PDBsum entry 2os2

Oxidoreductase

PDB id: 2os2

Contents

Protein chains

347 a.a. *

11 a.a. *

Ligands

OGA ×2

Metals

_NI ×2

_ZN ×2

Waters ×211

* Residue conservation analysis

PDB id:

2os2

Name:

Oxidoreductase

Title:

Crystal structure of jmjd2a complexed with histone h3 peptide trimethylated at lys36

Structure:

Jmjc domain-containing histone demethylation protein 3a. Chain: a, b. Synonym: jumonji domain-containing protein 2a. Engineered: yes. Histone 3 peptide. Chain: c, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: jmjd2a, jhdm3a, jmjd2, kiaa0677. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: synthetic peptide

Resolution:

2.30Å R-factor: 0.179 R-free: 0.226

Authors:

K.L.Kavanagh,S.S.Ng,E.Pilka,M.A.Mcdonough,P.Savitsky,F.Von Delft, C.H.Arrowsmith,J.Weigelt,A.Edwards,M.Sundstrom,C.J.Schofield, U.Oppermann,Structural Genomics Consortium (Sgc)

Key ref:

S.S.Ng et al. (2007). Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature, 448, 87-91. PubMed id: 17589501 DOI: 10.1038/nature05971

Date:

05-Feb-07 Release date: 13-Mar-07

Protein chains

O75164  (KDM4A_HUMAN) -  Lysine-specific demethylase 4A from Homo sapiens

Seq: 1064 a.a.

Struc: 347 a.a.

Protein chains

No UniProt id for this chain

Struc: 11 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.1.14.11.66 - [histone H3]-trimethyl-L-lysine(9) demethylase.
• Reaction: N₆,N₆,N₆-trimethyl-L-lysyl₉-[histone H3] + 2 2-oxoglutarate + 2 O2 = N₆-methyl-L-lysyl₉-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
• Enzyme class 3: Chains A, B: E.C.1.14.11.69 - [histone H3]-trimethyl-L-lysine(36) demethylase.
• Reaction: N₆,N₆,N₆-trimethyl-L-lysyl₃₆-[histone H3] + 2 2-oxoglutarate + 2 O2 = N₆-methyl-L-lysyl₃₆-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature05971

Nature 448:87-91 (2007)

PubMed id: 17589501

Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.

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

ABSTRACT

Post-translational histone modification has a fundamental role in chromatin biology and is proposed to constitute a 'histone code' in epigenetic regulation. Differential methylation of histone H3 and H4 lysyl residues regulates processes including heterochromatin formation, X-chromosome inactivation, genome imprinting, DNA repair and transcriptional regulation. The discovery of lysyl demethylases using flavin (amine oxidases) or Fe(II) and 2-oxoglutarate as cofactors (2OG oxygenases) has changed the view of methylation as a stable epigenetic marker. However, little is known about how the demethylases are selective for particular lysyl-containing sequences in specific methylation states, a key to understanding their functions. Here we reveal how human JMJD2A (jumonji domain containing 2A), which is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), discriminates between methylation states and achieves sequence selectivity for H3K9. We report structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. We propose a mechanism for achieving methylation state selectivity involving the orientation of the substrate methyl groups towards a ferryl intermediate. The results suggest distinct recognition mechanisms in different demethylase subfamilies and provide a starting point to develop chemical tools for drug discovery and to study and dissect the complexity of reversible histone methylation and its role in chromatin biology.

Selected figure(s)

Figure 3.
Figure 3: Mass spectra (MALDI–TOF) of JMJD2A demethylation reactions with native and modified histone peptides. a–d, H3K9; e, f, H3K27; g, h, H3K36. a, H3K9me3; b, H3K9me3 Gly12Ala–Gly13Ala; c, H3K9me3 Ser 10 phosphorylated; d, H3K9me3 Ser10Ala; e, H3K27me3; f, H3K27me3 Pro30Gly (glycine introduced as in H3K9 sequence); g, H3K36me3; h, H3K36me3 Pro38Ala.

Figure 4.
Figure 4: Active site and mechanism of JMJD2A. a, Stereoview omit 2F[o]-F[c] electron density maps contoured at 1 for H3K9me3 (blue) and H3K9me1 (red). The positions (a, b, c) for the three methyl groups of the H3K9me3 substrate are indicated with b projecting towards the metal-bound water. In the H3K9me1 structure the methyl group occupies position a with two water molecules (W1 and W2) close to the b and c positions. b, Outline of the catalytic cycle for JMJD2A showing the proposed ferryl and hemiaminal intermediates. Oxygen may bind at the position trans to His 276 or His 188.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 448, 87-91) copyright 2007.

Figures were selected by an automated process.