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(-) Description

Title :  SOLUTION STRUCTURE OF PDP1 PWWP DOMAIN REVEALS ITS UNIQUE BINDING SITES FOR METHYLATED H4K20 AND DNA
 
Authors :  Y. Qiu, J. Zhang, W. Zhang
Date :  07 Jan 11  (Deposition) - 21 Dec 11  (Release) - 21 Dec 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Histone Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Qiu, W. Zhang, C. Zhao, Y. Wang, W. Wang, J. Zhang, Z. Zhang, G. Li, Y. Shi, X. Tu, J. Wu
Solution Structure Of Pdp1 Pwwp Domain Reveals Its Unique Binding Sites For Methylated H4K20 And Dna
Biochem. J. 2011
PubMed-ID: 22150589  |  Reference-DOI: 10.1042/BJ20111885

(-) Compounds

Molecule 1 - PWWP DOMAIN-CONTAINING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET22B
    Expression System Vector Type: VECTOR
    Fragment: PWWP DOMAIN, RESIDUES 45-152
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synonym: SET9-ASSOCIATED FACTOR PDP1

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2L89)

(-) Sites  (0, 0)

(no "Site" information available for 2L89)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L89)

(-) 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, 20Phe A:95 -Pro A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L89)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PWWPPS50812 PWWP domain profile.PDP1_SCHPO52-114  1A:52-114
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PWWPPS50812 PWWP domain profile.PDP1_SCHPO52-114  1A:52-114

(-) Exons   (0, 0)

(no "Exon" information available for 2L89)

(-) 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:108
 aligned with PDP1_SCHPO | O59676 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:108
                                    54        64        74        84        94       104       114       124       134       144        
           PDP1_SCHPO    45 SADDRLNFGDRILVKAPGYPWWPALLLRRKETKDSLNTNSSFNVLYKVLFFPDFNFAWVKRNSVKPLLDSEIAKFLGSSKRKSKELIEAYEASKTPPDLKEESSTDEE 152
               SCOP domains d2l89a_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee.....eeeeeeeeeeeee........eeeeeeeee....eeeeehhh.eee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------PWWP  PDB: A:52-114 UniProt: 52-114                            -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2l89 A  45 SADDRLNFGDRILVKAPGYPWWPALLLRRKETKDSLNTNSSFNVLYKVLFFPDFNFAWVKRNSVKPLLDSEIAKFLGSSKRKSKELIEAYEASKTPPDLKEESSTDLE 152
                                    54        64        74        84        94       104       114       124       134       144
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L89)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L89)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (PDP1_SCHPO | O59676)
molecular function
    GO:1990889    H4K20me3 modified histone binding    Interacting selectively and non-covalently with a histone H4 in which the lysine residue at position 20 has been modified by trimethylation.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    GO:0031493    nucleosomal histone binding    Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
    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).
biological process
    GO:0006974    cellular response to DNA damage 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 a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0070510    regulation of histone H4-K20 methylation    Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 20 of histone H4.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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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    Phe A:95 - Pro A:96   [ RasMol ]  
 

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  2l89
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