5BUA

Lysine 120-acetylated P53 DNA binding domain in a complex with DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode.

Vainer, R.Cohen, S.Shahar, A.Zarivach, R.Arbely, E.

(2016) J Mol Biol 428: 3013-3025

  • DOI: 10.1016/j.jmb.2016.06.009
  • Primary Citation of Related Structures:  
    5BUA, 5LGY

  • PubMed Abstract: 
  • Normal cellular homeostasis depends on tight regulation of gene expression, which requires the modulation of transcription factors' DNA-binding specificity. That said, the mechanisms that allow transcription factors to distinguish between closely related response elements following different cellular signals are not fully understood ...

    Normal cellular homeostasis depends on tight regulation of gene expression, which requires the modulation of transcription factors' DNA-binding specificity. That said, the mechanisms that allow transcription factors to distinguish between closely related response elements following different cellular signals are not fully understood. In the tumor suppressor protein p53, acetylation of loop L1 residue Lys120 within the DNA-binding domain has been shown to promote the transcription of proapoptotic genes such as bax. Here, we report the crystal structures of Lys120-acetylated p53 DNA-binding domain in complex with a consensus response element and with the natural BAX response element. Our structural analyses reveal that Lys120 acetylation expands the conformational space of loop L1 in the DNA-bound state. Loop L1 flexibility is known to increase p53's DNA-binding specificity, and Lys120-acetylation-dependent conformational changes in loop L1 enable the formation of sequence-dependent DNA-binding modes for p53. Furthermore, binding to the natural BAX response element is accompanied by global conformational changes, deformation of the DNA helical structure, and formation of an asymmetric tetrameric complex. Based on these findings, we suggest a model for p53's Lys120 acetylation-dependent DNA-binding mode.


    Organizational Affiliation

    Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel; Department of Life-Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel. Electronic address: arbely@bgu.ac.il.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular tumor antigen p53A200Homo sapiensMutation(s): 0 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*GP*AP*CP*AP*TP*GP*TP*CP*C)-3')B10synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    C [auth A]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    ALY
    Query on ALY
    AL-PEPTIDE LINKINGC8 H16 N2 O3LYS
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.81 Å
    • R-Value Free: 0.213 
    • R-Value Work: 0.162 
    • R-Value Observed: 0.165 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 137.252α = 90
    b = 48.892β = 92.6
    c = 34.014γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    PHASERphasing
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2015-06-03 
    • Released Date: 2016-07-06 
    • Deposition Author(s): Arbely, E., Vainer, R.

    Funding OrganizationLocationGrant Number
    Concern FoundationUnited States--

    Revision History  (Full details and data files)

    • Version 1.0: 2016-07-06
      Type: Initial release
    • Version 1.1: 2016-08-17
      Changes: Database references