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Crystal structure of LSD1-CoREST in complex with a tranylcypromine derivative (MC2580, 14e)

Source organism: Homo sapiens
Biochemical function: enzyme binding
Biological process: negative regulation of DNA-templated transcription
Cellular component: DNA repair complex

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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)
PF00249
Domain description: Myb-like DNA-binding domain
Occurring in:
  1. REST corepressor 1
The deposited structure of PDB entry 2xas contains 2 copies of Pfam domain PF00249 (Myb-like DNA-binding domain) in REST corepressor 1. Showing 2 copies in chain B (some of the copies are out of the observed residue ranges!).

PF20878
Domain description: Helical region in REST corepressor
Occurring in:
  1. REST corepressor 1
The deposited structure of PDB entry 2xas contains 1 copy of Pfam domain PF20878 (Helical region in REST corepressor) in REST corepressor 1. Showing 1 copy in chain B.

PF01448
Domain description: ELM2 domain
Occurring in:
  1. REST corepressor 1
The deposited structure of PDB entry 2xas contains 1 copy of Pfam domain PF01448 (ELM2 domain) in REST corepressor 1. Showing 1 copy in chain B (this domain is out of the observed residue ranges!).

PF01593
Domain description: Flavin containing amine oxidoreductase
Occurring in:
  1. Lysine-specific histone demethylase 1A
The deposited structure of PDB entry 2xas 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 2xas contains 1 copy of Pfam domain PF04433 (SWIRM domain) in Lysine-specific histone demethylase 1A. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR001005
Domain description: SANT/Myb domain
Occurring in:
  1. REST corepressor 1
IPR000949
Domain description: ELM2 domain
Occurring in:
  1. REST corepressor 1
IPR036188
Domain description: FAD/NAD(P)-binding domain superfamily
Occurring in:
  1. Lysine-specific histone demethylase 1A
IPR009057
Domain description: Homeobox-like domain superfamily
Occurring in:
  1. Lysine-specific histone demethylase 1A
  2. REST corepressor 1
IPR017884
Domain description: SANT domain
Occurring in:
  1. REST corepressor 1
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
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
1.20.58.1880
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homology: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Occurring in:
  1. REST corepressor 1
The deposited structure of PDB entry 2xas contains 1 copy of CATH domain 1.20.58.1880 (Methane Monooxygenase Hydroxylase; Chain G, domain 1) in REST corepressor 1. Showing 1 copy in chain B.
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 2xas 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 2xas 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.

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