9EHI image
Deposition Date 2024-11-22
Release Date 2025-04-09
Last Version Date 2025-06-11
Entry Detail
PDB ID:
9EHI
Keywords:
Title:
Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.60 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Protein ENL
Gene (Uniprot):MLLT1
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Chain Length:145
Number of Molecules:16
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Histone H3.1
Gene (Uniprot):H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
Chain IDs:Q, R, S, T, U, V, W, X, Y, Z, AA (auth: a), BA (auth: b), CA (auth: c), DA (auth: d), EA (auth: e), FA (auth: f)
Chain Length:145
Number of Molecules:16
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A1BIE Q LYS modified residue
Ligand Molecules
Primary Citation
The YEATS domain is a selective reader of histone methacrylation.
Structure ? ? ? (2025)
PMID: 40339582 DOI: 10.1016/j.str.2025.04.010

Abstact

Metabolically regulated lysine acylation modifications in proteins play a major role in epigenetic processes and cellular homeostasis. A new type of histone acylation, lysine methacrylation, has recently been identified but remains poorly characterized. Here, we show that lysine methacrylation can be generated through metabolism of sodium methacrylate and enzymatically removed in cells, and that the YEATS domain but not bromodomain recognizes this modification. Structural and biochemical analyses reveal the π-π-π-stacking mechanism for binding of the YEATS domain of ENL to methacrylated histone H3K18 (H3K18mc). Using mass spectrometry proteomics, we demonstrate that methacrylate induces global methacrylation of a set of proteins that differs from the set of methacrylated proteins associated with valine metabolism. These findings suggest that high levels of methacrylate may potentially perturb cellular functions of these proteins by altering protein methacrylation profiles.

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Primary Citation of related structures