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PDBsum entry 3k3k

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protein ligands Protein-protein interface(s) links
Hormone receptor, signaling protein PDB id
3k3k
Jmol
Contents
Protein chains
183 a.a. *
Ligands
A8S
Waters ×380
* Residue conservation analysis
PDB id:
3k3k
Name: Hormone receptor, signaling protein
Title: Crystal structure of dimeric abscisic acid (aba) receptor py resistance 1 (pyr1) with aba-bound closed-lid and aba-free subunits
Structure: Abscisic acid receptor pyr1. Chain: a, b. Synonym: pyrabactin resistance 1, gene product at4g17870, r component of aba receptor 11, rcar11, gene product t6k21.50 engineered: yes
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: at4g17870, pyr1, t6k21.50. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.70Å     R-factor:   0.191     R-free:   0.237
Authors: A.S.Arvai,K.Hitomi,E.D.Getzoff
Key ref:
N.Nishimura et al. (2009). Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1. Science, 326, 1373-1379. PubMed id: 19933100 DOI: 10.1126/science.1181829
Date:
02-Oct-09     Release date:   17-Nov-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O49686  (PYR1_ARATH) -  Abscisic acid receptor PYR1
Seq:
Struc:
191 a.a.
183 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     regulation of protein serine/threonine phosphatase activity   3 terms 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1126/science.1181829 Science 326:1373-1379 (2009)
PubMed id: 19933100  
 
 
Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1.
N.Nishimura, K.Hitomi, A.S.Arvai, R.P.Rambo, C.Hitomi, S.R.Cutler, J.I.Schroeder, E.D.Getzoff.
 
  ABSTRACT  
 
The phytohormone abscisic acid (ABA) acts in seed dormancy, plant development, drought tolerance, and adaptive responses to environmental stresses. Structural mechanisms mediating ABA receptor recognition and signaling remain unknown but are essential for understanding and manipulating abiotic stress resistance. Here, we report structures of pyrabactin resistance 1 (PYR1), a prototypical PYR/PYR1-like (PYL)/regulatory component of ABA receptor (RCAR) protein that functions in early ABA signaling. The crystallographic structure reveals an alpha/beta helix-grip fold and homodimeric assembly, verified in vivo by coimmunoprecipitation. ABA binding within a large internal cavity switches structural motifs distinguishing ABA-free "open-lid" from ABA-bound "closed-lid" conformations. Small-angle x-ray scattering suggests that ABA signals by converting PYR1 to a more compact, symmetric closed-lid dimer. Site-directed PYR1 mutants designed to disrupt hormone binding lose ABA-triggered interactions with type 2C protein phosphatase partners in planta.
 
  Selected figure(s)  
 
