4GUS

Crystal structure of LSD2-NPAC with H3 in space group P3221

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation

Fang, R., Chen, F., Dong, Z., Hu, D., Barbera, A.J., Clark, E.A., Fang, J., Yang, Y., Mei, P., Rutenberg, M., Li, Z., Zhang, Y., Xu, Y., Yang, H., Wang, P., Simon, M.D., Zhou, Q., Li, J., Marynick, M.P., Li, X., Lu, H., Kaiser, U.B., Kingston, R.E., Xu, Y., Shi, Y.G.

(2013) Mol.Cell 49: 558-570

  • DOI: 10.1016/j.molcel.2012.11.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Dynamic regulation of histone methylation represents a fundamental epigenetic mechanism underlying eukaryotic gene regulation, yet little is known about how the catalytic activities of histone demethylases are regulated. Here, we identify and charact ...

    Dynamic regulation of histone methylation represents a fundamental epigenetic mechanism underlying eukaryotic gene regulation, yet little is known about how the catalytic activities of histone demethylases are regulated. Here, we identify and characterize NPAC/GLYR1 as an LSD2/KDM1b-specific cofactor that stimulates H3K4me1 and H3K4me2 demethylation. We determine the crystal structures of LSD2 alone and LSD2 in complex with the NPAC linker region in the absence or presence of histone H3 peptide, at resolutions of 2.9, 2.0, and 2.25 Å, respectively. These crystal structures and further biochemical characterization define a dodecapeptide of NPAC (residues 214-225) as the minimal functional unit for its cofactor activity and provide structural determinants and a molecular mechanism underlying the intrinsic cofactor activity of NPAC in stimulating LSD2-catalyzed H3K4 demethylation. Thus, these findings establish a model for how a cofactor directly regulates histone demethylation and will have a significant impact on our understanding of catalytic-activity-based epigenetic regulation.

    Organizational Affiliation: 

    Division of Endocrinology, Diabetes, and Hypertension, Department of Medicine and Department of Biological Chemistry & Molecular Pharmacology, Brigham and Women's Hospital and Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific histone demethylase 1B
A
776Homo sapiensMutation(s): 0 
Gene Names: KDM1B (AOF1, C6orf193, LSD2)
EC: 1.-.-.-
Find proteins for Q8NB78 (Homo sapiens)
Go to Gene View: KDM1B
Go to UniProtKB:  Q8NB78
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative oxidoreductase GLYR1
B
124Homo sapiensMutation(s): 0 
Gene Names: GLYR1 (HIBDL, NDF, NP60)
EC: 1.-.-.-
Find proteins for Q49A26 (Homo sapiens)
Go to Gene View: GLYR1
Go to UniProtKB:  Q49A26
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
C
21Homo sapiensMutation(s): 1 
Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens)
Go to Gene View: H3F3A H3F3B
Go to UniProtKB:  P84243
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD
Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD
Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.083α = 90.00
b = 101.083β = 90.00
c = 177.372γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references