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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRABACTIN-BOUND ABSCISIC ACID RECEPTOR PYL2 MUTANT A93F IN COMPLEX WITH TYPE 2C PROTEIN PHOSPHATASE ABI2
 
Authors :  X. E. Zhou, K. Melcher, L. -M. Ng, F. -F. Soon, Y. Xu, K. M. Suino-Powell, A J. Li, E. -L. Yong, H. E. Xu
Date :  22 Jun 10  (Deposition) - 25 Aug 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyl2, Pyrabactin, Abscisic Acid Receptor, Helix-Grip Fold, Type 2C Protein Phosphatase, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  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, H. E. Xu
Identification And Mechanism Of Aba Receptor Antagonism.
Nat. Struct. Mol. Biol. V. 17 1102 2010
PubMed-ID: 20729862  |  Reference-DOI: 10.1038/NSMB.1887

(-) Compounds

Molecule 1 - ABSCISIC ACID RECEPTOR PYL2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePYL2, RCAR14, AT2G26040, T19L18.15
    MutationYES
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymPYR1-LIKE PROTEIN 2, REGULATORY COMPONENTS OF ABA RECEPTOR 14
 
Molecule 2 - PROTEIN PHOSPHATASE 2C 77
    ChainsB
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneABI2, AT5G57050, MHM17.19
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymATPP2C77, PROTEIN PHOSPHATASE 2C ABI2, PP2C ABI2, PROTEIN ABSCISIC ACID-INSENSITIVE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2PYV1Ligand/Ion4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:7 , LYS A:64 , PHE A:93 , SER A:96 , GLU A:98 , PHE A:112 , TYR A:124 , PHE A:165 , VAL A:169 , ASN A:173 , HOH A:217 , HOH A:267BINDING SITE FOR RESIDUE PYV A 900
2AC2SOFTWAREHOH B:1 , ASP B:127 , ASP B:165 , ASP B:337 , ASP B:402 , ASN B:403BINDING SITE FOR RESIDUE MG B 424
3AC3SOFTWAREASP B:165 , ASP B:251 , SER B:252 , SER B:336 , ASP B:337BINDING SITE FOR RESIDUE MG B 425
4AC4SOFTWAREHOH B:11 , HOH B:75 , GLU B:126 , GLY B:166 , HOH B:428BINDING SITE FOR RESIDUE MG B 426

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys B:311 -Pro B:312

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.P2C77_ARATH112-411  1B:112-411
2PPM_1PS01032 PPM-type phosphatase domain signature.P2C77_ARATH160-168  1B:160-168

(-) Exons   (0, 0)

(no "Exon" information available for 3NMV)

(-) 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:176
 aligned with PYL2_ARATH | O80992 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:176
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           PYL2_ARATH    13 EEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------Polyketide_cyc2-3nmvA01 A:34-181                                                                                                                    ------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhhh..hhhhh...eeeeeeee.......eeeeee.......eeeeeeeeee....eeeeeeeee.......eeeeeeeeee......eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nmv A  13 SEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPFSTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHD 188
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with P2C77_ARATH | O04719 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:306
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408      
          P2C77_ARATH   109 CVPLYGVTSICGRRPEMEDSVSTIPRFLQVSSSSLLDGRVTNGFNPHLSAHFFGVYDGHGGSQVANYCRERMHLALTEEIVKEKPEFCDGDTWQEKWKKALFNSFMRVDSEIETVAHAPETVGSTSVVAVVFPTHIFVANCGDSRAVLCRGKTPLALSVDHKPDRDDEAARIEAAGGKVIRWNGARVFGVLAMSRSIGDRYLKPSVIPDPEVTSVRRVKEDDCLILASDGLWDVMTNEEVCDLARKRILLWHKKNAMAGEALLPAEKRGEGKDPAAMSAAEYLSKMALQKGSKDNISVVVVDLKGI 414
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----PP2C-3nmvB01 B:113-404                                                                                                                                                                                                                                                                              ---------- Pfam domains
         Sec.struct. author ....eeeeee........eeeeee.....------------...hhhhhheeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......ee.eeeeee...eeeeeee...eeeeee..eeee........hhhhhhhhhhh...eee...eee.........ee.hhhh.......eeeeee....eeeeeeehhhhhh..hhhhhhhhhhhhhhhhhh..--------------...hhhhhhhhhhhhhhhhhh.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---PPM_2  PDB: B:112-411 UniProt: 112-411                                                                                                                                                                                                                                                                      --- PROSITE (1)
                PROSITE (2) ---------------------------------------------------PPM_1    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nmv B 109 CVPLYGVTSICGRRPEMEDSVSTIPRFLQ------------NGFNPHLSAHFFGVYDGHGGSQVANYCRERMHLALTEEIVKEKPEFCDGDTWQEKWKKALFNSFMRVDSEIETVAHAPETVGSTSVVAVVFPTHIFVANCGDSRAVLCRGKTPLALSVDHKPDRDDEAARIEAAGGKVIRWNGARVFGVLAMSRSIGDRYLKPSVIPDPEVTSVRRVKEDDCLILASDGLWDVMTNEEVCDLARKRILLWHKKN--------------EGKDPAAMSAAEYLSKMALQKGSKDNISVVVVDLKGI 414
                                   118       128        |-         - |     158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358    |    -       378       388       398       408      
                                                      137          150                                                                                                                                                                                                                  363            378                                    

   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 3NMV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (26, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYL2_ARATH | O80992)
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.

Chain B   (P2C77_ARATH | O04719)
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: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:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0010205    photoinhibition    The mechanism by which high light intensity inhibits photosynthesis through inactivation of the D1 protein of photosystem II.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:1902456    regulation of stomatal opening    Any process that modulates the frequency, rate or extent of stomatal opening.
    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: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.
    GO:0006970    response to osmotic stress    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 stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
    GO:0009414    response to water deprivation    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 water deprivation stimulus, prolonged deprivation of water.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P2C77_ARATH | O047193ujk 3ujl
        PYL2_ARATH | O809923kaz 3kb0 3kb3 3kdh 3kdi 3kl1 3nj0 3nj1 3nmh 3nmp 3nmt 3nr4 3ns2 3ujl 4la7 4lg5 4lga 4lgb 5jnn

(-) Related Entries Specified in the PDB File

3nmh PYRABACTIN BOUND PYL2
3nmn
3nmp PYRABACTIN BOUND PYL2 A93F
3nmt PYRABACTIN BOUND PYL2 A93F IN COMPLEX WITH HAB1