PDBsum entry 3kv6

H3k4me3 binding protein, transferase

PDB id: 3kv6

Contents

Protein chain

447 a.a. *

Ligands

OXY ×2

AKG ×2

Metals

_ZN ×4

FE2 ×2

Waters ×165

* Residue conservation analysis

PDB id:

3kv6

Name:

H3k4me3 binding protein, transferase

Title:

Structure of kiaa1718, human jumonji demethylase, in complex with alpha-ketoglutarate

Structure:

Jmjc domain-containing histone demethylation protein 1d. Chain: a, d. Fragment: unp residues 1-488. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: jhdm1d, kiaa1718. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.89Å R-factor: 0.215 R-free: 0.253

Authors:

J.R.Horton,A.K.Upadhyay,H.H.Qi,X.Zhang,Y.Shi,X.Cheng

Key ref:

J.R.Horton et al. (2010). Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Biol, 17, 38-43. PubMed id: 20023638 DOI: 10.1038/nsmb.1753

Date:

29-Nov-09 Release date: 22-Dec-09

Protein chains

Q6ZMT4  (KDM7A_HUMAN) -  Lysine-specific demethylase 7A from Homo sapiens

Seq: 941 a.a.

Struc: 447 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.11.65 - [histone H3]-dimethyl-L-lysine(9) demethylase.
• Reaction: N₆,N₆-dimethyl-L-lysyl₉-[histone H3] + 2 2-oxoglutarate + 2 O2 = L-lysyl₉-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2

N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] (Bound ligand (Het Group name = AKG) corresponds exactly) + 2 × 2-oxoglutarate + 2 × O2 (Bound ligand (Het Group name = OXY) corresponds exactly) = L-lysyl(9)-[histone H3] + 2 × formaldehyde + 2 × succinate + 2 × CO2

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

reference

DOI no: 10.1038/nsmb.1753

Nat Struct Biol 17:38-43 (2010)

PubMed id: 20023638

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.

J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng.

ABSTRACT

Combinatorial readout of multiple covalent histone modifications is poorly understood. We provide insights into how an activating histone mark, in combination with linked repressive marks, is differentially 'read' by two related human demethylases, PHF8 and KIAA1718 (also known as JHDM1D). Both enzymes harbor a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. The presence of H3K4me3 on the same peptide as H3K9me2 makes the doubly methylated peptide a markedly better substrate of PHF8, whereas the presence of H3K4me3 has the opposite effect, diminishing the H3K9me2 demethylase activity of KIAA1718 without adversely affecting its H3K27me2 activity. The difference in substrate specificity between the two is explained by PHF8 adopting a bent conformation, allowing each of its domains to engage its respective target, whereas KIAA1718 adopts an extended conformation, which prevents its access to H3K9me2 by its jumonji domain when its PHD engages H3K4me3.

Selected figure(s)

Figure 1.
PHF8 PHD domain binding of H3K4me3 enhances its jumonji domain-mediated demethylation of H3K9me2.
(a) Schematic representation of PHF8. (b) Effect of H3K4me3 on the demethylation of H3K9me2 by PHF8. Top panels show progression of demethylation as a function of reaction time. Supplementary Figure 11a shows representative mass spectra at various time points. Bottom panels show kinetics of PHF8 on two peptide substrates, with calculated kinetic parameters. (c) ITC measurement of binding of PHF8 to doubly methylated H3[1–24]K4me3-K9me2 peptides, carried out under the conditions of 11 μM protein concentration and 0.2 mM peptide concentration in 100 mM NaCl and 50 mM HEPES, pH 7.0. (d) The inhibitory effect of adding an equimolar ratio of H3[1–12]K4me3 (top) or H3[1–21]K4me3 peptides (bottom) on the demethylation of H3[1–24]K9me2 by PHF8. (e) The PHD (blue) and jumonji (green) collaborate in binding the H3 peptide (magenta) containing H3K4me3 and H3K9me2. Omit electron densities, F[o] – F[c] (black mesh), contoured at 4σ above the mean, are shown for the trimethlyated H3K4me3 and dimethlyated H3K9me2, respectively. (f) The surface representation of PHF8, colored with blue (PHD), green (jumonji) and magenta (H3 peptide). (g) H3K4me3 binding in the cage, surrounded on four sides by Tyr14, Met20 and Trp29 of PHD (blue) and Ser354 of jumonji (green). The carbonyl oxygen of Ser354 is in van der Waals contact with one of the methyl groups. Tyr7 (in thin lines) covers the top of the cage. (h) H3K9me2 binds in the active site.

Figure 4.
KIAA1718 selectively demethylates H3K27me2 in the presence of H3K4me3 in cis.
(a) A model of KIAA1718 PHD on methylated H3K4 and its linked jumonji active site on a target lysine (left). Surface representation displayed as blue for positive, red for negative and white for neutral (right). The dashed line connects H3K4me3 bound in the aromatic cage and the target lysine in the jumonji domain. (b) The presence of H3K4 methylation in cis enhances KIAA1718 demethylase activities on H3K27me2. (c) When two peptide substrates were mixed in equimolar ratio, H3[1–35]K27me2 (left) and H3[1–35]K4me3-K27me2 (right), KIAA1718 selectively demethylated H3[1–35] peptides containing both H3K4me3 and H3K27me2 (right).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2010, 17, 38-43) copyright 2010.

Figures were selected by the author.