5TBN

Solution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.,Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany.,Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany.,Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany; Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA. Electronic address: mer.georges@mayo.edu.,Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: xbshi@mdanderson.org.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: tatiana.kutateladze@ucdenver.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHD finger protein 20
A
57Homo sapiensMutation(s): 0 
Gene Names: PHF20 (C20orf104, GLEA2, HCA58, NZF, TZP)
Find proteins for Q9BVI0 (Homo sapiens)
Go to Gene View: PHF20
Go to UniProtKB:  Q9BVI0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
C
12Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C
NON-POLYMERH2 N

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MLY
Query on MLY
C
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA132878

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-11-02
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Structure summary