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(-) Description

Title :  THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF
 
Authors :  P. B. Rupert, G. W. Daughdrill, B. Bowerman, B. W. Matthews
Date :  30 Mar 98  (Deposition) - 24 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Complex (Transcription Factor/Dna), Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. B. Rupert, G. W. Daughdrill, B. Bowerman, B. W. Matthews
A New Dna-Binding Motif In The Skn-1 Binding Domain-Dna Complex.
Nat. Struct. Biol. V. 5 484 1998
PubMed-ID: 9628487  |  Reference-DOI: 10.1038/NSB0698-484
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3')
    ChainsA
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA-BINDING DOMAIN OF SKN-1
    Cellular LocationNUCLEUS
    ChainsP
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentBINDING DOMAIN
    GeneSKN-1
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    SynonymDNA-BINDING DOMAIN OF TRANSCRIPTION FACTOR SKN-1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1LDA1Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO P:471 , VAL P:472 , GLU P:479 , MET P:480 , SER P:481 , GLU P:484 , GLU P:492BINDING SITE FOR RESIDUE LDA P 16

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIP_BASICPS00036 Basic-leucine zipper (bZIP) domain signature.SKN1_CAEEL596-611  1P:506-521

(-) Exons   (0, 0)

(no "Exon" information available for 1SKN)

(-) 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:DNA  Length:15
                                               
                 1skn A   1 TGACAATGTCATCCC  15
                                    10     

Chain B from PDB  Type:DNA  Length:15
                                               
                 1skn B   1 CAGGGATGACATTGT  15
                                    10     

Chain P from PDB  Type:PROTEIN  Length:74
 aligned with SKN1_CAEEL | P34707 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:74
                                   555       565       575       585       595       605       615    
           SKN1_CAEEL   546 GRQSKDEQLASDNELPVSAFQISEMSLSELQQVLKNESLSEYQRQLIRKIRRRGKNKVAARTCRQRRTDRHDKM 619
               SCOP domains d1sknp_ P: Skn-1                                                           SCOP domains
               CATH domains 1sknP00 P:456-529 Transcription Factor Skn-1; Chain P                      CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh......hhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------BZIP_BASIC      -------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1skn P 456 GRQSKDEQLASDNELPVSAFQISEMSLSELQQVLKNESLSEYQRQLIRKIRRRGKNKVAARTCRQRRTDRHDKM 529
                                   465       475       485       495       505       515       525    

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SKN)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (SKN1_CAEEL | P34707)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030544    Hsp70 protein binding    Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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:0001708    cell fate specification    The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0009880    embryonic pattern specification    The process that results in the patterns of cell differentiation that will arise in an embryo.
    GO:0001714    endodermal cell fate specification    The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an endoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
    GO:0048382    mesendoderm development    The process whose specific outcome is the progression of the mesendoderm over time, from its formation to the mature structure. In animal embryos, mesendoderm development gives rise to both mesoderm and endoderm tissues.
    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:1900409    positive regulation of cellular response to oxidative stress    Any process that activates or increases the frequency, rate or extent of cellular response to oxidative stress.
    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:0061408    positive regulation of transcription from RNA polymerase II promoter in response to heat stress    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0006990    positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response    The activation of genes whose promoters contain a specific sequence elements such as the unfolded protein response element (UPRE; consensus CAGCGTG) or the ER stress-response element (ERSE; CCAAN(N)9CCACG), as a result of signaling via the unfolded protein response.
    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:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0000303    response to superoxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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