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(-) Description

Title :  SOLUTION STRUCTURE OF THE DEAD RINGER ARID-DNA COMPLEX
 
Authors :  J. Iwahara, M. Iwahara, G. W. Daughdrill, J. Ford, R. T. Clubb
Date :  07 Jan 02  (Deposition) - 06 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (20x)
Keywords :  Arid, Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Iwahara, M. Iwahara, G. W. Daughdrill, J. Ford, R. T. Clubb
The Structure Of The Dead Ringer-Dna Complex Reveals How At-Rich Interaction Domains (Arids) Recognize Dna.
Embo J. V. 21 1197 2002
PubMed-ID: 11867548  |  Reference-DOI: 10.1093/EMBOJ/21.5.1197
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEAD RINGER PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentA/T RICH INTERACTION DOMAIN
    GeneDRI
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
 
Molecule 2 - 5'- D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 5'- D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'
    ChainsC
    EngineeredYES
    SyntheticYES

 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 1KQQ)

(-) Sites  (0, 0)

(no "Site" information available for 1KQQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARIDPS51011 ARID domain profile.DRI_DROME293-385  1A:22-114

(-) Exons   (0, 0)

(no "Exon" information available for 1KQQ)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:131
 aligned with DRI_DROME | Q24573 from UniProtKB/Swiss-Prot  Length:911

    Alignment length:131
                                   283       293       303       313       323       333       343       353       363       373       383       393       403 
            DRI_DROME   274 GWSFEEQFKQVRQLYEINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAAFTLRTQYMKYLYPYECEKKNLSTPAELQAAIDGNRREG 404
               SCOP domains d1kqqa_ A: DNA-binding domain from the dead ringer protein                                                                          SCOP domains
               CATH domains 1kqqA00 A:3-133  [code=1.10.150.60, no name defined]                                                                                CATH domains
               Pfam domains ----------------ARID-1kqqA01 A:19-110                                                                       ----------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........ee..ee..hhhhhhhhhh...hhhhhhh..hhhhhhh.........hhhhhhhhhhhh.hhhhhhh.....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------ARID  PDB: A:22-114 UniProt: 293-385                                                         ------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kqq A   3 GWSFEEQFKQVRQLYEINDDPKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSSITSAALTLRTQYMKYLYPYECEKKNLSTPAELQAAIDGNRREG 133
                                    12        22        32        42        52        62        72        82        92       102       112       122       132 

Chain B from PDB  Type:DNA  Length:15
                                               
                 1kqq B 401 CCTGTATTGATGTGG 415
                                   410     

Chain C from PDB  Type:DNA  Length:15
                                               
                 1kqq C 416 CCACATCAATACAGG 430
                                   425     

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  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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (DRI_DROME | Q24573)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    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.
    GO:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
biological process
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0009880    embryonic pattern specification    The process that results in the patterns of cell differentiation that will arise in an embryo.
    GO:0042063    gliogenesis    The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia.
    GO:0008049    male courtship behavior    The behavior of a male, for the purpose of attracting a sexual partner. An example of this process is found in Drosophila melanogaster.
    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:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    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:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    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:0045924    regulation of female receptivity    Any process that modulates the frequency, rate or extent of the willingness or readiness of a female to receive male advances.
    GO:0010906    regulation of glucose metabolic process    Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007431    salivary gland development    The process whose specific outcome is the progression of the salivary gland over time, from its formation to the mature structure. Salivary glands include any of the saliva-secreting exocrine glands of the oral cavity.
    GO:0007435    salivary gland morphogenesis    The process in which the anatomical structures of the salivary gland are generated and organized.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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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 Related Entries

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

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        DRI_DROME | Q245731c20

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