Figure 2.
View larger version (41K): [in this window] [in a new window] Fig. 2. Water-filled ABA-binding cavity. (A) ABA (purple ball-and-stick model, with red oxygen atoms) and adjacent, ordered water molecules (light blue spheres) inside the PYR1 cavity, shown with electron density (mesh). Omit Fo-Fc density for ABA contoured at 3 (dark blue) and 4 (magenta); 2Fo-Fc electron density for water molecules contoured at 1 (black). All maps were calculated after "shaking" coordinates to reduce phase bias. (B) Ordered water molecules (dark blue spheres) within the ABA-free subunit cavity, shown with associated 2Fo-Fc electron density, as in (A). ABA (purple) and water molecules (light blue) from the ABA-bound PYR1 subunit [shown in (A)] are superimposed showing conserved water positions. ABA displaces one water molecule (wat7) with the carboxylate, shifts a second (wat2' to wat2, as shown by arrow), and introduces or stabilizes a third (wat1), which interacts with the ABA carbonyl to stabilize lid closure. (C) Stereo view of PYR1 residues contributing to the ABA binding site. Hydrophobic side chains (green ball-and-stick model) surround the ABA ring, whereas hydrogen-bonded (red dashed lines) internal water molecules (light blue spheres) link ABA oxygen atoms (red) to PYR1 hydrophilic side chains (gray ball-and-stick model with red oxygen and blue nitrogen atoms) projecting into the binding cavity. Larger gray spheres show C atoms. Lys^59, Phe^61, Arg^79, Val^83, Leu^87, Pro^88, Ala^89, Ser^92, Glu^94, Ile^110, Leu^117, Tyr^120, Ser^122, Glu^141, Phe^159, Val^163, and Asn^167 contribute to forming this large internal cavity.
Figure 4.
View larger version (63K): [in this window] [in a new window] Fig. 4. ABA-induced subunit conformational changes. (A) Stereo image showing superposition of ABA-free (orange) and ABA-bound (green) PYR1 C traces. ABA-induced helix coiling by the Recoil motif (top right) is coupled to lid closure over ABA (purple with red oxygen atoms) by the Pro-Cap and Leu-Lock structural motifs (top left). (B) Enlarged view of ABA-triggered conformational changes in these three structural motifs that close the lid over bound ABA, colored as in (A). ABA (beneath center) triggers rotation of Phe^159 (arrow) to coil the Recoil motif into helix 3 (diagonal at right), switching the Arg^157 charge-charge interaction (circled) to a new partner within (rather than outside) this helix. Pro^88 isomerization from cis (orange, far left) to trans (green, center) converts the open-lid Pro-Cap to the closed-lid conformation, clamping Leu^87, Pro^88, and Ala^89 over ABA. Leu^117 (orange, top center) locks down (green, center) against ABA, closing the Leu-Lock and flipping the preceding Arg^116 side chain (orange, top center) toward the opposing subunit (forward and slightly to the right in this view) across the dimer interface (see also Fig. 1E).
 
