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(-) Description

Title :  CRYSTAL STRUCTURE OF (+)-ABA-BOUND PYL1 IN COMPLEX WITH ABI1
 
Authors :  K. Miyazono, T. Miyakawa, Y. Sawano, K. Kubota, M. Tanokura
Date :  08 Sep 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plant Hormone Receptor, Abscisic Acid, Pyl1, Abi1, Type 2C Protein Phosphatase, Abscisic Acid Signaling Pathway, Cell Membrane, Hydrolase, Magnesium, Manganese, Membrane, Metal-Binding, Nucleus, Protein Phosphatase, Hydrolase-Hormone Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Miyazono, T. Miyakawa, Y. Sawano, K. Kubota, H. J. Kang, A. Asano, Y. Miyauchi, M. Takahashi, Y. Zhi, Y. Fujita, T. Yoshida, K. Kodaira, K. Yamaguchi-Shinozaki, M. Tanokura
Structural Basis Of Abscisic Acid Signalling
Nature V. 462 609 2009
PubMed-ID: 19855379  |  Reference-DOI: 10.1038/NATURE08583

(-) Compounds

Molecule 1 - PROTEIN PHOSPHATASE 2C 56
    Chains: A
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 125-429
    Gene: ABI1
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATPP2C56, PROTEIN PHOSPHATASE 2C ABI1, PP2C ABI1, PROTEIN ABSCISIC ACID-INSENSITIVE 1
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN AT5G46790
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 28-210
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PYL1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1A8S1Ligand/Ion(2Z,4E)-5-[(1S)-1-HYDROXY-2,6,6-TRIMETHYL-4-OXOCYCLOHEX-2-EN-1-YL]-3-METHYLPENTA-2,4-DIENOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:9 , PHE B:88 , PRO B:115 , ALA B:116 , PHE B:135 , ILE B:137 , TYR B:147 , GLU B:171 , PHE B:189 , VAL B:193 , ILE B:194 , HOH B:234BINDING SITE FOR RESIDUE A8S B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JRQ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:153 -Ser A:154
2Gly A:269 -Lys A:270
3Lys A:321 -Pro A:322
4Met B:208 -Asn B:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JRQ)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.P2C56_ARATH128-422  1A:128-422
2PPM_1PS01032 PPM-type phosphatase domain signature.P2C56_ARATH172-180  1A:172-180

(-) Exons   (0, 0)

(no "Exon" information available for 3JRQ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:271
 aligned with P2C56_ARATH | P49597 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:299
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414         
          P2C56_ARATH   125 SVPLYGFTSICGRRPEMEDAVSTIPRFLQSSSGSMLDGRFDPQSAAHFFGVYDGHGGSQVANYCRERMHLALAEEIAKEKPMLCDGDTWLEKWKKALFNSFLRVDSEIESVAPETVGSTSVVAVVFPSHIFVANCGDSRAVLCRGKTALPLSVDHKPDREDEAARIEAAGGKVIQWNGARVFGVLAMSRSIGDRYLKPSIIPDPEVTAVKRVKEDDCLILASDGVWDVMTDEEACEMARKRILLWHKKNAVAGDASLLADERRKEGKDPAAMSAAEYLSKLAIQRGSKDNISVVVVDLK 423
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---PP2C-3jrqA01 A:128-415                                                                                                                                                                                                                                                                          -------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeee......--------..hhhhhheeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee.eeeeee...eeeeeee...eeeeee..eeee........hhhhhhhhhhh...eee...eee.........ee.hhhh.......eeeeee....eeeeeeehhhhhh..hhhhhhhhhhhhhhhh--------------------..hhhhhhhhhhhhhhhhhh.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PPM_2  PDB: A:128-422 UniProt: 128-422                                                                                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) -----------------------------------------------PPM_1    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jrq A 125 SVPLYGFTSICGRRPEMEDAVSTIPRFLQS--------RFDPQSAAHFFGVYDGHGGSQVANYCRERMHLALAEEIAKEKPMLCDGDTWLEKWKKALFNSFLRVDSEIESVAPETVGSTSVVAVVFPSHIFVANCGDSRAVLCRGKTALPLSVDHKPDREDEAARIEAAGGKVIQWNGARVFGVLAMSRSIGDRYLKPSIIPDPEVTAVKRVKEDDCLILASDGVWDVMTDEEACEMARKRILLW--------------------GKDPAAMSAAEYLSKLAIQRGSKDNISVVVVDLK 423
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364    |    -         -     | 394       404       414         
                                                       154      163                                                                                                                                                                                                           369                  390                                 

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with PYL1_ARATH | Q8VZS8 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:179
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
           PYL1_ARATH    32 LTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFEKEEEEERIWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMNR 210
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------Polyketide_cyc2-3jrqB01 B:57-206                                                                                                                      ---- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhh...hhhhh...eeeee...........eeeeee.......eeeeeeeeee....eeeeeeee........eeeeeeeee.------..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jrq B  32 LTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFE------RIWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMNR 210
                                    41        51        61        71        81        91       101       111       121       131       141       151     |   -  |    171       181       191       201         
                                                                                                                                                       157    164                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3JRQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JRQ)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PP2C (22)

(-) Gene Ontology  (26, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P2C56_ARATH | P49597)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
biological process
    GO:0009738    abscisic acid-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription.
    GO:0009788    negative regulation of abscisic acid-activated signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of abscisic acid (ABA) signaling.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0009787    regulation of abscisic acid-activated signaling pathway    Any process that modulates the frequency, rate or extent of abscisic acid (ABA) signaling.
    GO:0010119    regulation of stomatal movement    Any process that modulates the frequency, rate or extent of stomatal movement.
    GO:0009737    response to abscisic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abscisic acid stimulus.
    GO:0009409    response to cold    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (PYL1_ARATH | Q8VZS8)
molecular function
    GO:0010427    abscisic acid binding    Interacting selectively and non-covalently with abscisic acid, plant hormones that regulate aspects of plant growth.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004864    protein phosphatase inhibitor activity    Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0009738    abscisic acid-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0080163    regulation of protein serine/threonine phosphatase activity    Any process that modulates the frequency, rate or extent of protein serine/threonine phosphatase activity: catalysis of the reaction: protein serine/threonine phosphate + H2O = protein serine/threonine + phosphate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  3jrq
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  P2C56_ARATH | P49597
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        P2C56_ARATH | P49597: 3kdj 3nmn
        PYL1_ARATH | Q8VZS8: 3jrs 3kay 3kdj 3nef 3neg 3nmn

(-) Related Entries Specified in the PDB File

3jrs