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(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN ING1-LIKE PROTEIN BAC25079
 
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, Ing1-Like Protein, 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 Ing1-Like Protein Bac25079
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INHIBITOR OF GROWTH FAMILY, MEMBER 4
    ChainsA
    EngineeredYES
    Expression System PlasmidP030408-71
    Expression System Vector TypePLASMID
    FragmentPHD DOMAIN
    GeneRIKEN CDNA 1110062A16
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymING1-LIKE PROTEIN BAC25079

 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:32 , CYS A:37 , CYS A:59 , CYS A:62BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WEN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.ING4_MOUSE196-245  1A:16-65
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.ING4_MOUSE199-242  1A:19-62

(-) Exons   (0, 0)

(no "Exon" information available for 1WEN)

(-) 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:71
 aligned with ING4_MOUSE | Q8C0D7 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:130
                                                                                                                                                         249  
                                   131       141       151       161       171       181       191       201       211       221       231       241       | -
           ING4_MOUSE   122 DSSSSKGKKKGRTQKEKKAARARSKGKNSDEEAPKAAQKKLKLVRTSPEYGMPSVTFGSVHPSDVLDMPVDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQERKKK--   -
               SCOP domains d1wena_                                                            A: Inhibitor of growth protein 4, Ing4                          SCOP domains
               CATH domains 1wenA00                                                            A:1-71 Zinc/RING finger domain, C3HC4 (zinc finger)             CATH domains
               Pfam domains ----------------------------------------------------------------------------PHD-1wenA01 A:18-64                            ------- Pfam domains
         Sec.struct. author .......-----------------------------------------------------------.....................ee...........eehhhh............hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------ZF_PHD_2  PDB: A:16-65 UniProt: 196-245           ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------ZF_PHD_1  PDB: A:19-62 UniProt: 199-242     --------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wen A   1 GSSGSSG-----------------------------------------------------------DMPVDPNEPTYCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQESGPSSG  71
                                  |  -         -         -         -         -         -      | 11        21        31        41        51        61        71
                                  7                                                           8                                                               

   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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (ING4_MOUSE | Q8C0D7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006978    DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, resulting in the induction of the transcription of p21 (also known as WAF1, CIP1 and SDI1) or any equivalent protein, in response to the detection of DNA damage.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0043983    histone H4-K12 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone.
    GO:0043984    histone H4-K16 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
    GO:0043981    histone H4-K5 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 5 of the histone.
    GO:0043982    histone H4-K8 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 8 of the histone.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045926    negative regulation of growth    Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0006473    protein acetylation    The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
cellular component
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    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

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        ING4_MOUSE | Q8C0D71weu

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