5TAB

Crystal Structure of the PHD Finger of PHF20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation.

Klein, B.J.Wang, X.Cui, G.Yuan, C.Botuyan, M.V.Lin, K.Lu, Y.Wang, X.Zhao, Y.Bruns, C.J.Mer, G.Shi, X.Kutateladze, T.G.

(2016) Cell Rep 17: 1158-1170

  • DOI: 10.1016/j.celrep.2016.09.056
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PHF20 is a core component of the lysine acetyltransferase complex MOF (male absent on the first)-NSL (non-specific lethal) that generates the major epigenetic mark H4K16ac and is necessary for transcriptional regulation and DNA repair. The role of PH ...

    PHF20 is a core component of the lysine acetyltransferase complex MOF (male absent on the first)-NSL (non-specific lethal) that generates the major epigenetic mark H4K16ac and is necessary for transcriptional regulation and DNA repair. The role of PHF20 in the complex remains elusive. Here, we report on functional coupling between methylation readers in PHF20. We show that the plant homeodomain (PHD) finger of PHF20 recognizes dimethylated lysine 4 of histone H3 (H3K4me2) and represents an example of a native reader that selects for this modification. Biochemical and structural analyses help to explain this selectivity and the preference of Tudor2, another reader in PHF20, for dimethylated p53. Binding of the PHD finger to H3K4me2 is required for histone acetylation, accumulation of PHF20 at target genes, and transcriptional activation. Together, our findings establish a unique PHF20-mediated link between MOF histone acetyltransferase (HAT), p53, and H3K4me2, and suggest a model for rapid spreading of H4K16ac-enriched open chromatin.


    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
PHD finger protein 20
A
53Homo sapiensMutation(s): 1 
Gene Names: PHF20 (C20orf104, GLEA2, HCA58, NZF, TZP)
Find proteins for Q9BVI0 (Homo sapiens)
Go to Gene View: PHF20
Go to UniProtKB:  Q9BVI0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.118 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 46.739α = 90.00
b = 46.739β = 90.00
c = 50.928γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM100907, GM106416, GM101664

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references