ISDA

Deposition Date 2018-08-03

Release Date 2018-08-15

Last Version Date 2024-01-17

Entry Detail

PDB ID:

6H8P

Keywords:

OXIDOREDUCTASE

Title:

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.98 Å

R-Value Free:

0.21

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 21 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Lysine-specific demethylase 4A
Gene (Uniprot):KDM4A
Chain IDs:A, B
Chain Length:381
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:O75164 Pfam ID:PF02375, PF02373 EC:1.14.11.27

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H1.4
Gene (Uniprot):H1-4
Chain IDs:C, D
Chain Length:15
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P10412

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
M3L	C	LYS	modified residue

Ligand Molecules

GOL

OGA

Primary Citation

Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.

Walport, L.J, Hopkinson, R.J, Chowdhury, R, Zhang, Y, Bonnici, J, Schiller, R, Kawamura, A, Schofield, C.J, Ng, S.S, Kavanagh, K.L, McDonough, M.A, Butler, D, Pilka, E.S, Lienard, B.M, Bray, J.E, Savitsky, P, Gileadi, O, von Delft, F, Rose, N.R, Offer, J, Scheinost, J.C, Borowski, T, Sundstrom, M, Schofield, C.J, Oppermann, U.Show

FEBS Lett. 592 3264 3273 (2018)

PMID: 30156264 DOI: 10.1002/1873-3468.13231

Abstact

N-Methylation of lysyl residues is widely observed on histone proteins. Using isolated enzymes, we report mechanistic and structural studies on histone lysine demethylase (KDM)-catalysed demethylation of Nε -methylated lysine 26 on histone 1 isotype 4 (H1.4). The results reveal that methylated H1.4K26 is a substrate for all members of the KDM4 subfamily and that KDM4A-catalysed demethylation of H1.4K26me3 peptide is similarly efficient to that of H3K9me3. Crystallographic studies of an H1.4K26me3:KDM4A complex reveal a conserved binding geometry to that of H3K9me3. In the light of the high activity of the KDM4s on this mark, our results suggest JmjC KDM-catalysed demethylation of H1.4K26 may be as prevalent as demethylation on the H3 tail and warrants further investigation in cells.

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Primary Citation of related structures