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(-) Description

Title :  HOMEOBOX PROTEIN VND (VENTRAL NERVOUS SYSTEM DEFECTIVE PROTEIN)
 
Authors :  B. Xiang
Date :  16 Jun 99  (Deposition) - 06 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Helix-Turn-Helix, Dna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. J. Hwang, B. Xiang, J. M. Gruschus, K. Y. Nam, K. T. No, M. Nirenberg, J. A. Ferretti
Distortion Of The Three-Dimensional Structure Of The Vnd/Nk-2 Homeodomain Bound To Dna Induced By An Embryonically Lethal A35T Point Mutation.
Biochemistry V. 42 12522 2003
PubMed-ID: 14580198  |  Reference-DOI: 10.1021/BI030116I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (HOMEOBOX VENTRAL NERVOUS SYSTEM DEFECTIVE PROTEIN)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentVND/NK2 HOMEODOMAIN
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 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 1QRY)

(-) Sites  (0, 0)

(no "Site" information available for 1QRY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.VND_DROME543-603  1A:10-70
2HOMEOBOX_1PS00027 'Homeobox' domain signature.VND_DROME578-601  1A:45-68

(-) Exons   (0, 0)

(no "Exon" information available for 1QRY)

(-) 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:80
 aligned with VND_DROME | P22808 from UniProtKB/Swiss-Prot  Length:723

    Alignment length:85
                                   538       548       558       568       578       588       598       608     
            VND_DROME   529 GSGGGDANGSDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP 613
               SCOP domains d1     qrya_ A: VND/NK-2 protein                                                      SCOP domains
               CATH domains 1q     ryA00 A:1-80 Homeodomain-like                                                  CATH domains
               Pfam domains -----------------Homeobox-1qryA01 A:13-69                                 ----------- Pfam domains
         Sec.struct. author ..-----.................hhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------HOMEOBOX_2  PDB: A:10-70 UniProt: 543-603                    ---------- PROSITE (1)
                PROSITE (2) -------------------------------------------------HOMEOBOX_1  PDB: A:45-68------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1qry A   1 GS-----HMSDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEGHP  80
                             |     | 5        15        25        35        45        55        65        75     
                             2     3                                                                             

   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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (VND_DROME | P22808)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    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:0009953    dorsal/ventral pattern formation    The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0007398    ectoderm development    The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.
    GO:0021782    glial cell development    The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    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: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: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:0014019    neuroblast development    The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron.
    GO:0007400    neuroblast fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus.
    GO:0007389    pattern specification process    Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
    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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0007419    ventral cord development    The process whose specific outcome is the progression of the ventral cord over time, from its formation to the mature structure. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms.
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
        VND_DROME | P228081nk2 1nk3 1vnd

(-) Related Entries Specified in the PDB File

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