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Crystal structure of Lysine-specific demethylase1

Source organism: Homo sapiens
Biochemical function: flavin adenine dinucleotide binding
Biological process: regulation of DNA-templated transcription
Cellular component: nucleus

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EC 1.14.99.66: [Histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + acceptor + H(2)O = a [histone H3]-N(6)-methyl-L-lysine(4) + formaldehyde + reduced acceptor
Systematic name:
[Histone H3]-N(6),N(6)-dimethyl-L-lysine(4):acceptor oxidoreductase (demethylating)
Alternative Name(s):
  • Lysine-specific histone demethylase 1

GO terms

Sequence families

Pfam Protein families (Pfam)
PF01593
Domain description: Flavin containing amine oxidoreductase
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2z3y contains 1 copy of Pfam domain PF01593 (Flavin containing amine oxidoreductase) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.

PF04433
Domain description: SWIRM domain
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2z3y contains 1 copy of Pfam domain PF04433 (SWIRM domain) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR036188
Domain description: FAD/NAD(P)-binding domain superfamily
Occurring in:
  1. Lysine-specific histone demethylase 1A
IPR007526
Domain description: SWIRM domain
Occurring in:
  1. Lysine-specific histone demethylase 1A
IPR002937
Domain description: Amine oxidase
Occurring in:
  1. Lysine-specific histone demethylase 1A
IPR009057
Domain description: Homedomain-like superfamily
Occurring in:
  1. Lysine-specific histone demethylase 1A
IPR036388
Domain description: Winged helix-like DNA-binding domain superfamily
Occurring in:
  1. Lysine-specific histone demethylase 1A
IPR017366
Domain description: Lysine-specific histone demethylase
Occurring in:
  1. Lysine-specific histone demethylase 1A

Structure domains

CATH CATH domains
1.10.287.80
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Helix Hairpins
Homology: ATP synthase, gamma subunit, helix hairpin domain
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2z3y contains 1 copy of CATH domain 1.10.287.80 (Helix Hairpins) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.
1.10.10.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Arc Repressor Mutant, subunit A
Homology: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2z3y contains 1 copy of CATH domain 1.10.10.10 (Arc Repressor Mutant, subunit A) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.
SCOP SCOP annotations
51913
Class: Alpha and beta proteins (a/b)
Fold: FAD/NAD(P)-binding domain
Superfamily: FAD/NAD(P)-binding domain
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2z3y contains 1 copy of SCOP domain 51913 (FAD-linked reductases, N-terminal domain) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.
54394
Class: Alpha and beta proteins (a+b)
Fold: FAD-linked reductases, C-terminal domain
Superfamily: FAD-linked reductases, C-terminal domain
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2z3y contains 1 copy of SCOP domain 54394 (L-aminoacid/polyamine oxidase) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.
140222
Class: All alpha proteins
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2z3y contains 1 copy of SCOP domain 140222 (SWIRM domain) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.

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