Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 103.82 kDa 
• Atom Count: 6469 
• Modelled Residue Count: 804 
• Deposited Residue Count: 922 
• Unique protein chains: 3

2UXN

Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation

• PDB DOI: 10.2210/pdb2UXN/pdb

• Classification: OXIDOREDUCTASE/TRANSCRIPTION REGULATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-03-28 Released: 2007-05-29 
• Deposition Author(s): Yang, M., Culhane, J.C., Szewczuk, L.M., Gocke, C.B., Brautigam, C.A., Tomchick, D.R., Machius, M., Cole, P.A., Yu, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.272 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 

Literature

Structural Basis of Histone Demethylation by Lsd1 Revealed by Suicide Inactivation.

Yang, M., Culhane, J.C., Szewczuk, L.M., Gocke, C.B., Brautigam, C.A., Tomchick, D.R., Machius, M., Cole, P.A., Yu, H.

(2007) Nat Struct Mol Biol 14: 535

• PubMed: 17529991 
• DOI: 10.1038/nsmb1255
• Primary Citation of Related Structures:  
  2UXN


• PubMed Abstract: 
  

Histone methylation regulates diverse chromatin-templated processes, including transcription. The recent discovery of the first histone lysine-specific demethylase (LSD1) has changed the long-held view that histone methylation is a permanent epigenetic mark. LSD1 is a flavin adenine dinucleotide (FAD)-dependent amine oxidase that demethylates histone H3 Lys4 (H3-K4). However, the mechanism by which LSD1 achieves its substrate specificity is unclear. We report the crystal structure of human LSD1 with a propargylamine-derivatized H3 peptide covalently tethered to FAD. H3 adopts three consecutive gamma-turns, enabling an ideal side chain spacing that places its N terminus into an anionic pocket and positions methyl-Lys4 near FAD for catalysis. The LSD1 active site cannot productively accommodate more than three residues on the N-terminal side of the methyllysine, explaining its H3-K4 specificity. The unusual backbone conformation of LSD1-bound H3 suggests a strategy for designing potent LSD1 inhibitors with therapeutic potential.

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Related Citations: 

• Structural Basis for Corest-Dependent Demethylation of Nucleosomes by the Human Lsd1 Histone Demethylase
  Yang, M., Gocke, C.B., Luo, X., Borek, D., Tomchick, D.R., Machius, M., Otwinowski, Z., Yu, H.
  (2006) Mol Cell 23: 377

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Organizational Affiliation: 

Department of Pharmacology, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1	A	666	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
PHAROS:  O60341 GTEx:  ENSG00000004487

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST COREPRESSOR 1	B	235	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1, KIAA0071, RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0  Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0 GTEx:  ENSG00000089902

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3.1	C [auth E]	21	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA	D [auth A]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.272 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.949	α = 90
b = 178.646	β = 90
c = 234.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-28 
• Released Date: 2007-05-29 
Deposition Author(s): Yang, M., Culhane, J.C., Szewczuk, L.M., Gocke, C.B., Brautigam, C.A., Tomchick, D.R., Machius, M., Cole, P.A., Yu, H.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance