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(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN DNA-BINDING FAMILY PROTEIN AAM98074
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 May 04  (Deposition) - 25 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Phd Domain, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Phd Domain In Dna-Binding Family Protein Aam98074
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-BINDING FAMILY PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP030408-04
    Expression System Vector TypePLASMID
    FragmentPHD DOMAIN
    GeneRAFL09-09-B06
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsCELL FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:19 , CYS A:21 , HIS A:43 , CYS A:46BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:33 , CYS A:38 , CYS A:66 , CYS A:69BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WEW)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asn A:57 -Pro A:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WEW)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_1PS01359 Zinc finger PHD-type signature.SIZ1_ARATH115-165  1A:19-69

(-) Exons   (0, 0)

(no "Exon" information available for 1WEW)

(-) Sequences/Alignments

NMR Structure
   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:78
 aligned with SIZ1_ARATH | Q680Q4 from UniProtKB/Swiss-Prot  Length:884

    Alignment length:108
                                    97       107       117       127       137       147       157       167       177       187        
           SIZ1_ARATH    88 GQVSSDTSNLKVKGEPEDPFQPEIKVRCVCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTRADPFWVTVAHPLSPVRLTATTIPNDG 195
               SCOP domains d  1wewa     _   A: Sumoylation ligase E3, SIZ1                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .--.....-----.--......................eee........eeehhhh...................hhhh....---------------------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------ZF_PHD_1  PDB: A:19-69 UniProt: 115-165            ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1wew A   1 G--SSGSS-----G--EDPFQPEIKVRCVCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG---------------------PSSG  78
                            |  |   | -   |  | 11        21        31        41        51        61        71  |      -         -    |   
                            |  2   6     7  8                                                                74                    75   
                            1                                                                                                           

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WEW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WEW)

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (SIZ1_ARATH | Q680Q4)
molecular function
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0031668    cellular response to extracellular stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus.
    GO:0016036    cellular response to phosphate starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0010247    detection of phosphate ion    The series of events in which a phosphate ion stimulus is received by a cell and converted into a molecular signal.
    GO:0048589    developmental growth    The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
    GO:0009553    embryo sac development    The process whose specific outcome is the progression of the embryo sac over time, from its formation to the mature structure. The process begins with the meiosis of the megasporocyte to form four haploid megaspores. Three of the megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center. The two polar nuclei fuse resulting in a mononucleate diploid endosperm mother cell. The three antipodal cells degenerate.
    GO:0009908    flower development    The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.
    GO:0010286    heat acclimation    Any process that increases heat tolerance of an organism in response to high temperatures.
    GO:0009864    induced systemic resistance, jasmonic acid mediated signaling pathway    The series of molecular signals mediated by jasmonic acid involved in induced systemic resistance.
    GO:0009910    negative regulation of flower development    Any process that stops, prevents, or reduces the frequency, rate or extent of flower development.
    GO:0010113    negative regulation of systemic acquired resistance    Any process that stops, prevents, or reduces the frequency, rate or extent of systemic acquired resistance.
    GO:0048481    plant ovule development    The process whose specific outcome is the progression of the ovule over time, from its formation to the mature structure. The ovule is the structure in seed plants enclosing the female gametophyte, and is composed of the nucellus, one or two integuments, and the funiculus; it develops into the seed.
    GO:0010183    pollen tube guidance    The process in which the growth of pollen tube is directed towards the female gametophyte.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target 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:0040008    regulation of growth    Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
    GO:0090352    regulation of nitrate assimilation    Any process that modulates the rate, frequency, or extent of the uptake, from the environment, of nitrates, inorganic or organic salts and esters of nitric acid and the subsequent reduction of nitrate ion to other, less highly oxidized, inorganic nitrogenous substances.
    GO:2000070    regulation of response to water deprivation    Any process that modulates the frequency, rate or extent of response to water deprivation.
    GO:0010337    regulation of salicylic acid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving salicylic acid.
    GO:0050826    response to freezing    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 freezing stimulus, temperatures below 0 degrees Celsius.
    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.
cellular component
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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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