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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND TUDOR DOMAIN OF HUMAN PHF20 (HOMODIMER FORM)
 
Authors :  G. Cui, J. Lee, J. R. Thompson, M. V. Botuyan, G. Mer
Date :  13 Oct 10  (Deposition) - 22 Jun 11  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tudor Domain, Lysine-Methylated P53 Binding, Histone Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Cui, S. Park, A. I. Badeaux, D. Kim, J. Lee, J. R. Thompson, F. Yan, S. Kaneko, Z. Yuan, M. V. Botuyan, M. T. Bedford, J. Q. Cheng, G. Mer
Phf20 Is An Effector Protein Of P53 Double Lysine Methylation That Stabilizes And Activates P53.
Nat. Struct. Mol. Biol. V. 19 916 2012
PubMed-ID: 22864287  |  Reference-DOI: 10.1038/NSMB.2353

(-) Compounds

Molecule 1 - MEDULLOBLASTOMA ANTIGEN MU-MB-50.72
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTEV
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 84-147
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHD FINGER PROTEIN 20

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3P8D)

(-) Sites  (0, 0)

(no "Site" information available for 3P8D)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:96 -B:100
2A:100 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P8D)

(-) Exons   (0, 0)

(no "Exon" information available for 3P8D)

(-) 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:53
 aligned with PHF20_HUMAN | Q9BVI0 from UniProtKB/Swiss-Prot  Length:1012

    Alignment length:53
                                    94       104       114       124       134   
          PHF20_HUMAN    85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeee....eeeeee....eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3p8d A  85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
                                    94       104       114       124       134   

Chain A from PDB  Type:PROTEIN  Length:53
 aligned with Q7Z5E2_HUMAN | Q7Z5E2 from UniProtKB/TrEMBL  Length:550

    Alignment length:53
                                    94       104       114       124       134   
         Q7Z5E2_HUMAN    85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeee....eeeeee....eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3p8d A  85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
                                    94       104       114       124       134   

Chain B from PDB  Type:PROTEIN  Length:53
 aligned with PHF20_HUMAN | Q9BVI0 from UniProtKB/Swiss-Prot  Length:1012

    Alignment length:53
                                    94       104       114       124       134   
          PHF20_HUMAN    85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeee....eeeeee....eeeee...ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3p8d B  85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
                                    94       104       114       124       134   

Chain B from PDB  Type:PROTEIN  Length:53
 aligned with Q7Z5E2_HUMAN | Q7Z5E2 from UniProtKB/TrEMBL  Length:550

    Alignment length:53
                                    94       104       114       124       134   
         Q7Z5E2_HUMAN    85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeee....eeeeee....eeeee...ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3p8d B  85 SEFQINEQVLACWSDCRFYPAKVTAVNKDGTYTVKFYDGVVQTVKHIHVKAFS 137
                                    94       104       114       124       134   

   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 3P8D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P8D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P8D)

(-) Gene Ontology  (20, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PHF20_HUMAN | Q9BVI0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046972    histone acetyltransferase activity (H4-K16 specific)    Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 16) = CoA + histone H4 N6-acetyl-L-lysine (position 16). This reaction represents the addition of an acetyl group to the lysine at position 16 of histone H4.
    GO:0043995    histone acetyltransferase activity (H4-K5 specific)    Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 5) = CoA + histone H4 N6-acetyl-L-lysine (position 5).
    GO:0043996    histone acetyltransferase activity (H4-K8 specific)    Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 8) = CoA + histone H4 N6-acetyl-L-lysine (position 8).
    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: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:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0071339    MLL1 complex    A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

Chain A,B   (Q7Z5E2_HUMAN | Q7Z5E2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHF20_HUMAN | Q9BVI02ldm 3q1j 3qii 3sd4 5tab 5tbn

(-) Related Entries Specified in the PDB File

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