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(-) Description

Title :  SOLUTION STRUCTURE OF THE BRINKER DNA BINDING DOMAIN IN COMPLEX WITH THE OMB ENHANCER
 
Authors :  F. Cordier, B. Hartmann, M. Rogowski, M. Affolter, S. Grzesiek
Date :  05 Apr 06  (Deposition) - 29 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (20x)
Keywords :  Protein-Dna Complex, Helix-Turn-Helix Motif, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Cordier, B. Hartmann, M. Rogowski, M. Affolter, S. Grzesiek
Dna Recognition By The Brinker Repressor - An Extreme Case Of Coupling Between Binding And Folding
J. Mol. Biol. V. 361 659 2006
PubMed-ID: 16876822  |  Reference-DOI: 10.1016/J.JMB.2006.06.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BRINKER CG9653-PA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-22B(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentBRINKER DNA BINDING DOMAIN (RESIDUES 43-101)
    GeneBRINKER
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymBRINKER NUCLEAR REPRESSOR
 
Molecule 2 - 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3'
    ChainsB
    EngineeredYES
    SynonymDNA OPTOMOTOR BLIND (OMB) ENHANCER
    SyntheticYES
 
Molecule 3 - 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3'
    ChainsC
    EngineeredYES
    SynonymDNA OPTOMOTOR BLIND (OMB) ENHANCER
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:59
 aligned with Q9XTN4_DROME | Q9XTN4 from UniProtKB/TrEMBL  Length:704

    Alignment length:59
                                    52        62        72        82        92         
         Q9XTN4_DROME    43 GSRRIFTPHFKLQVLESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCESNLRSSVANN 101
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 2glo A  43 GSRRIFTPHFKLQVLESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCESNLRSSVANN 101
                                    52        62        72        82        92         

Chain B from PDB  Type:DNA  Length:12
                                            
                 2glo B   1 TGAGGCGTCAAC  12
                                    10  

Chain C from PDB  Type:DNA  Length:12
                                            
                 2glo C  13 GTTGACGCCTCA  24
                                    22  

   Legend:   → Mismatch (orange background)
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    → 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)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (Q9XTN4_DROME | Q9XTN4)
molecular function
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0001158    enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0035212    cell competition in a multicellular organism    Competitive interactions within multicellular organisms between cell populations that differ in growth rates, leading to the elimination of the slowest-growing cells.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0061328    posterior Malpighian tubule development    The process whose specific outcome is the progression of the posterior Malpighian tubule over time, from its formation to the mature structure. The pair of posterior tubules arise from a ventrolateral region of the embryonic hindgut and project backwards through the body cavity. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which connects with the posterior part of the gut.
    GO:0030510    regulation of BMP signaling pathway    Any process that modulates the frequency, rate or extent of the activity of any BMP receptor signaling pathway.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0007432    salivary gland boundary specification    Determination of where the salivary gland forms, the total number of salivary gland cells and how many cells are allocated to each of the specialised cell types within the salivary gland.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007472    wing disc morphogenesis    The process in which the anatomical structures derived from the wing disc are generated and organized. This includes the transformation of a wing imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into recognizable adult structures including the wing hinge, wing blade and pleura.
cellular component
    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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