor, which in turn binds to and inhibits a protein phosphatase 2C [1][2][3]. See ABA Signaling Pathway for a scheme of the pathway, which includes activation of a SNRK2 protein kinase.

ABA receptors are small (150-200 residues) soluble proteins that are found in the cytoplasm and nucleus of plant cells. In the absence of ABA, they are dimers[4][5][6]. Upon binding ABA in a water-filled pocket, a gate loop closes over the pocket and is latched by another loop. This conformational change apparently loosens the bonds between the monomers and shifts the equilibrium between the dimer and free monomers towards free monomers. Also, a binding site for a protein phosphatase 2Cs is formed. The ABA-bound receptor binds to the protein phosphatase and inhibits its activity. The interaction occurs near the active site of the phosphatase and phosphatase residues serve to lock the gate of the receptor. This mechanism has been dubbed “gate-latch-lock”, and is described in recent reviews[7][8][9].

Six members of the PYR/PYL/RCAR family of proteins (PYR1/RCAR11: PYL1/RCAR12, PYL2/RCAR14, PYL3/RCAR13, PYL8/RCAR3, PYL9/RCAR1) have been shown to bind a protein phosphatase 2C in the presence of ABA[1][3][5][10][11]. The names of proteins are from Pyrabactin resistance/Pyrabactin-like or regulatory components of ABA receptor.

The structure of ABA receptors[2][4][10][12][13] places them in the START group (e.g. lipid transport domain of human MLN64, 1em2) of the Bet v1(Betula verrucosa pollen allergen, 1bv1) family of proteins [14]. This helix grip structure consists of a large antiparallel beta sheet flanked by alpha helices. The ABA binding pocket is formed between the sheet and one of the helices, with loops serving as the gate and latch at the entrance of the pocket.

The following scenes examine the structures of receptor monomers and dimers, with and without bound ABA, and of a receptor-protein phosphatase 2C complex. The top row compares the structures of PYL2 in the unliganded, ABA-bound, and ABA plus PP2C(HAB1)-bound states. The bottom row shows dimers of PYR and PYL3. The PYR dimer has one monomer unliganded and the other bound to ABA. PYL3 with bound ABA crystallized in two configurations: cis, with the two monomers head-to-head; and trans, with the two monomers head-to-toe.

Left panel

Top - apo PYL2 3kdh
Bottom - PYR1 dimer 3k3k

Middle panel

Top - ABA bound to PYL2 3kdi or PYR1 3k3k
Bottom - Apo PYL 3 dimer 3klx

Right panel

Top - PYL2.ABA bound to HAB1 3ujl
Bottom - PYL3.ABA dimer

3kdh - apo-Pyl2


3kdh scenes
PYL2 is shown as a monomer. See below for receptor dimers.
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.
is in a trans peptide bond unlike Pro88 in the empty subunit of Pyr1 dimer (below)

3kdi - ABA bound to PYL2


3kdi scenes
ABA (CPK spheres) binds to a water-filled (not shown) pocket of PYL2.
The gate folds over ABA and interacts with the latch.
is in the trans configuration as is Pro88 of the ABA-bound subunit of the Pyr1 dimer (below)


3ujl - PYR2-HAB1


3ujl scenes
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.
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).

3k3k scene
in which one monomer is bound to ABA. The native form of the receptor is a dimer[4][5][6].


3klx scene





4dsc scene




PYR/PYL/RCAR structures

At is Arabidopsis thaliana

Apo structures

3k3k, AtPYR1 dimer, one monomer is bound to ABA and the other unliganded
3kay, apo AtPYL1
3kdh, 3kaz, 3kl1 apo AtPYL2
3klx, Apo AtPYL3
4jdl, Apo AtPYL5
3rt2, 3uqh apo AtPYL10


Structures with (+)-ABA
3k90, AtPYR1.ABA
3k3k, AtPyr1 dimer, one monomer is bound to ABA and the other unliganded
3jrs, AtPYL1.ABA
3kdi, 3kb0 AtPYL2.ABA
4dsb, 4dsc AtPYL3 with ABA
3oqu, AtPYL9.ABA
3r6p, AtPYL10.ABA


Structures with (-)-ABA
4jda, AtPYL3 with (-)-ABA


Structures with pyrabactin
3njo, AtPYR1.Pyrabactin
3nef, 3neg, 3nr4 AtPYL1.pyrabactin
3nj0, 3ns2 AtPYL2.Pyrabactin
3nj1, AtPYL2 V114I mutant.Pyrabactin
3nmh, AtPYL2 in complex with pyrabactin
3nmp, AtPYL2 mutant A93F in complex with pyrabactin
3oji, AtPYL3 with pyrabactin(?)