  The above figures are reprinted by permission from the AAAs: Science (2009, 326, 1373-1379) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23396808 S.Classen, G.L.Hura, J.M.Holton, R.P.Rambo, I.Rodic, P.J.McGuire, K.Dyer, M.Hammel, G.Meigs, K.A.Frankel, and J.A.Tainer (2013).
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.
  J Appl Crystallogr, 46, 1.  
21549957 F.Hauser, R.Waadt, and J.I.Schroeder (2011).
Evolution of abscisic Acid synthesis and signaling mechanisms.
  Curr Biol, 21, R346-R355.  
21241020 K.Kaufmann, C.Smaczniak, S.de Vries, G.C.Angenent, and R.Karlova (2011).
Proteomics insights into plant signaling and development.
  Proteomics, 11, 744-755.  
20493758 A.S.Raghavendra, V.K.Gonugunta, A.Christmann, and E.Grill (2010).
ABA perception and signalling.
  Trends Plant Sci, 15, 395-401.  
20507903 D.Schneidman-Duhovny, M.Hammel, and A.Sali (2010).
FoXS: a web server for rapid computation and fitting of SAXS profiles.
  Nucleic Acids Res, 38, W540-W544.  
20729860 F.C.Peterson, E.S.Burgie, S.Y.Park, D.R.Jensen, J.J.Weiner, C.A.Bingman, C.E.Chang, S.R.Cutler, G.N.Phillips, and B.F.Volkman (2010).
Structural basis for selective activation of ABA receptors.
  Nat Struct Mol Biol, 17, 1109-1113.
PDB codes: 3nj0 3nj1 3njo
20851666 G.R.Hicks, and N.V.Raikhel (2010).
Advances in dissecting endomembrane trafficking with small molecules.
  Curr Opin Plant Biol, 13, 706-713.  
  20948817 J.Muschietti, and S.McCormick (2010).
Abscisic acid (ABA) receptors: light at the end of the tunnel.
  F1000 Biol Rep, 2, 0.  
20522527 J.P.Klingler, G.Batelli, and J.K.Zhu (2010).
ABA receptors: the START of a new paradigm in phytohormone signalling.
  J Exp Bot, 61, 3199-3210.  
20050303 K.Baumann (2010).
Signalling: ABA's greatest hits.
  Nat Rev Mol Cell Biol, 11, 2.  
20713515 K.E.Hubbard, N.Nishimura, K.Hitomi, E.D.Getzoff, and J.I.Schroeder (2010).
Early abscisic acid signal transduction mechanisms: newly discovered components and newly emerging questions.
  Genes Dev, 24, 1695-1708.  
20733066 K.G.Kline, G.A.Barrett-Wilt, and M.R.Sussman (2010).
In planta changes in protein phosphorylation induced by the plant hormone abscisic acid.
  Proc Natl Acad Sci U S A, 107, 15986-15991.  
20729862 K.Melcher, Y.Xu, L.M.Ng, X.E.Zhou, F.F.Soon, V.Chinnusamy, K.M.Suino-Powell, A.Kovach, F.S.Tham, S.R.Cutler, J.Li, E.L.Yong, J.K.Zhu, and H.E.Xu (2010).
Identification and mechanism of ABA receptor antagonism.
  Nat Struct Mol Biol, 17, 1102-1108.
PDB codes: 3nmh 3nmn 3nmp 3nmt 3nmv
20927106 L.B.Sheard, X.Tan, H.Mao, J.Withers, G.Ben-Nissan, T.R.Hinds, Y.Kobayashi, F.F.Hsu, M.Sharon, J.Browse, S.Y.He, J.Rizo, G.A.Howe, and N.Zheng (2010).
Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor.
  Nature, 468, 400-405.
PDB codes: 3ogk 3ogl 3ogm
20975223 S.Classen, I.Rodic, J.Holton, G.L.Hura, M.Hammel, and J.A.Tainer (2010).
Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system.
  J Synchrotron Radiat, 17, 774-781.  
21124925 S.L.Hutson, E.Mui, K.Kinsley, W.H.Witola, M.S.Behnke, K.El Bissati, S.P.Muench, B.Rohrman, S.R.Liu, R.Wollmann, Y.Ogata, A.Sarkeshik, J.R.Yates, and R.McLeod (2010).
T. gondii RP promoters & knockdown reveal molecular pathways associated with proliferation and cell-cycle arrest.
  PLoS One, 5, e14057.  
20590451 S.Lumba, S.Cutler, and P.McCourt (2010).
Plant nuclear hormone receptors: a role for small molecules in protein-protein interactions.
  Annu Rev Cell Dev Biol, 26, 445-469.  
20192755 S.R.Cutler, P.L.Rodriguez, R.R.Finkelstein, and S.R.Abrams (2010).
Abscisic acid: emergence of a core signaling network.
  Annu Rev Plant Biol, 61, 651-679.  
20192751 T.H.Kim, M.Böhmer, H.Hu, N.Nishimura, and J.I.Schroeder (2010).
Guard cell signal transduction network: advances in understanding abscisic acid, CO2, and Ca2+ signaling.
  Annu Rev Plant Biol, 61, 561-591.  
20409277 T.Hirayama, and K.Shinozaki (2010).
Research on plant abiotic stress responses in the post-genome era: past, present and future.
  Plant J, 61, 1041-1052.  
20980270 T.Umezawa, K.Nakashima, T.Miyakawa, T.Kuromori, M.Tanokura, K.Shinozaki, and K.Yamaguchi-Shinozaki (2010).
Molecular basis of the core regulatory network in aba responses: sensing, signaling and transport.
  Plant Cell Physiol, 51, 1821-1839.  
20561255 Y.Liu, J.He, Z.Chen, X.Ren, X.Hong, and Z.Gong (2010).
ABA overly-sensitive 5 (ABO5), encoding a pentatricopeptide repeat protein required for cis-splicing of mitochondrial nad2 intron 3, is involved in the abscisic acid response in Arabidopsis.
  Plant J, 63, 749-765.  
19965746 M.R.Sussman, and G.N.Phillips (2009).
How plant cells go to sleep for a long, long time.
  Science, 326, 1356-1357.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.