PDBsum entry 3b95

Transferase/structural protein

PDB id: 3b95

Contents

Protein chains

236 a.a. *

Ligands

ALA-ARG-THR

ALA-ARG-MLY-SER-THR-GLY-GLY

SO4 ×10

Waters ×28

* Residue conservation analysis

PDB id:

3b95

Name:

Transferase/structural protein

Title:

Euhmt1 (glp) ankyrin repeat domain (structure 2)

Structure:

Euchromatic histone-lysine n-methyltransferase 1. Chain: a, b. Fragment: ankyrin repeat domains. Engineered: yes. Histone h3 n-terminal peptide. Chain: p. Fragment: h3 amino terminus peptide. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ehmt1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.99Å R-factor: 0.195 R-free: 0.238

Authors:

R.E.Collins,J.R.Horton,X.Cheng

Key ref:

R.E.Collins et al. (2008). The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Biol, 15, 245-250. PubMed id: 18264113 DOI: 10.1038/nsmb.1384

Date:

02-Nov-07 Release date: 12-Feb-08

Protein chains

Q9H9B1  (EHMT1_HUMAN) -  Histone-lysine N-methyltransferase EHMT1 from Homo sapiens

Seq: 1298 a.a.

Struc: 236 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.- - ?????
• Enzyme class 2: E.C.2.1.1.367 - [histone H3]-lysine(9) N-methyltransferase.
• Reaction: L-lysyl₉-[histone H3] + S-adenosyl-L-methionine = N₆-methyl-L- lysyl₉-[histone H3] + S-adenosyl-L-homocysteine + H⁺

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

Added reference

DOI no: 10.1038/nsmb.1384

Nat Struct Biol 15:245-250 (2008)

PubMed id: 18264113

The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules.

R.E.Collins, J.P.Northrop, J.R.Horton, D.Y.Lee, X.Zhang, M.R.Stallcup, X.Cheng.

ABSTRACT

Histone modifications have important roles in transcriptional control, mitosis and heterochromatin formation. G9a and G9a-like protein (GLP) are euchromatin-associated methyltransferases that repress transcription by mono- and dimethylating histone H3 at Lys9 (H3K9). Here we demonstrate that the ankyrin repeat domains of G9a and GLP bind with strong preference to N-terminal H3 peptides containing mono- or dimethyl K9. X-ray crystallography revealed the basis for recognition of the methylated lysine by a partial hydrophobic cage with three tryptophans and one acidic residue. Substitution of key residues in the cage eliminated the H3 tail interaction. Hence, G9a and GLP contain a new type of methyllysine binding module (the ankyrin repeat domains) and are the first examples of protein (histone) methyltransferases harboring in a single polypeptide the activities that generate and read the same epigenetic mark.

Selected figure(s)

Figure 1.
(a,b) Peptide pull-down assays with peptides that were unmodified (U) or mono-, di- or trimethylated (1, 2 or 3) at K4 or K9 (H3 1–21) or at K27 (H3 21–44) using G9a full-length (FL, residues 1–1263) or fragments containing the SET domain (residues 936–1263 of G9a) or the ankyrin repeats (ANK, residues 730–965 of G9a and 734–968 of GLP). Proteins were detected by SDS-PAGE and autoradiography. 1/10, 10% input. Shorter exposures of H3K9me1 and H3K9me2 binding are shown below each panel. (c,d) Binding of G9a and GLP ankyrin repeats with N-terminal fluoresceinated H3 peptides (residues 1–15), as determined by fluorescence polarization.

Figure 2.
(a) The helix-turn-helix- -turn structure of G9a-like protein (GLP) ankyrin repeats. The H3 peptide (gray) binds between the fourth and fifth repeats. For convenience, G9a residue numbers are shown (Supplementary Fig. 2). (b) H3K9me2 binds in a partial hydrophobic cage. Peptide binding is further specified by the interactions with H3 Ser10, Thr11, Gly12 and Gly13. (c) Peptide pull-down assays with H3 peptides (residues 1–21) using G9a wild-type (WT) or mutant ankyrin repeats. H3 peptides were either unmodified (U), or mono-, di- or trimethylated (1, 2 and 3). 1/10, 10% input. (d) Structural comparison of GLP ankyrin repeats with (green) and without (blue) bound peptide.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 245-250) copyright 2008.

Figures were selected by an automated process.