Structures with (+)-ABA or homolog and a PP2C
3qn1, AtPYR1.ABA - AtHAB1
3zvu, AtPYR1 H60P mutant .ABA - AtHAB1
3kb3, AtPYL1.ABA - HAB1
3jrq, 3kdj AtPYL1.ABA - ABI1
3ujl, AtPYL2.ABA - AtABI2
4lga, 4lgb AtPYL2.ABA mimic - AtHAB1
4ds8, AtPYL3.ABA complex with AtHAB1 3rt0, AtPYL10.ABA - AtHAB1


Structures with pyrabactin or homolog and a PP2C
4la7, 4lg5 AtPYL2.Quinabactin - AtHAB1
3nmn, AtPYL1.pyrabactin in complex with AtABI1
3nmt, AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase AtHAB1
3nmv, AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase AtABI1

References

  1. 1.0 1.1 Ma Y, Szostkiewicz I, Korte A, Moes D, Yang Y, Christmann A, Grill E. Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science. 2009 May 22;324(5930):1064-8. doi: 10.1126/science.1172408. Epub 2009, Apr 30. PMID:19407143 doi:10.1126/science.1172408
  2. 2.0 2.1 Santiago J, Rodrigues A, Saez A, Rubio S, Antoni R, Dupeux F, Park SY, Marquez JA, Cutler SR, Rodriguez PL. Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs. Plant J. 2009 Nov;60(4):575-88. doi: 10.1111/j.1365-313X.2009.03981.x. Epub 2009 , Jul 16. PMID:19624469 doi:10.1111/j.1365-313X.2009.03981.x
  3. 3.0 3.1 Park SY, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues A, Chow TF, Alfred SE, Bonetta D, Finkelstein R, Provart NJ, Desveaux D, Rodriguez PL, McCourt P, Zhu JK, Schroeder JI, Volkman BF, Cutler SR. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science. 2009 May 22;324(5930):1068-71. doi: 10.1126/science.1173041. Epub 2009, Apr 30. PMID:19407142 doi:10.1126/science.1173041
  4. 4.0 4.1 4.2 Nishimura N, Hitomi K, Arvai AS, Rambo RP, Hitomi C, Cutler SR, Schroeder JI, Getzoff ED. Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science. 2009 Dec 4;326(5958):1373-9. Epub 2009 Oct 22. PMID:19933100
  5. 5.0 5.1 5.2 Zhang X, Zhang Q, Xin Q, Yu L, Wang Z, Wu W, Jiang L, Wang G, Tian W, Deng Z, Wang Y, Liu Z, Long J, Gong Z, Chen Z. Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism. Structure. 2012 May 9;20(5):780-90. PMID:22579247 doi:10.1016/j.str.2012.02.019
  6. 6.0 6.1 Miyakawa T, Fujita Y, Yamaguchi-Shinozaki K, Tanokura M. Structure and function of abscisic acid receptors. Trends Plant Sci. 2013 May;18(5):259-66. doi: 10.1016/j.tplants.2012.11.002. Epub, 2012 Dec 22. PMID:23265948 doi:10.1016/j.tplants.2012.11.002
  7. Joshi-Saha A, Valon C, Leung J. A brand new START: abscisic acid perception and transduction in the guard cell. Sci Signal. 2011 Nov 29;4(201):re4. doi: 10.1126/scisignal.2002164. PMID:22126965 doi:http://dx.doi.org/10.1126/scisignal.2002164
  8. Melcher K, Zhou XE, Xu HE. Thirsty plants and beyond: structural mechanisms of abscisic acid perception and signaling. Curr Opin Struct Biol. 2010 Dec;20(6):722-9. doi: 10.1016/j.sbi.2010.09.007. Epub, 2010 Oct 14. PMID:20951573 doi:10.1016/j.sbi.2010.09.007
  9. Santiago J, Dupeux F, Betz K, Antoni R, Gonzalez-Guzman M, Rodriguez L, Marquez JA, Rodriguez PL. Structural insights into PYR/PYL/RCAR ABA receptors and PP2Cs. Plant Sci. 2012 Jan;182:3-11. doi: 10.1016/j.plantsci.2010.11.014. Epub 2010 Dec , 7. PMID:22118610 doi:10.1016/j.plantsci.2010.11.014
  10. 10.0 10.1 Melcher K, Ng LM, Zhou XE, Soon FF, Xu Y, Suino-Powell KM, Park SY, Weiner JJ, Fujii H, Chinnusamy V, Kovach A, Li J, Wang Y, Li J, Peterson FC, Jensen DR, Yong EL, Volkman BF, Cutler SR, Zhu JK, Xu HE. A gate-latch-lock mechanism for hormone signalling by abscisic acid receptors. Nature. 2009 Dec 3;462(7273):602-8. PMID:19898420 doi:10.1038/nature08613
  11. Antoni R, Gonzalez-Guzman M, Rodriguez L, Peirats-Llobet M, Pizzio GA, Fernandez MA, De Winne N, De Jaeger G, Dietrich D, Bennett MJ, Rodriguez PL. PYRABACTIN RESISTANCE1-LIKE8 plays an important role for the regulation of abscisic acid signaling in root. Plant Physiol. 2013 Feb;161(2):931-41. doi: 10.1104/pp.112.208678. Epub 2012 Dec , 14. PMID:23370718 doi:10.1104/pp.112.208678
  12. Miyazono K, Miyakawa T, Sawano Y, Kubota K, Kang HJ, Asano A, Miyauchi Y, Takahashi M, Zhi Y, Fujita Y, Yoshida T, Kodaira KS, Yamaguchi-Shinozaki K, Tanokura M. Structural basis of abscisic acid signalling. Nature. 2009 Dec 3;462(7273):609-14. PMID:19855379 doi:10.1038/nature08583
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  14. Radauer C, Lackner P, Breiteneder H. The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. BMC Evol Biol. 2008 Oct 15;8:286. doi: 10.1186/1471-2148-8-286. PMID:18922149 doi:http://dx.doi.org/10.1186/1471-2148-8-286

See Also

[1] Abscisic Acid in Wikipedia

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Alice Harmon

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