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(-) Description

Title :  SOLUTION STRUCTURE OF THE BROMODOMAIN OF PEREGRIN
 
Authors :  R. Hatta, F. Hayashi, K. Izumi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Dec 05  (Deposition) - 09 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Four-Helix Bundle, Transcription Activator, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hatta, F. Hayashi, K. Izumi, M. Yoshida, S. Yokoyama
Solution Structure Of The Bromodomain Of Peregrin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEREGRIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: P050314-10
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN
    Gene: BRPF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1, BR140 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2D9E)

(-) Sites  (0, 0)

(no "Site" information available for 2D9E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D9E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D9E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D9E)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.BRPF1_HUMAN645-715  1A:20-90
2BROMODOMAIN_1PS00633 Bromodomain signature.BRPF1_HUMAN650-707  1A:25-82

(-) Exons   (0, 0)

(no "Exon" information available for 2D9E)

(-) 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:121
 aligned with BRPF1_HUMAN | P55201 from UniProtKB/Swiss-Prot  Length:1214

    Alignment length:270
                                   583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843
          BRPF1_HUMAN   574 GRDSEDKNWALKEQLKSWQRLRHDLERARLLVELIRKREKLKRETIKVQQIAMEMQLTPFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMGIDFETGMHIPHSLAGDEATHHTEDAAEEERLVLLENQKHLPVEEQLKLLLERLDEVNASKQSVGRSRRAKMIKKEMTALRRKLAHQRETGRDGPERHGPSSRG 843
               SCOP domains d2d9e                                                    a_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....----------------------------------------------------hhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..------------------------------------------------------------------------------------------------....-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------BROMODOMAIN_2  PDB: A:20-90 UniProt: 645-715                           -------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------BROMODOMAIN_1  PDB: A:25-82 UniProt: 650-707              ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2d9e A   1 GSSGS----------------------------------------------------SGFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMGS------------------------------------------------------------------------------------------------GPSS-G 121
                                |    -         -         -         -         -       | 8        18        28        38        48        58        68        78        88        98       108       | -         -         -         -         -         -         -         -         -         -    |  121
                                5                                                    6                                                                                                           116                                                                                              117  | |
                                                                                                                                                                                                                                                                                                     120 |
                                                                                                                                                                                                                                                                                                       121
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D9E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D9E)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (BRPF1_HUMAN | P55201)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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:0070776    MOZ/MORF histone acetyltransferase complex    A histone acetyltransferase complex that has histone H3 acetyltransferase and coactivator activities. Subunits of the human complex include MYST3/MOZ, MYST4/MORF, ING5, EAF6 and one of BRPF1, BRD1/BRPF2 and BRPF3.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRPF1_HUMAN | P55201: 2rs9 2x35 2x4w 2x4x 2x4y 3l42 3mo8 4lc2 4qyd 4qyl 4uye 5c6s 5c7n 5c85 5c87 5c89 5d7x 5dy7 5dya 5dyc 5e3d 5e3g 5em3 5epr 5eps 5eq1 5erc 5etb 5etd 5ev9 5eva 5ewc 5ewd 5ewh 5ewv 5eww 5ffv 5ffw 5ffy 5fg4 5fg5 5g4r 5g4s 5t4u 5t4v

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