PDBsum entry: 2g46

Transferase

PDB id: 2g46

Contents

Protein chains

119 a.a. *

21 a.a. *

Ligands

SAH ×2

* Residue conservation analysis

PDB id:

2g46

Name:

Transferase

Title:

Structure of vset in complex with mek27 h3 pept. And cofactor product sah

Structure:

Pbcv-1 histone h3-lys 27 methyltransferase. Chain: a, b. Synonym: vset. Engineered: yes. Mek27 h3 peptide. Chain: c, d. Engineered: yes

Source:

Paramecium bursaria chlorella virus 1. Organism_taxid: 10506. Gene: a612l. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes

NMR struc:

20 models

Authors:

C.M.Qian,L.Zheng,M.M.Zhou

Key ref:

C.Qian et al. (2006). Structural insights of the specificity and catalysis of a viral histone H3 lysine 27 methyltransferase. J Mol Biol, 359, 86-96. PubMed id: 16603186 DOI: 10.1016/j.jmb.2006.03.006

Date:

21-Feb-06 Release date: 05-Dec-06

Protein chains

O41094  (O41094_PBCV1) -  Histone H3K27 methylase

Seq: 119 a.a.

Struc: 119 a.a.

Protein chains

O24165  (O24165_TOBAC) -  Histone H3 (Fragment)

Seq: 38 a.a.

Struc: 21 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biological process: methylation (1 term)
• Biochemical function: protein binding (2 terms)

DOI no: 10.1016/j.jmb.2006.03.006

J Mol Biol 359:86-96 (2006)

PubMed id: 16603186

Structural insights of the specificity and catalysis of a viral histone H3 lysine 27 methyltransferase.

C.Qian, X.Wang, K.Manzur, Sachchidanand, A.Farooq, L.Zeng, R.Wang, M.M.Zhou.

ABSTRACT

SET domain lysine methyltransferases are known to catalyze site and state-specific methylation of lysine residues in histones that is fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. Here we report the three-dimensional solution structure of the SET domain histone lysine methyltransferase (vSET) from Paramecium bursaria chlorella virus 1 bound to cofactor S-adenosyl-L-homocysteine and a histone H3 peptide containing mono-methylated lysine 27. The dimeric structure, mimicking an enzyme/cofactor/substrate complex, yields the structural basis of the substrate specificity and methylation multiplicity of the enzyme. Our results from mutagenesis and enzyme kinetics analyses argue that a general base mechanism is less likely for lysine methylation by SET domains; and that the only invariant active site residue tyrosine 105 in vSET facilitates methyl transfer from cofactor to the substrate lysine by aligning intermolecular interactions in the lysine access channel of the enzyme.

Selected figure(s)

Figure 2.
Figure 2. The three-dimensional structure of the tertiary complex of vSET with cofactor SAH and H3-K27me peptide. (a) Stereoview of superimposition of backbone atoms (N, C^α and C′) of 20 lowest energy NMR structures of the vSET/SAH/H3-K27me. For clarity, only residues A25–A31 of the H3 peptide are depicted in the final structures. (b) Ribbon diagrams of the vSET/SAH/H3-K27me tertiary complex structure, shown in front view as in (a) (left panel) and top view with 90° rotation (right panel). vSET, SAH and H3-K27me peptide are color-coded in blue, green and pink, respectively. The peptide residues shown in this structure are T22-G33. (c) Surface electrostatic potential representation of the vSET protein in tertiary complex with SAH and H3-K27me peptide, depicted in a front view as in (b). (d) Comparison of the apo and ternary complex structures of vSET. The structures were superimposed with the secondary structural elements only. (e) The backbone {^1H}–^15N heteronuclear NOEs of vSET in the free form (lower panel) and in the tertiary complex with SAH and H3-K27me peptide (top panel). Error bars represent the standard deviation of NOE values measured in three data sets. (f) The regions of vSET that exhibited increased backbone dynamics upon ternary complex formation, as indicated by reduced {^1H}–^15N heteronuclear NOEs in (e), are highlighted in red in the Ribbon diagram of the vSET structure. Figure 2. The three-dimensional structure of the tertiary complex of vSET with cofactor SAH and H3-K27me peptide. (a) Stereoview of superimposition of backbone atoms (N, C^α and C′) of 20 lowest energy NMR structures of the vSET/SAH/H3-K27me. For clarity, only residues A25–A31 of the H3 peptide are depicted in the final structures. (b) Ribbon diagrams of the vSET/SAH/H3-K27me tertiary complex structure, shown in front view as in (a) (left panel) and top view with 90° rotation (right panel). vSET, SAH and H3-K27me peptide are color-coded in blue, green and pink, respectively. The peptide residues shown in this structure are T22-G33. (c) Surface electrostatic potential representation of the vSET protein in tertiary complex with SAH and H3-K27me peptide, depicted in a front view as in (b). (d) Comparison of the apo and ternary complex structures of vSET. The structures were superimposed with the secondary structural elements only. (e) The backbone {^1H}–^15N heteronuclear NOEs of vSET in the free form (lower panel) and in the tertiary complex with SAH and H3-K27me peptide (top panel). Error bars represent the standard deviation of NOE values measured in three data sets. (f) The regions of vSET that exhibited increased backbone dynamics upon ternary complex formation, as indicated by reduced {^1H}–^15N heteronuclear NOEs in (e), are highlighted in red in the Ribbon diagram of the vSET structure.

Figure 4.
Figure 4. The molecular determinants of H3-K27 methylation by vSET. The geometry and molecular environment of the lysine access channel in SET domains is shown for (a), vSET in the apo form; (b) vSET in the ternary complex; (c) DIM-5; (d) Set7/9; and (e) SET8. The SET domain protein residues are color-coded in gray, blue and red for carbon, nitrogen and oxygen, respectively, whereas the residues of the histone peptide substrates including substrate lysine are color-coded in green for carbon and nitrogen. Figure 4. The molecular determinants of H3-K27 methylation by vSET. The geometry and molecular environment of the lysine access channel in SET domains is shown for (a), vSET in the apo form; (b) vSET in the ternary complex; (c) DIM-5; (d) Set7/9; and (e) SET8. The SET domain protein residues are color-coded in gray, blue and red for carbon, nitrogen and oxygen, respectively, whereas the residues of the histone peptide substrates including substrate lysine are color-coded in green for carbon and nitrogen.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 86-96) copyright 2006.

Figures were selected by an automated process.