4GUQ

Structure of mutS139F p73 DNA binding domain complexed with 20BP DNA response element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.302 
  • R-Value Observed: 0.303 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Transactivation specificity is conserved among p53 family proteins and depends on a response element sequence code.

Ciribilli, Y.Monti, P.Bisio, A.Nguyen, H.T.Ethayathulla, A.S.Ramos, A.Foggetti, G.Menichini, P.Menendez, D.Resnick, M.A.Viadiu, H.Fronza, G.Inga, A.

(2013) Nucleic Acids Res 41: 8637-8653

  • DOI: 10.1093/nar/gkt657
  • Primary Citation of Related Structures:  
    4GUQ

  • PubMed Abstract: 
  • Structural and biochemical studies have demonstrated that p73, p63 and p53 recognize DNA with identical amino acids and similar binding affinity. Here, measuring transactivation activity for a large number of response elements (REs) in yeast and human cell lines, we show that p53 family proteins also have overlapping transactivation profiles ...

    Structural and biochemical studies have demonstrated that p73, p63 and p53 recognize DNA with identical amino acids and similar binding affinity. Here, measuring transactivation activity for a large number of response elements (REs) in yeast and human cell lines, we show that p53 family proteins also have overlapping transactivation profiles. We identified mutations at conserved amino acids of loops L1 and L3 in the DNA-binding domain that tune the transactivation potential nearly equally in p73, p63 and p53. For example, the mutant S139F in p73 has higher transactivation potential towards selected REs, enhanced DNA-binding cooperativity in vitro and a flexible loop L1 as seen in the crystal structure of the protein-DNA complex. By studying, how variations in the RE sequence affect transactivation specificity, we discovered a RE-transactivation code that predicts enhanced transactivation; this correlation is stronger for promoters of genes associated with apoptosis.


    Organizational Affiliation

    Laboratory of Transcriptional Networks, Centre for Integrative Biology (CIBIO), University of Trento, TN, 38060 Italy, Molecular Mutagenesis and DNA Repair Unit, IRCSS Azienda Ospedaliera Universitaria San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Genoa 16132, Italy, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA and Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIEHS, NIH, RTP, NC, 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor protein p73C [auth A], D [auth B]210Homo sapiensMutation(s): 1 
Gene Names: human p73P73TP73
UniProt & NIH Common Fund Data Resources
Find proteins for O15350 (Homo sapiens)
Explore O15350 
Go to UniProtKB:  O15350
PHAROS:  O15350
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')A [auth E], B [auth F]10N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    E [auth A], F [auth B]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.70 Å
    • R-Value Free: 0.316 
    • R-Value Work: 0.302 
    • R-Value Observed: 0.303 
    • Space Group: P 61
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 172.498α = 90
    b = 172.498β = 90
    c = 34.093γ = 120
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    PHASERphasing
    REFMACrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-08-14
      Type: Initial release
    • Version 1.1: 2013-10-23
      Changes: Database references