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(-) Description

Title :  HIGH-RESOLUTION PYRABACTIN-BOUND PYL1 STRUCTURE
 
Authors :  N. Yan
Date :  08 Jun 10  (Deposition) - 16 Jun 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pyl1, Pyrabactin, Hormone Receptor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Hao, P. Yin, C. Yan, X. Yuan, W. Li, Z. Zhang, L. Liu, J. Wang, N. Yan
Functional Mechanism Of The Aba Agonist Pyrabactin
J. Biol. Chem. V. 285 28946 2010
PubMed-ID: 20554531  |  Reference-DOI: 10.1074/JBC.M110.149005

(-) Compounds

Molecule 1 - ABSCISIC ACID RECEPTOR PYL1
    Chains: A, B
    EC Number: 3.1.3.16
    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
    Fragment: UNP RESIDUES 20-221
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PYL1, PYR1-LIKE PROTEIN 1, ABI1-BINDING PROTEIN 6, REGULATORY COMPONENTS OF ABA RECEPTOR 9

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PYV1Ligand/Ion4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PYV1Ligand/Ion4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PYV-1Ligand/Ion4-BROMO-N-(PYRIDIN-2-YLMETHYL)NAPHTHALENE-1-SULFONAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:68 , VAL A:87 , ALA A:95 , SER A:98 , GLU A:100 , HIS A:121 , LEU A:123 , TYR A:126 , VAL A:172 , HOH A:206 , HOH A:235BINDING SITE FOR RESIDUE PYV A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:117 -Gly A:118
2Asp B:10 -Leu B:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NEF)

(-) 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:182
 aligned with PYL1_ARATH | Q8VZS8 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:187
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       
           PYL1_ARATH    24 HHQTMPSDLTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFEKEEEEERIWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMNR 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhh...hhhhh...eeeee...........eeeeee.......eeeeeeeeee....eeeeee..........eeeeeeeee..-----..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nef A   3 HHQTMPSDLTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFEK-----RIWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMNR 189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    |    -|      152       162       172       182       
                                                                                                                                                                137   143                                              


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with PYL1_ARATH | Q8VZS8 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:183
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
           PYL1_ARATH    30 SDLTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFEKEEEEERIWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMNRNN 212
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------Polyketide_cyc2-3nefB01 B:36-185                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) ---------------------------Polyketide_cyc2-3nefB02 B:36-185                                                                                                                      ------ Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......eeeeeeeeee..hhhhhhhhhh...hhhhh...eeeee...........eeeeee.......eeeeeeeeee....eeeeeeee........eeeeeeeee..------.eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nef B   9 SDLTQDEFTQLSQSIAEFHTYQLGNGRCSSLLAQRIHAPPETVWSVVRRFDRPQIYKHFIKSCNVSEDFEMRVGCTRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVTTVHRFEK------IWTVVLESYVVDVPEGNSEEDTRLFADTVIRLNLQKLASITEAMNRNN 191
                                    18        28        38        48        58        68        78        88        98       108       118       128        |-     | 148       158       168       178       188   
                                                                                                                                                          137    144
   Legend:   → Mismatch (orange background)
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  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 3NEF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Bet_V_1_like (93)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,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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 Related Entries

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

UniProtKB/Swiss-Prot
        PYL1_ARATH | Q8VZS8: 3jrq 3jrs 3kay 3kdj 3neg 3nmn

(-) Related Entries Specified in the PDB File

3kdh APO-PYL2
3kdi (+)-ABA BOUND PYL2
3kdj (+)-ABA-BOUND PYL1 AND ABI1
3neg PYRABACTIN-BOUND PYL1 AT 2.8A