Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.30 kDa 
• Atom Count: 5153 
• Residue Count: 647 
• Unique protein chains: 1

2H94

Crystal Structure and Mechanism of human Lysine-Specific Demethylase-1

• DOI: 10.2210/pdb2H94/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-08 Released: 2006-07-04 
• Deposition Author(s): Stavropoulos, P., Blobel, G., Hoelz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.281 
• R-Value Work: 0.229 
• R-Value Observed: 0.281 

Literature

Crystal structure and mechanism of human lysine-specific demethylase-1.

Stavropoulos, P., Blobel, G., Hoelz, A.

(2006) Nat Struct Mol Biol 13: 626-632

• PubMed: 16799558 
• DOI: 10.1038/nsmb1113
• Primary Citation of Related Structures:  
  2H94


• PubMed Abstract: 
  

The reversible methylation of specific lysine residues in histone tails is crucial in epigenetic gene regulation. LSD1, the first known lysine-specific demethylase, selectively removes monomethyl and dimethyl, but not trimethyl modifications of Lys4 or Lys9 of histone-3. Here, we present the crystal structure of LSD1 at 2.9-A resolution. LSD1 forms a highly asymmetric, closely packed domain structure from which a long helical 'tower' domain protrudes. The active site cavity is spacious enough to accommodate several residues of the histone tail substrate, but does not appear capable of recognizing the different methylation states of the substrate lysine. This supports the hypothesis that trimethylated lysine is chemically rather than sterically discriminated. We present a biochemical analysis of LSD1 mutants that identifies crucial residues in the active site cavity and shows the importance of the SWIRM and tower domains for catalysis.

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Organizational Affiliation: 

Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1	A	664	Homo sapiens	Mutation(s): 0  Gene Names: AOF2, KDM1A, KDM1, KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
NIH Common Fund Data Resources
PHAROS  O60341 GTEx  ENSG00000004487

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HG	A	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.281 
• R-Value Work: 0.229 
• R-Value Observed: 0.281 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.943	α = 90
b = 187.943	β = 90
c = 108.741	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-08 
• Released Date: 2006-07-04 
Deposition Author(s): Stavropoulos, P., Blobel, G., Hoelz, A.

Revision History 

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description