2UXN

Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation


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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1038/nsmb1255
  • Structures With Same Primary Citation

  • 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 epigenet ...

    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
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A666Homo sapiensMutation(s): 0 
Gene Names: KDM1AAOF2KDM1KIAA0601LSD1
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REST COREPRESSOR 1B235Homo sapiensMutation(s): 0 
Gene Names: RCOR1KIAA0071RCOR
Find proteins for Q9UKL0 (Homo sapiens)
Explore Q9UKL0 
Go to UniProtKB:  Q9UKL0
NIH Common Fund Data Resources
PHAROS  Q9UKL0
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3.1E21Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDA
Query on FDA

Download CCD File 
A
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 = 119.949α = 90
b = 178.646β = 90
c = 234.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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