PDBsum entry: 1n3j

Transferase

PDB id: 1n3j

Contents

Protein chains

119 a.a. *

* Residue conservation analysis

PDB id:

1n3j

Name:

Transferase

Title:

Structure and substrate of a histone h3 lysine methyltransferase from paramecium bursaria chlorella virus 1

Structure:

Histone h3 lysine methyltransferase. Chain: a, b. Synonym: a612l. Engineered: yes

Source:

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

NMR struc:

1 models

Authors:

K.L.Manzur,A.Farooq,L.Zeng,O.Plotnikova,Sachchidanand, A.W.Koch,M.-M.Zhou

Key ref:

K.L.Manzur et al. (2003). A dimeric viral SET domain methyltransferase specific to Lys27 of histone H3. Nat Struct Biol, 10, 187-196. PubMed id: 12567185 DOI: 10.1038/nsb898

Date:

28-Oct-02 Release date: 28-Jan-03

Protein chains

O41094  (O41094_PBCV1) -  Histone H3K27 methylase

Seq: 119 a.a.

Struc: 119 a.a.

 Gene Ontology (GO) functional annotation 

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

DOI no: 10.1038/nsb898

Nat Struct Biol 10:187-196 (2003)

PubMed id: 12567185

A dimeric viral SET domain methyltransferase specific to Lys27 of histone H3.

K.L.Manzur, A.Farooq, L.Zeng, O.Plotnikova, A.W.Koch, Sachchidanand, M.M.Zhou.

ABSTRACT

Site-specific lysine methylation of histones by SET domains is a hallmark for epigenetic control of gene transcription in eukaryotic organisms. Here we report that a SET domain protein from Paramecium bursaria chlorella virus can specifically di-methylate Lys27 in histone H3, a modification implicated in gene silencing. The solution structure of the viral SET domain reveals a butterfly-shaped head-to-head symmetric dimer different from other known protein methyltransferases. Each subunit consists of a Greek-key antiparallel beta-barrel and a three-stranded open-faced sandwich that mediates the dimer interface. Cofactor S-adenosyl-L-methionine (SAM) binds at the opening of the beta-barrel, and amino acids C-terminal to Lys27 in H3 and in the flexible C-terminal tail of the enzyme confer the specificity of this viral histone methyltransferase.

Selected figure(s)

Figure 2.
Figure 2. Histone methyltransferase activity of vSET. a, HMTase activity of vSET for free histones measured in the in vitro HMTase assay (lower panel). Relative amount of free histones used in the HMTase assay are shown in an SDS-PAGE gel (upper panel). When judged on the basis of molecular weight, the weak signal in the H2B lane in the fluorogram (indicated by an asterisk, lower panel) is probably due to H3 contamination in the H2B protein sample obtained from the manufacturer. b, HMTase activity of vSET measured against histone H3 peptides in a reaction condition similar to that of (a). The amino acid sequences of H3 peptides are shown below the enzyme activity plot, where Me[2]K and pS stand for N -di-methylated lysine and phosphorylated serine, respectively. c, vSET binding to H3 peptides. Superimposition of 2D 1H/15N HSQC spectra of vSET shows representative protein backbone resonances in the absence (black) and the presence (red) of H3 peptide containing residues 1 -20 (left column) or 15 -30 (right column). d, HPLC analysis of the enzyme kinetics of vSET. The HPLC stacking plot depicts time-dependent formation of mono- and di-methylated -Lys27 H3 peptides (residues 15 -30) catalyzed by vSET. Elution peaks were confirmed by MALDI-TOF mass spectrometry analysis. HPLC peaks corresponding to the non-, mono- and di-methylated -Lys27 H3 peptides are marked by solid dot, solid square and asterisk, respectively. e, Effect of amino acid changes of the histone H3 sequence on the lysine methylation by vSET. The reaction condition was similar to that of (b). Lys4 in substrate 3 was changed to Ala to ensure a direct comparison of methylation between Lys9 and Lys27. f, HMTase activity of vSET in the presence of varying amounts of urea and sodium chloride, measured using the H3-peptide substrate (amino acids 15 -30) as described (see Methods).

Figure 4.
Figure 4. Three-dimensional structure of the vSET dimer. a, Stereo view (front view) of ribbon depiction of the averaged minimized NMR structure of the vSET dimer. Orientation of the structure is similar to that of Fig. 3b. The two adjacent subunits of the dimer are colored in red and blue. Domain I of the antiparallel -barrel and domain II of the open-faced -sandwich are indicated. b, Side view of the vSET dimer. c, Top view of the vSET dimer looking down the two-fold axis. d, The dimer interface showing side chain contacts between the adjacent subunits. The side chains are color-coded in orange and green for the subunits in red and blue, respectively.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 187-196) copyright 2003.

Figures were selected by an automated process.