3Q06

An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity.

Petty, T.J.Emamzadah, S.Costantino, L.Petkova, I.Stavridi, E.S.Saven, J.G.Vauthey, E.Halazonetis, T.D.

(2011) EMBO J 30: 2167-2176

  • DOI: 10.1038/emboj.2011.127
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The p53 tumour suppressor gene, the most frequently mutated gene in human cancer, encodes a transcription factor that contains sequence-specific DNA binding and homo-tetramerization domains. Interestingly, the affinities of p53 for specific and non-s ...

    The p53 tumour suppressor gene, the most frequently mutated gene in human cancer, encodes a transcription factor that contains sequence-specific DNA binding and homo-tetramerization domains. Interestingly, the affinities of p53 for specific and non-specific DNA sites differ by only one order of magnitude, making it hard to understand how this protein recognizes its specific DNA targets in vivo. We describe here the structure of a p53 polypeptide containing both the DNA binding and oligomerization domains in complex with DNA. The structure reveals that sequence-specific DNA binding proceeds via an induced fit mechanism that involves a conformational switch in loop L1 of the p53 DNA binding domain. Analysis of loop L1 mutants demonstrated that the conformational switch allows DNA binding off-rates to be regulated independently of affinities. These results may explain the universal prevalence of conformational switching in sequence-specific DNA binding proteins and suggest that proteins like p53 rely more on differences in binding off-rates, than on differences in affinities, to recognize their specific DNA sites.


    Organizational Affiliation

    Department of Molecular Biology, University of Geneva, Geneva, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular tumor antigen p53
A, B, C, D
231Homo sapiensMutation(s): 17 
Gene Names: TP53P53
Find proteins for P04637 (Homo sapiens)
Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
DNA (26-MER)K26N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
DNA (26-MER)L26N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.591α = 90
b = 169.363β = 90
c = 55.336γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Other
  • Version 1.3: 2017-07-26
    Changes: Refinement description, Source and taxonomy