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Lysine-specific histone demethylase: Difference between revisions

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== Function ==
== Function ==
'''Lysine-specific histone demethylase 1 or 1A''' (LSD1) is a flavin-dependent oxidase that catalyzes the removal of methyl groups from mono- and dimethylated lysine 4 of histone H3.  LSD1 is a nuclear homolog of amine oxidase.  LSD contains a SWIRM domain which is a small a-helical domain which binds DNA.  It functions as histone demethylase and transcriptional corepressor.  LSD1 demethylation occurs via a reaction which produces formaldehyde.  LSD1 is a component of transcriptional co-repressor complex which also contains CoREST (co-repressor of element-1-silencing transcription factor)<ref>PMID:22339659</ref>.<br />
'''Lysine-specific histone demethylase 1 or 1A''' (LSD1) is a flavin-dependent oxidase that catalyzes the removal of methyl groups from mono- and dimethylated lysine 4 of histone H3.  LSD1 is a nuclear homolog of amine oxidase.  LSD contains a SWIRM domain which is a small a-helical domain which binds DNA.  It functions as histone demethylase and transcriptional corepressor.  LSD1 demethylation occurs via a reaction which produces formaldehyde.  LSD1 is a component of transcriptional co-repressor complex which also contains CoREST (co-repressor of element-1-silencing transcription factor)<ref>PMID:22339659</ref>.<br />
'''Lysine-specific histone demethylase 2 or 1B''' (LSD2) is a flavin-dependent oxidase that catalyzes the removal of methyl groups from mono- and dimethylated lysine 9 of histone H3.<br />
See also [[Lysine-specific demethylase 1 (LSD-1)]].<br />
'''Lysine-specific histone demethylase 5A or KDM5A''' is essential for the repression of astrocyte differentiation<ref>PMID:29212818</ref>.<br />
*'''Lysine-specific histone demethylase 2 or 1B''' (LSD2) is a flavin-dependent oxidase that catalyzes the removal of methyl groups from mono- and dimethylated lysine 9 of histone H3.<br />
'''Lysine-specific histone demethylase 5B or KDM5B or retinoblastoma-binding protein Rbbp2 homolog''' (LSD5B) is a JmjC domain containing histone demethylase and is an improtant component of DNA repair
*'''Lysine-specific histone demethylase 5A or KDM5A''' is essential for the repression of astrocyte differentiation<ref>PMID:29212818</ref>.<br />
*'''Lysine-specific histone demethylase 5B or KDM5B or retinoblastoma-binding protein Rbbp2 homolog''' (LSD5B) is a JmjC domain containing histone demethylase and is an improtant component of DNA repair


