Crystal structure of histone K79 methyltransferase Dot1p from yeast

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase

Sawada, K.Yang, Z.Horton, J.R.Collins, R.E.Zhang, X.Cheng, X.

(2004) J Biol Chem 279: 43296-43306

  • DOI: https://doi.org/10.1074/jbc.M405902200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Methylation of Lys79 on histone H3 by Dot1p is important for gene silencing. The elongated structure of the conserved core of yeast Dot1p contains an N-terminal helical domain and a seven-stranded catalytic domain that harbors the binding site for the methyl-donor and an active site pocket sided with conserved hydrophobic residues. The S-adenosyl-L-homocysteine exhibits an extended conformation distinct from the folded conformation observed in structures of SET domain histone lysine methyltransferases. A catalytic asparagine (Asn479), located at the bottom of the active site pocket, suggests a mechanism similar to that employed for amino methylation in DNA and protein glutamine methylation. The acidic, concave cleft between the two domains contains two basic residue binding pockets that could accommodate the outwardly protruding basic side chains around Lys79 of histone H3 on the disk-like nucleosome surface. Biochemical studies suggest that recombinant Dot1 proteins are active on recombinant nucleosomes, free of any modifications.

  • Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specific
A, B, C
433Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DOT1
EC: (PDB Primary Data), (UniProt)
Find proteins for Q04089 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04089 
Go to UniProtKB:  Q04089
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04089
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SAH

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
C14 H20 N6 O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.07α = 90
b = 146.275β = 97.68
c = 75.412γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance