Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 103819.83 
• Atom Count: 6418 
• Residue Count: 922 
• Unique protein chains: 3

2UXN

Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation

• DOI: 10.2210/pdb2UXN/pdb

• Classification: OXIDOREDUCTASE/TRANSCRIPTION REGULATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• 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.

---

Experimental Data Snapshot

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

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


• 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.

---

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




---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1	A	666	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A (AOF2, KDM1, KIAA0601, LSD1) EC: 1.-.-.-
Find proteins for O60341 (Homo sapiens) Go to Gene View: KDM1A Go to UniProtKB:  O60341

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
REST COREPRESSOR 1	B	235	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1 (KIAA0071, RCOR)
Find proteins for Q9UKL0 (Homo sapiens) Go to Gene View: RCOR1 Go to UniProtKB:  Q9UKL0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HISTONE H3.1	E	21	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens) Go to Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Go to UniProtKB:  P68431

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FDA	A	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LYP	E	NON-POLYMER	C10 H22 N2 O2		LYS

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 119.949	α = 90.00
b = 178.646	β = 90.00
c = 234.930	γ = 90.00

Software Package:

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

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
  Type: Advisory, Version format compliance