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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PYR1 ABSCISIC ACID RECEPTOR IN COMPLEX WITH THE HAB1 TYPE 2C PHOSPHATASE CATALYTIC DOMAIN
 
Authors :  K. Betz, F. Dupeux, J. Santiago, J. A. Marquez
Date :  07 Feb 11  (Deposition) - 16 Mar 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Start Domain, Bet V Domain, Pyr/Pyl/Rcar, Pp2C, Abscisic Acid Hormone Receptor, Type 2C Protein Phosphatase, Plant Stress Response, Abiotic Stress, Abscisic Acid Binding, Type 2C Protein Phosphatase Binding, Intracellular, Nucleus, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Dupeux, R. Antoni, K. Betz, J. Santiago, M. Gonzalez-Guzman, L. Rodriguez, S. Rubio, S. Y. Park, S. R. Cutler, P. L. Rodriguez, J. A. Marquez
Modulation Of Abscisic Acid Signaling In Vivo By An Engineered Receptor-Insensitive Protein Phosphatase Type 2C Allele.
Plant Physiol. V. 156 106 2011
PubMed-ID: 21357183  |  Reference-DOI: 10.1104/PP.110.170894

(-) Compounds

Molecule 1 - ABSCISIC ACID RECEPTOR PYR1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneABIP6, AT4G17870, PYR1, RCAR11, T6K21.50
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymABI1-BINDING PROTEIN 6, PROTEIN PYRABACTIN RESISTANCE 1, REGULATORY COMPONENTS OF ABA RECEPTOR 11
 
Molecule 2 - PROTEIN PHOSPHATASE 2C 16
    ChainsB
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAT1G72770, F28P22.4, HAB1, P2C-HA
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymATPP2C16, ATP2C-HA, PROTEIN HYPERSENSITIVE TO ABA 1, PROTEIN PHOSPHATASE 2C HAB1, PP2C HAB1

 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
1A8S1Ligand/Ion(2Z,4E)-5-[(1S)-1-HYDROXY-2,6,6-TRIMETHYL-4-OXOCYCLOHEX-2-EN-1-YL]-3-METHYLPENTA-2,4-DIENOIC ACID
2MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:59 , PHE A:61 , VAL A:83 , ALA A:89 , PHE A:108 , ILE A:110 , TYR A:120 , PHE A:159 , VAL A:163 , HOH A:197 , HOH A:205 , HOH A:234 , HOH A:266 , HOH A:293BINDING SITE FOR RESIDUE A8S A 192
2AC2SOFTWAREHOH B:16 , HOH B:24 , ASP B:243 , ASP B:432 , ASP B:492 , HOH B:669BINDING SITE FOR RESIDUE MN B 1
3AC3SOFTWAREHOH B:11 , HOH B:33 , HOH B:125 , ASP B:243 , GLY B:244 , HOH B:669BINDING SITE FOR RESIDUE MN B 2
4AC4SOFTWAREHOH B:89 , ASP B:346 , LYS B:365 , ASP B:432 , HOH B:575 , HOH B:647BINDING SITE FOR RESIDUE MN B 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QN1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys B:406 -Pro B:407

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QN1)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PPM_2PS51746 PPM-type phosphatase domain profile.P2C16_ARATH189-501  1B:189-501
2PPM_1PS01032 PPM-type phosphatase domain signature.P2C16_ARATH238-246  1B:238-246

(-) Exons   (0, 0)

(no "Exon" information available for 3QN1)

