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(-) Description

Title :  POLYHOMEOTIC SAM DOMAIN STRUCTURE
 
Authors :  C. A. Kim, M. Gingery, R. M Pilpa, J. U. Bowie
Date :  28 Jan 02  (Deposition) - 05 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Sam Domain, Polycomb Group, Polymer, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Kim, M. Gingery, R. M. Pilpa, J. U. Bowie
The Sam Domain Of Polyhomeotic Forms A Helical Polymer.
Nat. Struct. Biol. V. 9 453 2002
PubMed-ID: 11992127
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYHOMEOTIC
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSAM DOMAIN
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1KW4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KW4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KW4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KW4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.PHP_DROME1513-1577  1A:17-79

(-) Exons   (0, 0)

(no "Exon" information available for 1KW4)

(-) 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:70
 aligned with PHP_DROME | P39769 from UniProtKB/Swiss-Prot  Length:1589

    Alignment length:70
                                  1515      1525      1535      1545      1555      1565      1575
           PHP_DROME   1506 DRPPISSWSVDDVSNFIRELPGCQDYVDDFIQQEIDGQALLLLKEKHLVNAMGMKLGPALKIVAKVESIK 1575
               SCOP domains d1kw4a_ A: Polyhomeotic                                                SCOP domains
               CATH domains 1kw4A00 A:10-79 Transcription Factor, Ets-1                            CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SAM_DOMAIN  PDB: A:17-79 UniProt: 1513-1577                     PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                1kw4 A   10 DRPPISSWSVDDVSNFIRELPGCQDYVDDFIQQEIDGQALLRLKEKHLVNAmGmKLGPALKIVAKVESIK   79
                                    19        29        39        49        59 | |    69        79
                                                                              61-MSE              
                                                                                63-MSE            

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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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KW4)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHP_DROME | P39769)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0044547    DNA topoisomerase binding    Interacting selectively and non-covalently with a DNA topoisomerase.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    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:0021954    central nervous system neuron development    The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
    GO:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0016458    gene silencing    Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.
    GO:0030708    germarium-derived female germ-line cyst encapsulation    Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the germarium. An example of this process is found in Drosophila melanogaster.
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0030713    ovarian follicle cell stalk formation    Development of ovarian follicle cells to create the interfollicular stalks that connect the egg chambers of progressive developmental stages. An example of this process is found in Drosophila melanogaster.
    GO:0035075    response to ecdysone    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 ecdysone stimulus.
    GO:0035186    syncytial blastoderm mitotic cell cycle    Mitotic division cycles 10 to 13 of the insect embryo. This is the second phase of the syncytial period where nuclei divide in a common cytoplasm without cytokinesis. The majority of migrating nuclei reach the embryo surface during cycle 10, after which they divide less synchronously than before, and the syncytial blastoderm cycles lengthen progressively.
cellular component
    GO:0035102    PRC1 complex    A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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
        PHP_DROME | P397691pk1

(-) Related Entries Specified in the PDB File

1ji7 ETS-RELATED PROTEIN TEL1