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(-) Description

Title :  STRUCTURE OF LIGAND-FREE PYL2
 
Authors :  P. Yin, H. Fan, Q. Hao, X. Yuan, N. Yan
Date :  22 Oct 09  (Deposition) - 10 Nov 09  (Release) - 15 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Pyl2, Hormone Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Yin, H. Fan, Q. Hao, X. Yuan, D. Wu, Y. Pang, C. Yan, W. Li, J. Wang, N. Yan
Structural Insights Into The Mechanism Of Abscisic Acid Signaling By Pyl Proteins
Nat. Struct. Mol. Biol. V. 16 1230 2009
PubMed-ID: 19893533  |  Reference-DOI: 10.1038/NSMB.1730
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN AT2G26040
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PYL2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3KDH)

(-) Sites  (0, 0)

(no "Site" information available for 3KDH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:117 -Glu A:118
2Asn A:135 -Gln A:136
3Gly B:116 -Gly B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KDH)

(-) Exons   (0, 0)

(no "Exon" information available for 3KDH)

(-) Sequences/Alignments

Asymmetric 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:189
 aligned with PYL2_ARATH | O80992 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
           PYL2_ARATH     2 SSSPAVKGLTDEEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHDDE 190
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhhh..hhhhh...eeeeeeee.......eeeeee......eeeeeeeeeee....eeeeee..........eeeeeeeee........eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdh A   2 SSSPAVKGLTDEEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHDDE 190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with PYL2_ARATH | O80992 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:184
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    
           PYL2_ARATH     6 AVKGLTDEEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHDD 189
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhhh..hhhhh...eeeeeeee.......eeeeee......eeeeeeeeeee....eeeeeeee........eeeeeeeeee......eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdh B   6 AVKGLTDEEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHDD 189
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    


Chain C from PDB  Type:PROTEIN  Length:188
 aligned with PYL2_ARATH | O80992 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        
           PYL2_ARATH     2 SSSPAVKGLTDEEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHDD 189
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------Polyketide_cyc2-3kdhC01 C:34-181                                                                                                                    -------- Pfam domains (1)
           Pfam domains (2) --------------------------------Polyketide_cyc2-3kdhC02 C:34-181                                                                                                                    -------- Pfam domains (2)
           Pfam domains (3) --------------------------------Polyketide_cyc2-3kdhC03 C:34-181                                                                                                                    -------- Pfam domains (3)
         Sec.struct. author .........hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhhh..hhhhh...eeeeeeee.......eeeeee......eeeeeeeeeee....eeeeee..........eeeeeeeeee......eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdh C   2 SSSPAVKGLTDEEQKTLEPVIKTYHQFEPDPTTCTSLITQRIHAPASVVWPLIRRFDNPERYKHFVKRCRLISGDGDVGSVREVTVISGLPASTSTERLEFVDDDHRVLSFRVVGGEHRLKNYKSVTSVNEFLNQDSGKVYTVVLESYTVDIPEGNTEEDTKMFVDTVVKLNLQKLGVAATSAPMHDD 189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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 3KDH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Bet_V_1_like (93)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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.

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  Sites
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  Cis Peptide Bonds
    Asn A:135 - Gln A:136   [ RasMol ]  
    Gly A:117 - Glu A:118   [ RasMol ]  
    Gly B:116 - Gly B:117   [ RasMol ]  
 
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  3kdh
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  PYL2_ARATH | O80992
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYL2_ARATH | O80992: 3kaz 3kb0 3kb3 3kdi 3kl1 3nj0 3nj1 3nmh 3nmp 3nmt 3nmv 3nr4 3ns2 3ujl 4la7 4lg5 4lga 4lgb 5jnn

(-) Related Entries Specified in the PDB File

3kdi (+)-ABA BOUND PYL2
3kdj (+)-ABA-BOUND PYL1 AND ABI1