4GUQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.302 

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

  • 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 huma ...

    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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tumor protein p73
A, B
210Homo sapiensMutation(s): 1 
Gene Names: TP73 (P73)
Find proteins for O15350 (Homo sapiens)
Go to Gene View: TP73
Go to UniProtKB:  O15350
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')E,F10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.302 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 172.498α = 90.00
b = 172.498β = 90.00
c = 34.093γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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