PDBsum entry: 3f9w

Transferase

PDB id: 3f9w

Contents

Protein chains

160 a.a. *

Ligands

LYS-ARG-HIS-ARG-LYS-VAL-LEU-ARG-ASP ×2

LYS-ARG-HIS-ARG-LYS-VAL-LEU-ARG ×2

SAH ×4

Waters ×1022

* Residue conservation analysis

PDB id:

3f9w

Name:

Transferase

Title:

Structural insights into lysine multiple methylation by set domain methyltransferases, set8-y334f / h4-lys20 / adohcy

Structure:

Histone-lysine n-methyltransferase setd8. Chain: a, b, c, d. Fragment: set domain: unp residues 232-393. Synonym: h4-k20-hmtase setd8, set domain-containing protein 8, pr/set domain-containing protein 07, pr/set07, pr-set7, lysine n-methyltransferase 5a. Engineered: yes. Mutation: yes. Histone h4.

Source:

Homo sapiens. Organism_taxid: 9606. Gene: setd8, kmt5a, prset7, set07, set8. Expressed in: escherichia coli. Synthetic: yes. Other_details: synthetic peptide corresponding to residues 16-25 of human histone h4

Resolution:

1.60Å R-factor: 0.164 R-free: 0.206

Authors:

J-F.Couture,L.M.A.Dirk,J.S.Brunzelle,R.L.Houtz,R.C.Trievel

Key ref:

J.F.Couture et al. (2008). Structural origins for the product specificity of SET domain protein methyltransferases. Proc Natl Acad Sci U S A, 105, 20659-20664. PubMed id: 19088188 DOI: 10.1073/pnas.0806712105

Date:

14-Nov-08 Release date: 25-Nov-08

Protein chains

Q9NQR1  (SETD8_HUMAN) -  N-lysine methyltransferase SETD8

Seq: 393 a.a.

Struc: 160 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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

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

Added reference

DOI no: 10.1073/pnas.0806712105

Proc Natl Acad Sci U S A 105:20659-20664 (2008)

PubMed id: 19088188

Structural origins for the product specificity of SET domain protein methyltransferases.

J.F.Couture, L.M.Dirk, J.S.Brunzelle, R.L.Houtz, R.C.Trievel.

ABSTRACT

SET domain protein lysine methyltransferases (PKMTs) regulate transcription and other cellular functions through site-specific methylation of histones and other substrates. PKMTs catalyze the formation of monomethylated, dimethylated, or trimethylated products, establishing an additional hierarchy with respect to methyllysine recognition in signaling. Biochemical studies of PKMTs have identified a conserved position within their active sites, the Phe/Tyr switch, that governs their respective product specificities. To elucidate the mechanism underlying this switch, we have characterized a Phe/Tyr switch mutant of the histone H4 Lys-20 (H4K20) methyltransferase SET8, which alters its specificity from a monomethyltransferase to a dimethyltransferase. The crystal structures of the SET8 Y334F mutant bound to histone H4 peptides bearing unmodified, monomethyl, and dimethyl Lys-20 reveal that the phenylalanine substitution attenuates hydrogen bonding to a structurally conserved water molecule adjacent to the Phe/Tyr switch, facilitating its dissociation. The additional space generated by the solvent's dissociation enables the monomethyllysyl side chain to adopt a conformation that is catalytically competent for dimethylation and furnishes sufficient volume to accommodate the dimethyl epsilon-ammonium product. Collectively, these results indicate that the Phe/Tyr switch regulates product specificity through altering the affinity of an active-site water molecule whose dissociation is required for lysine multiple methylation.

Selected figure(s)

Figure 2.
Structures of the active sites of native SET8 and the Y334F mutant bound to AdoHcy and H4K20, H4K20me1, and H4K20me2 peptides. His-18 in histone H4 forms 1 wall of the channel and was omitted to provide an unobstructed view of the active site. SET8, histone H4, and AdoHcy are delineated by gray, gold, and green carbon atoms, respectively. The Y334F mutation is highlighted in magenta. (Insets) Shown are the F[O] − F[C] omit map electron densities for the various K20 side chains contoured at 2.0 σ. Conventional and CH^…O hydrogen bonds are depicted as orange and cyan dashes, respectively. (A) Native SET8–H4K20–AdoHcy complex (Protein Data Bank ID code 1ZKK). (B) SET8 Y334F–H4K20–AdoHcy. (C) SET8 Y334F–H4K20me1–AdoHcy. (D) SET8 Y334F–H4K20me2–AdoHcy.

Figure 4.
Model for H4K20 dimethylation by the SET8 Y334F mutant. (A) First methyltransfer reaction. In the SET8 Y334F–H4K20–AdoMet complex, AdoMet was modeled in the active site by using the AdoHcy coordinates (Fig. 2 color scheme with hydrogens rendered in cyan). The S[N]2 reaction distance and bond angle corresponding to the H4K20 ε-amine group and the AdoMet methyl group and sulfonium cation are noted. Fig. S6 illustrates the hydrogen bonding to the K20 ε-amine. (B) Second methyltransfer reaction. In this substrate complex, the H4K20me1 side chain is modeled with its methyl group projecting into the vacated water binding site, which is inferred from the coordinates of the corresponding methyl group in the H4K20me2 product complex (Fig. 2D). This orientation aligns the K20me1 ε-amine for methyltransfer with AdoMet.

Figures were selected by the author.