1ML9 | pdb_00001ml9

Structure of the Neurospora SET domain protein DIM-5, a histone lysine methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb1ML9/pdb

• Classification: TRANSFERASE
• Organism(s): Neurospora crassa
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-08-30 Released: 2002-10-23 
• Deposition Author(s): Zhang, X., Tamaru, H., Khan, S.I., Horton, J.R., Keefe, L.J., Selker, E.U., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.258 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 

Literature

Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase

Zhang, X., Tamaru, H., Khan, S.I., Horton, J.R., Keefe, L.J., Selker, E.U., Cheng, X.

(2002) Cell 111: 117-127

• PubMed: 12372305 
• DOI: https://doi.org/10.1016/s0092-8674(02)00999-6
• Primary Citation Related Structures: 
  1ML9


• PubMed Abstract: 
  

  AdoMet-dependent methylation of histones is part of the "histone code" that can profoundly influence gene expression. We describe the crystal structure of Neurospora DIM-5, a histone H3 lysine 9 methyltranferase (HKMT), determined at 1.98 A resolution, as well as results of biochemical characterization and site-directed mutagenesis of key residues. This SET domain protein bears no structural similarity to previously characterized AdoMet-dependent methyltransferases but includes notable features such as a triangular Zn3Cys9 zinc cluster in the pre-SET domain and a AdoMet binding site in the SET domain essential for methyl transfer. The structure suggests a mechanism for the methylation reaction and provides the structural basis for functional characterization of the HKMT family and the SET domain.

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Organizational Affiliation: 
• Department of Biochemistry, School of Medicine, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.93 kDa 
• Atom Count: 2,043 
• Modeled Residue Count: 260 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3 methyltransferase DIM-5	A	302	Neurospora crassa	Mutation(s): 0  EC: 2.1.1.43 (PDB Primary Data), 2.1.1.355 (UniProt)
UniProt
Find proteins for Q8X225 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q8X225  Go to UniProtKB:  Q8X225

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	Unknown ligand PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.258 (Depositor) 
• R-Value Work:  0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.73	α = 90
b = 81.56	β = 90
c = 101.27	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
X-PLOR	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-23 
Deposition Author(s): Zhang, X., Tamaru, H., Khan, S.I., Horton, J.R., Keefe, L.J., Selker, E.U., Cheng, X.

Revision History  

• Version 1.0: 2002-10-23
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2025-02-12
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary