PDBsum entry: 1n6a

Transferase

PDB id: 1n6a

Contents

Protein chain

234 a.a. *

Ligands

SAM

Waters ×212

* Residue conservation analysis

PDB id:

1n6a

Name:

Transferase

Title:

Structure of set7/9

Structure:

Set domain-containing protein 7. Chain: a. Fragment: residues 108-366. Synonym: set7/9 methyltransferase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.194 R-free: 0.217

Authors:

T.W.Kwon,J.H.Chang,E.Kwak,C.W.Lee,A.Joachimiak,Y.C.Kim, J.Lee,Y.Cho

Key ref:

T.Kwon et al. (2003). Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet. EMBO J, 22, 292-303. PubMed id: 12514135 DOI: 10.1093/emboj/cdg025

Date:

09-Nov-02 Release date: 04-Feb-03

Protein chain

Q8WTS6  (SETD7_HUMAN) -  Histone-lysine N-methyltransferase SETD7

Seq: 366 a.a.

Struc: 234 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.43 - Histone-lysine N-methyltransferase.
• Reaction: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N₆-methyl-L-lysine-[histone]

S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]

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

Added reference

DOI no: 10.1093/emboj/cdg025

EMBO J 22:292-303 (2003)

PubMed id: 12514135

Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet.

T.Kwon, J.H.Chang, E.Kwak, C.W.Lee, A.Joachimiak, Y.C.Kim, J.Lee, Y.Cho.

ABSTRACT

The methylation of lysine residues of histones plays a pivotal role in the regulation of chromatin structure and gene expression. Here, we report two crystal structures of SET7/9, a histone methyltransferase (HMTase) that transfers methyl groups to Lys4 of histone H3, in complex with S-adenosyl-L-methionine (AdoMet) determined at 1.7 and 2.3 A resolution. The structures reveal an active site consisting of: (i) a binding pocket between the SET domain and a c-SET helix where an AdoMet molecule in an unusual conformation binds; (ii) a narrow substrate-specific channel that only unmethylated lysine residues can access; and (iii) a catalytic tyrosine residue. The methyl group of AdoMet is directed to the narrow channel where a substrate lysine enters from the opposite side. We demonstrate that SET7/9 can transfer two but not three methyl groups to unmodified Lys4 of H3 without substrate dissociation. The unusual features of the SET domain-containing HMTase discriminate between the un- and methylated lysine substrate, and the methylation sites for the histone H3 tail.

Selected figure(s)

Figure 2.
Figure 2 Overall structure of SET7/9 -AdoMet. (A) The 2.3 Å SET7/9L structure is shown in a ribbon representation. A bound AdoMet molecule is shown in a ball-and-stick model (oxygen, red; carbon, cyan; nitrogen, blue; and sulfur, green). The n-, SET and c-SET regions in the C-terminal domain are coloured in yellow, red and green, respectively. (B) Topological diagrams of secondary structure elements. Loops forming the active site pocket are in red. The AdoMet-binding site is indicated. The colour scheme is identical to that in (A). (C) Stereo diagram showing an extensive van der Waals contacts network between the SET and c-SET region. The AdoMet is coloured in cyan, and the residues from SET and c-SET domains are in yellow. Other atoms are shown in the same colour as in (A).

Figure 4.
Figure 4 A channel at the active site pocket. (A) A surface representation showing the location of the putative lysine-binding channel and a conserved shallow groove for the substrate-binding site (indicated by an arrow). See the text for sites 1, 2 and 3. The colouring scheme is identical to that in Figure 3A. AdoMet is shown in a bond model. The N-terminal domain is not coloured since it is not homologous to those of other SET-containing HMTases (Figure 1B). (B) A diagram showing the substrate-specific channel in SET7/9S. Key residues discussed in the text are shown in a ball-and-stick model. The AdoMet molecule is shown with the same colour scheme as in Figure 3B. (C) SET7/9 methylates unmethylated H3 peptide but cannot add methyl group(s) to already methylated peptide. An N-terminal peptide with amino acids 1 -8 of unmodified, mono- or dimethylated H3-K4 was used for the assay of SET7/9 HMTase activity. The full-length SET7/9 was used for the assay. (D) Methylation specificity of SET7/9. Histone H3 (Roche) was methylated by SET7/9. The reaction products were resolved by SDS -PAGE, blotted to nitrocellulose and probed with either a H3-K4 mono- or dimethyl antibody, or a H3-K4 trimethyl antibody as indicated. The H3-K4, K9 trimethyl antibody also gave the same result as that of the H3-K4 trimethyl antibody (data not shown).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 292-303) copyright 2003.

Figures were selected by the author.