6O7G

Solution structure of MLL4 PHD6 domain in complex with histone H4K16ac peptide


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF.

Zhang, Y.Jang, Y.Lee, J.E.Ahn, J.Xu, L.Holden, M.R.Cornett, E.M.Krajewski, K.Klein, B.J.Wang, S.P.Dou, Y.Roeder, R.G.Strahl, B.D.Rothbart, S.B.Shi, X.Ge, K.Kutateladze, T.G.

(2019) Nat Commun 10: 2314-2314

  • DOI: 10.1038/s41467-019-10324-8

  • PubMed Abstract: 
  • Histone methyltransferase MLL4 is centrally involved in transcriptional regulation and is often mutated in human diseases, including cancer and developmental disorders. MLL4 contains a catalytic SET domain that mono-methylates histone H3K4 and seven ...

    Histone methyltransferase MLL4 is centrally involved in transcriptional regulation and is often mutated in human diseases, including cancer and developmental disorders. MLL4 contains a catalytic SET domain that mono-methylates histone H3K4 and seven PHD fingers of unclear function. Here, we identify the PHD6 finger of MLL4 (MLL4-PHD6) as a selective reader of the epigenetic modification H4K16ac. The solution NMR structure of MLL4-PHD6 in complex with a H4K16ac peptide along with binding and mutational analyses reveal unique mechanistic features underlying recognition of H4K16ac. Genomic studies show that one third of MLL4 chromatin binding sites overlap with H4K16ac-enriched regions in vivo and that MLL4 occupancy in a set of genomic targets depends on the acetyltransferase activity of MOF, a H4K16ac-specific acetyltransferase. The recognition of H4K16ac is conserved in the PHD7 finger of paralogous MLL3. Together, our findings reveal a previously uncharacterized acetyllysine reader and suggest that selective targeting of H4K16ac by MLL4 provides a direct functional link between MLL4, MOF and H4K16 acetylation.


    Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. tatiana.kutateladze@ucdenver.edu.,Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA. kai.ge@nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase 2D
B
64Homo sapiensMutation(s): 0 
Gene Names: KMT2D (ALR, MLL2, MLL4)
EC: 2.1.1.43
Find proteins for O14686 (Homo sapiens)
Go to Gene View: KMT2D
Go to UniProtKB:  O14686
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
A
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A
NON-POLYMERH2 N

--

ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection, Database references