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(-) Description

Title :  STRUCTURE OF ARISTALESS HOMEODOMAIN IN COMPLEX WITH DNA
 
Authors :  Y. Takamura, K. Miyazono, K. Nagata, K. Saigo, T. Kojima, M. Tanokura
Date :  02 Feb 10  (Deposition) - 28 Apr 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Homeodomain, Protein-Dna Complex, Developmental Protein, Dna-Binding, Homeobox, Nucleus, Gene Regulation-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Miyazono, Y. Zhi, Y. Takamura, K. Nagata, K. Saigo, T. Kojima, M. Tanokura
Cooperative Dna-Binding And Sequence-Recognition Mechanism Of Aristaless And Clawless
Embo J. V. 29 1613 2010
PubMed-ID: 20389279  |  Reference-DOI: 10.1038/EMBOJ.2010.53

(-) Compounds

Molecule 1 - HOMEOBOX PROTEIN ARISTALESS
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HOMEOBOX, RESIDUES 87-144
    Gene: AL, CG3935
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - 5'-D(*GP*GP*GP*TP*TP*TP*AP*AP*TP*TP*AP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*CP*CP*TP*AP*AP*TP*TP*AP*AP*AP*CP*CP*C)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG B:1 , DG B:13 , HOH B:17BINDING SITE FOR RESIDUE ACT B 1428

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LNQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LNQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LNQ)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.AL_DROME118-141  1A:118-141

(-) Exons   (0, 0)

(no "Exon" information available for 3LNQ)

(-) 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:58
 aligned with AL_DROME | Q06453 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:58
                                    96       106       116       126       136        
             AL_DROME    87 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 144
               SCOP domains d3lnqa_ A: automated matches                               SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains Homeobox-3lnqA01 A:87-142                               -- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------HOMEOBOX_1              --- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 3lnq A  87 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 144
                                    96       106       116       126       136        


Chain B from PDB  Type:DNA  Length:14
                                              
                 3lnq B   1 GGGTTTAATTAGGG  14
                                    10    


Chain C from PDB  Type:DNA  Length:14
                                              
                 3lnq C   1 CCCTAATTAAACCC  14
                                    10
   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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LNQ)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AL_DROME | Q06453)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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.
biological process
    GO:0048800    antennal morphogenesis    The process in which the anatomical structures of the antenna are generated and organized.
    GO:0022416    chaeta development    The process whose specific outcome is the progression of a chaeta over time, from its formation to the mature structure. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
    GO:0035015    elongation of arista core    The increase in length of the aristal core. The arista is the terminal segment of the antenna and consists of a central core and a series of lateral extensions.
    GO:0007480    imaginal disc-derived leg morphogenesis    The process in which the anatomical structures of a leg derived from an imaginal disc are generated and organized. A leg is a limb on which an animal walks and stands. An example of this is found in Drosophila melanogaster.
    GO:0035218    leg disc development    Progression of the leg imaginal disc over time, from its initial formation through to its metamorphosis to form adult structures including the leg, coxa and ventral thoracic pleura.
    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: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:0045747    positive regulation of Notch signaling pathway    Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway.
    GO:0007449    proximal/distal pattern formation, imaginal disc    The establishment, maintenance and elaboration of the proximal/distal 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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AL_DROME | Q06453: 3a01 3a02

(-) Related Entries Specified in the PDB File

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