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 
  • R-Value Observed: 0.209 

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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:  
    4GU1, 4GUR, 4GUS, 4GUT, 4GUU

  • 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 characterize NPAC/GLYR1 as an LSD2/KDM1b-specific cofactor that stimulates H3K4me1 and H3K4me2 demethylation ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific histone demethylase 1BA776Homo sapiensMutation(s): 0 
Gene Names: LSD2, KDM1B, AOF1, C6orf193
EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
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Find proteins for Q8NB78 (Homo sapiens)
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Go to UniProtKB:  Q8NB78
PHAROS:  Q8NB78
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UniProt GroupQ8NB78
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative oxidoreductase GLYR1B124Homo sapiensMutation(s): 0 
Gene Names: GLYR1, HIBDL, NDF, NP60, NPAC
EC: 1
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Find proteins for Q49A26 (Homo sapiens)
Explore Q49A26 
Go to UniProtKB:  Q49A26
PHAROS:  Q49A26
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UniProt GroupQ49A26
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3C21Homo sapiensMutation(s): 1 
Gene Names: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
PHAROS:  P84243
Entity Groups  
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UniProt GroupP84243
Protein Feature View
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
D [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
IOD
Query on IOD
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E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-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 
  • R-Value Observed: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.083α = 90
b = 101.083β = 90
c = 177.372γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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