(-) 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:179
 aligned with PYR1_ARATH | O49686 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           PYR1_ARATH     1 MPSELTPEERSELKNSIAEFHTYQLDPGSCSSLHAQRIHAPPELVWSIVRRFDKPQTYKHFIKSCSVEQNFEMRVGCTRDVIVISGLPANTSTERLDILDDERRVTGFSIIGGEHRLTNYKSVTTVHRFEKENRIWTVVLESYVVDMPEGNSEDDTRMFADTVVKLNLQKLATVAEAMARN 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------Polyketide_cyc-3qn1A01 A:38-172                                                                                                        --------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhh...hhhhh...eeeee..--.......eeeeee.......eeeeeeeeee....eeeeeeee........eeeeeeeeeee..eeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qn1 A   1 MASELTPEERSELKNSIAEFHTYQLDPGSCSSLHAQRIHAPPELVWSIVRRFDKPQTYKHFIKSCSVE--FEMRVGCTRDVIVISGLPANTSTERLDILDDERRVTGFSIIGGEHRLTNYKSVTTVHRFEKENRIWTVVLESYVVDMPEGNSEDDTRMFADTVVKLNLQKLATVAEAMARN 181
                                    10        20        30        40        50        60       | -|       80        90       100       110       120       130       140       150       160       170       180 
                                                                                              68 71                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with P2C16_ARATH | Q9CAJ0 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:321
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504 
          P2C16_ARATH   185 DCIPLWGTVSIQGNRSEMEDAFAVSPHFLKLPIKMLMGDHEGMSPSLTHLTGHFFGVYDGHGGHKVADYCRDRLHFALAEEIERIKDELCKRNTGEGRQVQWDKVFTSCFLTVDGEIEGKIGRAVVGSSDKVLEAVASETVGSTAVVALVCSSHIVVSNCGDSRAVLFRGKEAMPLSVDHKPDREDEYARIENAGGKVIQWQGARVFGVLAMSRSIGDRYLKPYVIPEPEVTFMPRSREDECLILASDGLWDVMNNQEVCEIARRRILMWHKKNGAPPLAERGKGIDPACQAAADYLSMLALQKGSKDNISIIVIDLKAQR 505
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----PP2C-3qn1B01 B:190-494                                                                                                                                                                                                                                                                                           ----------- Pfam domains
         Sec.struct. author .....eeeeee........eeeeeeeeeeeee.hhh.----------.eeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.------------hhhhhhhhhhhhhhhhhhhhh......................ee.eeeeee...eeeeeee...eeeeee..eeee........hhhhhhhhhhh...eee...eee.........ee.hhhh.......eeeeee....eeeeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh..----.....hhhhhhhhhhhhhhhhhh.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PPM_2  PDB: B:189-501 UniProt: 189-501                                                                                                                                                                                                                                                                                   ---- PROSITE (1)
                PROSITE (2) -----------------------------------------------------PPM_1    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qn1 B 185 DCIPLWGTVSIQGNRSEMEDAFAVSPHFLKLPIKMLM----------THLTGHFFGVYDGHGGHKVADYCRDRLHFALAEEIERIK------------QVQWDKVFTSCFLTVDGEIEGKIGRAVVGSSDKVLEAVASETVGSTAVVALVCSSHIVVSNCGDSRAVLFRGKEAMPLSVDHKPDREDEYARIENAGGKVIQWQGARVFGVLAMSRSIGDRYLKPYVIPEPEVTFMPRSREDECLILASDGLWDVMNNQEVCEIARRRILMWHKKNGAP----RGKGIDPACQAAADYLSMLALQKGSKDNISIIVIDLKAQR 505
                                   194       204       214      |  -       234       244       254       264     |   -       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454      |  - |     474       484       494       504 
                                                              221        232                                   270          283                                                                                                                                                                               461  466                                       

   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 3QN1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QN1)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (20, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYR1_ARATH | O49686)
molecular function
    GO:0010427    abscisic acid binding    Interacting selectively and non-covalently with abscisic acid, plant hormones that regulate aspects of plant growth.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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   (P2C16_ARATH | Q9CAJ0)
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:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P2C16_ARATH | Q9CAJ03kb3 3nmt 3rt0 3ujg 3zvu 4ds8 4la7 4lg5 4lga 4lgb 4wvo 5jo1 5jo2
        PYR1_ARATH | O496863k3k 3k90 3njo 3wg8 3zvu 4wvo

(-) Related Entries Specified in the PDB File

3k3k CRYSTAL STRUCTURE OF THE DIMERIC ABSCISIC ACID RECEPTOR PYR1
3k90 CRYSTAL STRUCTURE OF THE DIMERIC ABSCISIC ACID RECEPTOR PYR1
3njo CRYSTAL STRUCTURE OF PYR1 IN COMPLEX WITH PYRABACTIN
3nmt CRYSTAL STRUCTURE OF THE HAB1 PHOSPHATASE CATALYTIC DOMAIN IN COMPLEX WITH THE ABSICSIC ACID RECEPTOR PYL2