Entry
Name
[histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase;
KDM1 (gene name);
LSD1 (gene name);
lysine-specific histone demethylase 1
Class
Oxidoreductases;
Acting on paired donors, with incorporation or reduction of molecular oxygen;
Miscellaneous
BRITE hierarchy
Sysname
[histone H3]-N6,N6-dimethyl-L-lysine4:acceptor oxidoreductase (demethylating)
Reaction(IUBMB)
a [histone H3]-N6,N6-dimethyl-L-lysine4 + 2 acceptor + 2 H2O = a [histone H3]-L-lysine4 + 2 formaldehyde + 2 reduced acceptor (overall reaction) [RN:
R12462 ];
(1a) a [histone H3]-N6,N6-dimethyl-L-lysine4 + acceptor + H2O = a [histone H3]-N6-methyl-L-lysine4 + formaldehyde + reduced acceptor [RN:
R12463 ];
(1b) a [histone H3]-N6-methyl-L-lysine4 + acceptor + H2O = a [histone H3]-L-lysine4 + formaldehyde + reduced acceptor [RN:
R12464 ]
Reaction(KEGG)
Substrate
[histone H3]-N6,N6-dimethyl-L-lysine4;
acceptor [CPD:
C00028 ];
H2O [CPD:
C00001 ];
[histone H3]-N6-methyl-L-lysine4
Product
[histone H3]-L-lysine4;
formaldehyde [CPD:
C00067 ];
reduced acceptor [CPD:
C00030 ];
[histone H3]-N6-methyl-L-lysine4
Comment
The enzyme specifically removes methyl groups from mono- and dimethylated lysine4 of histone 3. During the reaction the substrate is oxidized by the FAD cofactor of the enzyme to generate the corresponding imine, which is subsequently hydrolysed in the form of formaldehyde.The enzyme is similar to flavin amine oxidases, and differs from all other known histone lysine demethylases, which are iron(II)- and 2-oxoglutarate-dependent dioxygenases. The physiological electron acceptor is not known with certainty. In vitro the enzyme can use oxygen, which is reduced to hydrogen peroxide, but generation of hydrogen peroxide in the chromatin environment is unlikely as it will result in oxidative damage of DNA.
History
EC 1.14.99.66 created 2019
Orthology
K11450 [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase
Genes
CJC : 100406478(KDM1A) 103787766
MBEZ : 129538204(KDM1A) 129559913
SHAB : 115615991 115616143(KDM1A)
XLA : 100127344(kdm1a.S) 108708259(kdm1a.L)
SANH : 107694865 107697707
CAUA : 113098446 113117536
CGIB : 127933332 127976370
MASI : 127411423 127455097
SASA : 106562352 106610674
STRU : 115162572 115172875
OMY : 110498149(kdm1a) 110505285
SALP : 111968924 112068085
SNH : 120023537(kdm1a) 120060168
CCLU : 121538976 121545121
ARUT : 117413319 117414103 117962911
CMK : 103179609(kdm1a) 121849774
DME : Dmel_CG17149(Su(var)3-3)
DSI : Dsimw501_GD14861(Dsim_GD14861)
ASTE : 118505889 118516469
HAW : 110370308(Su(var)3-3)
CCRN : 123296727 123301095
CSEC : 111864370 111865515
BROR : 134541268 134541884
RSAN : 119371688 119377057
DPTE : 113789474 113795938
PMEO : 129587433 129587466
MMER : 123563686 128549072
SHX : MS3_00009234(KDM1A_1)
DOSA : Os08t0143400-01(Os08g0143400)
TAES : 123147418 123157372 123165349
PVIR : 120678932 120711365
» show all
Taxonomy
Reference
Authors
Forneris F, Binda C, Vanoni MA, Mattevi A, Battaglioli E
Title
Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process.
Journal
Sequence
Reference
Authors
Forneris F, Battaglioli E, Mattevi A, Binda C
Title
New roles of flavoproteins in molecular cell biology: histone demethylase LSD1 and chromatin.
Journal
Sequence
Other DBs