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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE BICOID HOMEODOMAIN BOUND TO THE CONSENSUS DNA BINDING SITE TAATCC
 
Authors :  J. M. Baird-Titus, M. Rance, K. Clark-Baldwin, J. Ma, D. Vrushank
Date :  18 May 05  (Deposition) - 14 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,P  (20x)
Keywords :  Protein-Dna Complex, Double Helix, Helix-Turn-Helix, Homeodomain, Dna-Binding Domain, K50, Recognition Helix, Transcription Factor, Translational Control, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Baird-Titus, K. Clark-Baldwin, V. Dave, C. A. Caperelli, J. Ma, M. Rance
The Solution Structure Of The Native K50 Bicoid Homeodomain Bound To The Consensus Taatcc Dna-Binding Site.
J. Mol. Biol. V. 356 1137 2006
PubMed-ID: 16406070  |  Reference-DOI: 10.1016/J.JMB.2005.12.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMEOTIC BICOID PROTEIN
    Chains: P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41A-NOVAGEN
    Expression System Strain: BL21STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HOMEODOMAIN (RESIDUES 97-163)
    Gene: BCD
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: PRD-4
 
Molecule 2 - 5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3'
    Chains: A
    Engineered: YES
    Other Details: CONSENSUS DNA BINDING SITE SENSE STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3'
    Chains: B
    Engineered: YES
    Other Details: CONSENSUS DNA BINDING SITE ANTI-SENSE STRAND
    Synthetic: YES

 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 1ZQ3)

(-) Sites  (0, 0)

(no "Site" information available for 1ZQ3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZQ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZQ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZQ3)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.BCD_DROME130-153  1P:35-58

(-) Exons   (0, 0)

(no "Exon" information available for 1ZQ3)

(-) 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:DNA  Length:13
                                             
                 1zq3 A  69 GCTCTAATCCCCG  81
                                    78   


Chain B from PDB  Type:DNA  Length:13
                                             
                 1zq3 B  82 CGGGGATTAGAGC  94
                                    91   


Chain P from PDB  Type:PROTEIN  Length:68
 aligned with BCD_DROME | P09081 from UniProtKB/Swiss-Prot  Length:494

    Alignment length:68
                                   105       115       125       135       145       155        
            BCD_DROME    96 RPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKDQS 163
               SCOP domains -d1zq3p1 P:2-68 Homeotic bicoid protein                              SCOP domains
               CATH domains 1zq3P00 P:1-68 Homeodomain-like                                      CATH domains
               Pfam domains --Homeobox-1zq3P01 P:3-59                                  --------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------HOMEOBOX_1  PDB: P:35-58---------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1zq3 P   1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKDQS  68
                                    10        20        30        40        50        60
   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  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain P   (BCD_DROME | P09081)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0016015    morphogen activity    Acts as a trigger for a pattern specification process when present at a specific concentration within a gradient.
    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: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.
    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:0045182    translation regulator activity    Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
    GO:0030371    translation repressor activity    Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0007355    anterior region determination    Specification of the anterior (head and thoracic segments) of the embryo by the gap genes; exemplified in insects by the actions of hunchback gene product.
    GO:0009948    anterior/posterior axis specification    The establishment, maintenance and elaboration of 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:0008595    anterior/posterior axis specification, embryo    The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote.
    GO:0008358    maternal determination of anterior/posterior axis, embryo    The specification of the anterior/posterior axis of the embryo by gradients of maternally-transcribed gene products; exemplified in insects by the morphogens, bicoid and nanos.
    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:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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: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:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0007367    segment polarity determination    Division of the 14 parasegments of the embryo into anterior and posterior compartments; exemplified by the actions of the segment polarity gene products.
    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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