Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.07 kDa 
• Atom Count: 617 
• Modelled Residue Count: 78 
• Deposited Residue Count: 81 
• Unique protein chains: 1

2LDM

Solution structure of human PHF20 Tudor2 domain bound to a p53 segment containing a dimethyllysine analog p53K370me2

• PDB DOI: 10.2210/pdb2LDM/pdb
• BMRB: 17673

• Classification: TRANSCRIPTION/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-30 Released: 2012-05-30 
• Deposition Author(s): Cui, G., Botuyan, M., Mer, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53.

Cui, G., Park, S., Badeaux, A.I., Kim, D., Lee, J., Thompson, J.R., Yan, F., Kaneko, S., Yuan, Z., Botuyan, M.V., Bedford, M.T., Cheng, J.Q., Mer, G.

(2012) Nat Struct Mol Biol 19: 916-924

• PubMed: 22864287 
• DOI: 10.1038/nsmb.2353
• Primary Citation of Related Structures:  
  2LDM, 3P8D, 3SD4


• PubMed Abstract: 
  

PHF20 is a multidomain protein and subunit of a lysine acetyltransferase complex that acetylates histone H4 and p53 but whose function is unclear. Using biochemical, biophysical and cellular approaches, we determined that PHF20 is a direct regulator of p53. A Tudor domain in PHF20 recognized p53 dimethylated at Lys370 or Lys382 and a homodimeric form of this Tudor domain could associate with the two dimethylated sites on p53 with enhanced affinity, indicating a multivalent interaction. Association with PHF20 promotes stabilization and activation of p53 by diminishing Mdm2-mediated p53 ubiquitylation and degradation. PHF20 contributes to upregulation of p53 in response to DNA damage, and ectopic expression of PHF20 in different cell lines leads to phenotypic changes that are hallmarks of p53 activation. Overall our work establishes that PHF20 functions as an effector of p53 methylation that stabilizes and activates p53.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	81	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M2L	A	L-PEPTIDE LINKING	C7 H16 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2LDM Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-30 
• Released Date: 2012-05-30 
Deposition Author(s): Cui, G., Botuyan, M., Mer, G.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-08-08
  Changes: Database references
• Version 1.2: 2012-08-15
  Changes: Database references
• Version 1.3: 2012-10-03
  Changes: Database references