== Relevance ==
== Relevance ==
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</StructureSection>
</StructureSection>
==3D structures of lysine-specific histone demethylase==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
*lysine-specific histone demethylase 1A
**[[2com]], [[2l3d]] - hLSD1 SWIRM domain – human – NMR<br />
**[[5it3]], [[6e1f]] - hLSD1 SWIRM domain<br />
**[[2h94]], [[2dw4]], [[2z3y]], [[2z5u]], [[4fwe]], [[4fwj]], [[4gu1]] – hLSD1<br />
**[[2hko]] – hLSD1 (mutant)<br />
**[[2ejr]], [[3abt]], [[3abu]] – hLSD1 + tranylcypromine derivative<br />
**[[4gut]], [[4guu]] – hLSD1 + oxidoreductase<br />
**[[6nqu]] – hLSD1 + inhibitor<br />
**[[6nr5]] – hLSD1 + phenelzine sulfate<br />
*LSD1 complex with histone H3 peptide
**[[4fwf]] – hLSD1 + histone 3.1 peptide<br />
*LSD1 complex with CoREST
**[[2iw5]], [[2uxn]], [[2uxx]] - hLSD1 SWIRM + amine oxidase domains + CoREST SANT1 and SANT2 domains<br />
**[[2v1d]], [[5x60]], [[5h6r]], [[5h6q]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + histone H3 residues 2-22 (mutant)<br />
**[[2x0l]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + histone H3 residues 1-16<br />
**[[2xaf]], [[2xag]], [[2xah]], [[2xaj]], [[2xaq]], [[2xas]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + tranylcypromine derivative<br />
**[[2y48]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + zinc finger protein SNAIL N terminal<br />
**[[3zms]], [[3zmt]], [[3zmu]], [[3zmv]], [[3zmz]], [[3zn0]], [[3zn1]] - hLSD1 residues 123-852 + CoREST SANT1 and SANT2 domains + zinc finger protein IA-1 peptide <br />
**[[4bay]] - hLSD1 residues 192-876 + CoREST residues 308-440 <br />
**[[4kum]] - hLSD1 SWIRM + FAD domains + CoREST residues 289-485 <br />
**[[4czz]] - hLSD1 + CoREST <br />
**[[5l3b]], [[5l3c]], [[5l3d]],  - hLSD1 (mutant) + CoREST <br />
**[[4uv8]], [[4uv9]], [[4uva]], [[4uvb]], [[4uvc]] - hLSD1 + CoREST + irreversible inhibitor<br />
**[[5l3e]], [[5lbq]], [[5lgn]], [[5lgt]], [[5lgu]], [[5lhg]], [[5lhh]], [[5lhi]] - hLSD1 + CoREST + reversible inhibitor<br />
**[[5l3f]], [[5l3g]] - hLSD1 + CoREST + polmyxin peptide<br />
**[[4xbf]] - hLSD1 + CoREST + RNA<br />
**[[4uxn]], [[5yjb]] - hLSD1 + CoREST + pyrrolydine inhibitor<br />
*lysine-specific histone demethylase 1B
**[[4gu1]] – hLSD2<br />
**[[4gur]], [[4gus]], [[4hsu]] – hLSD2 + NPAC + histone 3.3 peptide <br />
**[[4gut]] – hLSD2 + NPAC  <br />
**[[4guu]] – hLSD2 + NPAC + tranylcypromine <br />
**[[4gu0]] – hLSD2 + histone 3.3 peptide <br />
**[[6r25]], [[6r1u]] – hLSD2 + NPAC + histones 3,4,2A,2B + DNA – Cryo EM <br />
*lysine-specific histone demethylase 5B or JARID1B or KDM5B.  Domains: zinc finger 1 306-360; PHD-type zinc finger 1487-1544; ARID 94-208; JmjC 26-101 + 374-772
**[[2ma5]] – hLSD5B zinc finger domain 3 - NMR<br />
**[[2mny]] – hLSD5B zinc finger domain 1 - NMR<br />
**[[2mnz]] – hLSD5B zinc finger domain 1 + histone 3 peptide - NMR<br />
**[[2eqy]] – hLSD5B ARID domain - NMR<br />
**[[5a3p]] – hLSD5B JmjC domain <br />
**[[5lwb]], [[5lw9]], [[5fun]], [[5fz0]], [[5fzk]], [[5fzl]], [[5fz9]], [[5fza]], [[5fzb]], [[5fzc]], [[5fyt]], [[5fyu]], [[5fyy]], [[5fyz]], [[5fz3]], [[5fz4]], [[5fz6]], [[5fz7]], [[5fpl]], [[5fpu]], [[5a3n]], [[5a3t]], [[5a3w]], [[6ein]], [[6eiu]], [[6eiy]], [[6ej0]], [[6ej1]], [[6ek6]], [[5fzm]], [[5fzi]], [[5fzg]], [[5fzf]], [[5fze]], [[5fzd]], [[5fz8]], [[5fyb]] – hLSD5B JmjC domain + inhibitor<br />
**[[5fzh]], [[5fz1]] – hLSD5B JmjC domain + ligand<br />
**[[5fup]], [[5fys]] – hLSD5B JmjC domain + oxoglutarate<br />
**[[5fyv]] – hLSD5B JmjC domain + oxaloacetate<br />
**[[5fy9]] – hLSD5B JmjC domain + pyruvate<br />
**[[5fy5]] – hLSD5B JmjC domain + fumarate<br />
**[[5fy4]] – hLSD5B JmjC domain + succinate<br />
**[[5fv3]], [[5a1f]] – hLSD5B JmjC domain + oxalyl glycine<br />
**[[6h4z]], [[6h50]], [[6h51]], [[6h52]] – hLSD5B JmjC domain + inhibitor<br />
*lysine-specific histone demethylase 2A or KDM2A 
**[[4bbq]] – hKDM2A residues 567-681<br />
**[[6c16]], [[6byh]] – hKDM2A residues 888-932 + SKP1 + polyubiquitin <br />
**[[4tn7]], [[4qxh]], [[4qxc]], [[4qxb]], [[4qx8]], [[4qx7]], [[4qwn]] – hKDM2A residues 36-364 + histone peptide <br />
*lysine-specific histone demethylase 2B or KDM2Bsee [[Jumanji domain-containing protein 3D structures]] 
*lysine-specific histone demethylase 4A or KDM4A see [[Jumanji domain-containing protein 3D structures]]
*lysine-specific histone demethylase 4D see [[Jumanji domain-containing protein 3D structures]] 
**[[6ete]], [[6fuk]], [[6ful]] – hKDM6A + inhibitor<br />
*lysine-specific histone demethylase 6A 
**[[6g8f]], [[6fuk]], [[6ful]] – hKDM6A + inhibitor<br />
*lysine-specific histone demethylase Ref6 see [[Jumanji domain-containing protein 3D structures]]


}}
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Jaime Prilusky, Joel L. Sussman
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