4X34

Crystal structure of the 53BP1 tandem tudor domain in complex with p53K381acK382me2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

An Acetyl-Methyl Switch Drives a Conformational Change in p53.

Tong, Q., Mazur, S.J., Rincon-Arano, H., Rothbart, S.B., Kuznetsov, D.M., Cui, G., Liu, W.H., Gete, Y., Klein, B.J., Jenkins, L., Mer, G., Kutateladze, A.G., Strahl, B.D., Groudine, M., Appella, E., Kutateladze, T.G.

(2015) Structure 23: 322-331

  • DOI: 10.1016/j.str.2014.12.010

  • PubMed Abstract: 

    • Individual posttranslational modifications (PTMs) of p53 mediate diverse p53-dependent responses; however, much less is known about the combinatorial action of adjacent modifications. Here, we describe crosstalk between the early DNA damage response ...

    Individual posttranslational modifications (PTMs) of p53 mediate diverse p53-dependent responses; however, much less is known about the combinatorial action of adjacent modifications. Here, we describe crosstalk between the early DNA damage response mark p53K382me2 and the surrounding PTMs that modulate binding of p53 cofactors, including 53BP1 and p300. The 1.8 Å resolution crystal structure of the tandem Tudor domain (TTD) of 53BP1 in complex with p53 peptide acetylated at K381 and dimethylated at K382 (p53K381acK382me2) reveals that the dual PTM induces a conformational change in p53. The α-helical fold of p53K381acK382me2 positions the side chains of R379, K381ac, and K382me2 to interact with TTD concurrently, reinforcing a modular design of double PTM mimetics. Biochemical and nuclear magnetic resonance analyses show that other surrounding PTMs, including phosphorylation of serine/threonine residues of p53, affect association with TTD. Our findings suggest a novel PTM-driven conformation switch-like mechanism that may regulate p53 interactions with binding partners.

    Organizational Affiliation: 

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor suppressor p53-binding protein 1
A, B
120Homo sapiensMutation(s): 0 
Gene Names: TP53BP1
Find proteins for Q12888 (Homo sapiens)
Go to Gene View: TP53BP1
Go to UniProtKB:  Q12888
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THR-SER-ARG-HIS-ALY-MLY-LEU-MET-PHE-LYS
C, D
10Homo sapiensMutation(s): 0 
Gene Names: TP53 (P53)
Find proteins for P04637 (Homo sapiens)
Go to Gene View: TP53
Go to UniProtKB:  P04637
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
C, D
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
MLY
Query on MLY
C, D
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 58.891α = 90.00
b = 110.939β = 90.00
c = 96.915γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM101664 (T.G.K.)

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-09-09
    Type: Data collection
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Derived calculations