Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.24 kDa 
• Atom Count: 2262 
• Modelled Residue Count: 280 
• Deposited Residue Count: 280 
• Unique protein chains: 2

2G46

structure of vSET in complex with meK27 H3 Pept. and cofactor product SAH

• PDB DOI: 10.2210/pdb2G46/pdb
• BMRB: 6997

• Classification: TRANSFERASE
• Organism(s): Paramecium bursaria Chlorella virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-02-21 Released: 2006-12-05 
• Deposition Author(s): Qian, C.M., Zheng, L., Zhou, M.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

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

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

(2006) J Mol Biol 359: 86-96

• PubMed: 16603186 
• DOI: 10.1016/j.jmb.2006.03.006
• Primary Citation of Related Structures:  
  2G46


• PubMed 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.

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Organizational Affiliation: 

Department of Molecular Physiology and Biophysics, Mount Sinai School of Medicine, New York University, NY 10029, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PBCV-1 histone H3-Lys 27 methyltransferase	A, C [auth B]	119	Paramecium bursaria Chlorella virus 1	Mutation(s): 0  Gene Names: A612L
UniProt
Find proteins for O41094 (Paramecium bursaria Chlorella virus 1) Explore O41094  Go to UniProtKB:  O41094

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
meK27 H3 Peptide	B [auth C], D	21	N/A	Mutation(s): 0
UniProt
Find proteins for O24165 (Nicotiana tabacum) Explore O24165  Go to UniProtKB:  O24165

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	B [auth C], D	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2G46 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-21 
• Released Date: 2006-12-05 
Deposition Author(s): Qian, C.M., Zheng, L., Zhou, M.M.

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations