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(-) Description

Title :  SOLUTION STRUCTURE OF THE THIRD HELIX OF ANTENNAPEDIA HOMEODOMAIN DERIVATIVE [W6F,W14F]
 
Authors :  A. Czajlik, E. Mesko, B. Penke, A. Perczel
Date :  06 Feb 02  (Deposition) - 20 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (39x)
Keywords :  Irregular Helix, Turn-Like Parts, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Czajlik, E. Mesko, B. Penke, A. Perczel
Investigation Of Penetratin Peptides. Part 1. The Environment Dependent Conformational Properties Of Penetratin And Two Of Its Derivatives.
J. Pept. Sci. V. 8 151 2002
PubMed-ID: 11991205  |  Reference-DOI: 10.1002/PSC.380
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTENNAPEDIA PROTEIN
    ChainsA
    EngineeredYES
    MutationYES
    Other DetailsTHIS SEQUENCE WAS SYNTHETIZED IN SOLID- PHASE USING THE BOC-CHEMISTRY. THE SEQUENCE OF THIS PEPTIDE IS BASED ON A SEQUENCE NATURALLY FOUND IN DROSOPHILA MELANOGASTER (FRUIT FLY).
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (39x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1KZ2)

(-) Sites  (0, 0)

(no "Site" information available for 1KZ2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KZ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KZ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 1KZ2)

(-) 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:16
 aligned with ZEN1_DROME | P09089 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:16
                                   141      
           ZEN1_DROME   132 RQVKIWFQNRRMKFKK 147
               SCOP domains d1kz2a_ A:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains Homeobox-1kz2A01 Pfam domains
         Sec.struct. author .hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1kz2 A   1 RQIKIFFQNRRMKFKK  16
                                    10      

   Legend:   → Mismatch (orange background)
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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
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1KZ2)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (ZEN1_DROME | P09089)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
biological process
    GO:0007378    amnioserosa formation    Formation of the amnioserosa, an epithelium that occupies a hole in the embryonic dorsal epidermis. This occurs by the transformation of a narrow strip of cells at the dorsal midline of the blastoderm from columnar to squamous cells, accompanied by a lateral shift.
    GO:0048749    compound eye development    The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye.
    GO:0009950    dorsal/ventral axis specification    The establishment, maintenance and elaboration of the dorsal/ventral axis. 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:0007450    dorsal/ventral pattern formation, imaginal disc    The establishment, maintenance and elaboration of the dorsal/ventral axis of the imaginal disc. Imaginal disks are masses of hypodermic cells, carried by the larvae of some insects after leaving the egg, from which masses the wings and legs of the adult are subsequently formed.
    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: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: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: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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(-) Related Entries Specified in the PDB File

1hom 1HOM CONTAINS THE ENTIRE HOMEODOMAIN
1kz5 THIRD HELIX OF ANTENNAPEDIA HOMEODOMAIN DERIVATIVE, 4 DELETIONS
1kzo THIRD HELIX OF ANTENNAPEDIA HOMEODOMAIN