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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIZATION DOMAIN OF DOUBLESEX PROTEIN FROM D. MELANOGASTER
 
Authors :  M. A. Weiss, J. R. Bayrer, Z. Wan, B. Li, N. B. Phillips
Date :  01 Jun 05  (Deposition) - 09 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Doublesex, Uba Domain, Dimerization, Sex Determination, Transcription Factor, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Bayrer, W. Zhang, M. A. Weiss
Dimerization Of Doublesex Is Mediated By A Cryptic Ubiquitin-Associated Domain Fold: Implications For Sex-Specific Gene Regulation
J. Biol. Chem. V. 280 32989 2005
PubMed-ID: 16049008  |  Reference-DOI: 10.1074/JBC.M507990200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DOUBLESEX PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DIMERIZATION DOMAIN
    Gene: DSX
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 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 1ZV1)

(-) Sites  (0, 0)

(no "Site" information available for 1ZV1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZV1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZV1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZV1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZV1)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZV1)

(-) 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:59
 aligned with DSX_DROME | P23023 from UniProtKB/Swiss-Prot  Length:549

    Alignment length:123
                                   362       372       382       392       402       412       422       432       442       452       462       472   
            DSX_DROME   353 QDVFLDYCQKLLEKFRYPWELMPLMYVILKDADANIEEASRRIEEARVEINRTVAQIYYNYYTPMALVNGAPMYLTYPSIEQGRYGAHFTHLPLTQICPPTPEPLALSRSPSSPSGPSAVHNQ 475
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh--------------------------------hh----------------------h..----------... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zv1 A   6 QDVFLDYCQKLLEKFRYPWELMPLMYVILKDADANIEEASRRIEEGQYVVN--------------------------------EY----------------------SRQ----------HNL  64
                                    15        25        35        45        55|        -         -         -   ||    -         -       |61         -|  
                                                                             56                               57|                     59 |         62  
                                                                                                               58                       61             


Chain B from PDB  Type:PROTEIN  Length:59
 aligned with DSX_DROME | P23023 from UniProtKB/Swiss-Prot  Length:549

    Alignment length:123
                                   362       372       382       392       402       412       422       432       442       452       462       472   
            DSX_DROME   353 QDVFLDYCQKLLEKFRYPWELMPLMYVILKDADANIEEASRRIEEARVEINRTVAQIYYNYYTPMALVNGAPMYLTYPSIEQGRYGAHFTHLPLTQICPPTPEPLALSRSPSSPSGPSAVHNQ 475
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DSX_dimer-1zv1B01 B:6-50                     ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) DSX_dimer-1zv1B02 B:6-50                     ------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh--------------------------------hh----------------------h..----------... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zv1 B   6 QDVFLDYCQKLLEKFRYPWELMPLMYVILKDADANIEEASRRIEEGQYVVN--------------------------------EY----------------------SRQ----------HNL  64
                                    15        25        35        45        55|        -         -         -   ||    -         -       |61         -|  
                                                                             56                               57|                     59 |         62  
                                                                                                               58                       61
   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 1ZV1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZV1)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DSX_dimer] (3)

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DSX_DROME | P23023)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016199    axon midline choice point recognition    The recognition of molecules at the central nervous system midline choice point by an axon growth cone; this choice point determines whether the growth cone will cross the midline.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0007619    courtship behavior    The behavioral interactions between organisms for the purpose of attracting sexual partners.
    GO:0045497    female analia development    The process whose specific outcome is the progression of the analia of the female over time, from formation to the mature structure. The analia is the posterior-most vertral appendage that develops from the genital disc. An example of this process is found in Drosophila melanogaster.
    GO:0046660    female sex differentiation    The establishment of the sex of a female organism by physical differentiation.
    GO:0019101    female somatic sex determination    The determination of sex and sexual phenotypes in a female organism's soma.
    GO:0035215    genital disc development    Progression of the genital imaginal disc over time, from its initial formation through to its metamorphosis to form the adult terminalia, comprising the entire set of internal and external genitalia and analia. Both sexes of Drosophila have a single genital disc formed from the female and male genital primordia, and the anal primordium. The anal primordium develops in both sexes, forming either male or female analia. However, only one of the genital primordia develops in each sex, forming either the male or the female genitalia.
    GO:0007483    genital disc morphogenesis    The process in which the anatomical structures derived from the genital disc are generated and organized. This includes the transformation of a genital imaginal disc from a monolayered epithelium in the larvae of holometabolous insects into the recognizable adult genital structures, the anal plates and the hind gut.
    GO:0035263    genital disc sexually dimorphic development    The sex-specific patterns of primoridia growth and differentiation in the genital imaginal disc. The anal primordium of the genital disc develops in both sexes, but depending on the genetic sex gives rise to either male or female analia. Depending on the genetic sex, only one of the two genital primordia develop. In females the female genital primordium develops and gives rise to the female genitalia whereas the male primordium is repressed. Conversely, in males the male genital primordium develops and gives rise to the male genitalia whereas the female genital primordium is repressed.
    GO:0007486    imaginal disc-derived female genitalia development    The process whose specific outcome is the progression of the female genitalia over time, from formation as part of the genital disc to the mature structure. An example of this is found in Drosophila melanogaster.
    GO:0007485    imaginal disc-derived male genitalia development    The process whose specific outcome is the progression of the male genitalia over time, from formation as part of the genital disc to the mature structure. An example of this is found in Drosophila melanogaster.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0045496    male analia development    The process whose specific outcome is the progression of the analia of the male over time, from formation to the mature structure. The analia is the posterior-most vertral appendage that develops from the genital disc. An example of this process is found in Drosophila melanogaster.
    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:0045433    male courtship behavior, veined wing generated song production    The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.
    GO:0046661    male sex differentiation    The establishment of the sex of a male organism by physical differentiation.
    GO:0019102    male somatic sex determination    The determination of sex and sexual phenotypes in a male organism's soma.
    GO:0048086    negative regulation of developmental pigmentation    Any process that decreases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0045570    regulation of imaginal disc growth    Any process that modulates the frequency, rate or extent of the growth of the imaginal disc.
    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.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045498    sex comb development    The process whose specific outcome is the progression of the sex comb over time, from its formation to the mature structure. The sex combs are the male specific chaetae located on the prothoracic tarsal segment of the prothoracic leg.
    GO:0007530    sex determination    Any process that establishes and transmits the specification of sexual status of an individual organism.
    GO:0007548    sex differentiation    The establishment of the sex of an organism by physical differentiation.
    GO:0048071    sex-specific pigmentation    Establishment of a pattern of pigment in one sex that is not observed in the other sex.
    GO:0018993    somatic sex determination    The determination of sex and sexual phenotypes in an organism's soma.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    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)

UniProtKB/Swiss-Prot
        DSX_DROME | P23023: 1lpv 2jz0 2jz1

(-) Related Entries Specified in the PDB File

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