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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF ADPA, THE GLOBAL TRANSCRIPTIONAL FACTOR, IN COMPLEX WITH A TARGET DNA
 
Authors :  M. D. Yao, J. Ohtsuka, K. Nagata, K. Miyazono, Y. Ohnishi, M. Tanokura
Date :  22 Feb 13  (Deposition) - 18 Sep 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  H-T-H Motif, Sequence-Specific Dna Binding Transcription Factor Activity, Dna-Binding, Intracellular, Transcription Activator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Yao, J. Ohtsuka, K. Nagata, K. Miyazono, Y. Zhi, Y. Ohnishi, M. Tanokura
Complex Structure Of The Dna-Binding Domain Of Adpa, The Global Transcription Factor In Streptomyces Griseus, And A Target Duplex Dna Reveals The Structural Basis Of Its Tolerant Dna Sequence Specificity
J. Biol. Chem. V. 288 31019 2013
PubMed-ID: 24019524  |  Reference-DOI: 10.1074/JBC.M113.473611

(-) Compounds

Molecule 1 - ADPA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN, RESIDUES 215-340
    Gene: ADPA
    Organism Scientific: STREPTOMYCES GRISEUS
    Organism Taxid: 1911
 
Molecule 2 - DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)- 3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*GP*GP*TP*TP*GP*GP*CP*GP*GP*GP*TP*TP*CP*AP*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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3W6V)

(-) Sites  (0, 0)

(no "Site" information available for 3W6V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W6V)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:111
 aligned with Q9S166_STRGR | Q9S166 from UniProtKB/TrEMBL  Length:405

    Alignment length:111
                                   239       249       259       269       279       289       299       309       319       329       339 
         Q9S166_STRGR   230 SDPLAEVVAWALEHLHEQFDVETLAARAYMSRRTFDRRFRSLTGSAPLQWLITQRVLQAQRLLETSDYSVDEVAGRCGFRSPVALRGHFRRQLGSSPAAYRAAYRARRPQG 340
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3w6v A 230 SDPLAEVVAWALEHLHEQFDVETLAARAYMSRRTFDRRFRSLTGSAPLQWLITQRVLQAQRLLETSDYSVDEVAGRCGFRSPVALRGHFRRQLGSSPAAYRAAYRARRPQG 340
                                   239       249       259       269       279       289       299       309       319       329       339 


Chain B from PDB  Type:DNA  Length:16
                                                
                 3w6v B  -3 CTGTGAACCCGCCAAC  12
                                     6      


Chain C from PDB  Type:DNA  Length:16
                                                
                 3w6v C  -3 AGGTTGGCGGGTTCAC  12
                                     6
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3W6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W6V)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9S166_STRGR | Q9S166)
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: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: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.

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