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Jumonji domain-containing protein: Difference between revisions

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<StructureSection load='2p5b' size='340' side='right' caption='Structure of human Jumonji domain-containing protein 2a catalytic domain complex with oxalylglycine, Fe+2 ion, Zn+2 ion (grey) and histone H3 peptide with trimethyllysine (aqua and wheat) (PDB code [[2p5b]]).' scene=''>
<StructureSection load='' size='350' side='right' caption='Structure of human Jumonji domain-containing protein 2a catalytic domain complex with oxalylglycine, Fe+2 ion (orange), Zn+2 ion (grey) and histone H3 peptide (aqua) with trimethyllysine (magenta) (PDB code [[2p5b]]).' scene='59/596434/Cv/1'>
 
SEE ALSO [[Lysine-specific histone demethylase]]
== Function ==
== Function ==
*'''Jumonji domain-containing protein 2a''' (Jmjd2a) or '''KDM4A''' catalyzes the demethylation of trimethylated histone H3 at lysine residues 9 and 36 producing the dimethylated form.  Jmjd2a domains contain: N-terminal, catalytic core (residues 1-350), 2 TUDOR domains which recognize dimethylated Arg (residues 895-1011) , 2 PHD-type zinc fingers and C-terminal domain.  Jmjd2a is Fe+2 and α-ketoglutarate dependent.  Methylation of histones in the chromatin  is involved in regulation of gene activity, chromatin structure and epigenetic memory<ref>PMID:16677698</ref>.<br />
*'''Jumonji domain-containing protein 2a''' (Jmjd2a) or '''KDM4A''' or '''Lysine-specific demethylase''' catalyzes the demethylation of trimethylated histone H3 at lysine residues 9 and 36 producing the dimethylated form.  Jmjd2a domains contain: N-terminal, catalytic core (residues 1-350), 2 TUDOR domains which recognize dimethylated Arg (residues 895-1011) , 2 PHD-type zinc fingers and C-terminal domain.  Jmjd2a is Fe+2 and α-ketoglutarate dependent.  Methylation of histones in the chromatin  is involved in regulation of gene activity, chromatin structure and epigenetic memory<ref>PMID:16677698</ref>.<br />
*'''Jumonji domain-containing protein 2b''' (Jmjd2b) or '''KDM4B''' and '''Jumonji domain-containing protein 2d''' (Jmjd2d) or '''KDM4D''' catalyze the demethylation of trimethylated histone H3 at lysine residues 9 producing the dimethylated form. <br />
*'''Jumonji domain-containing protein 2b''' (Jmjd2b) or '''KDM4B''' and '''Jumonji domain-containing protein 2d''' (Jmjd2d) or '''KDM4D''' catalyze the demethylation of trimethylated histone H3 at lysine residues 9 producing the dimethylated form. <br />
*'''Jumonji domain-containing protein 3''' (Jmjd3) or '''KDM6B''' and '''Jumonji domain-containing protein 2d''' (Jmjd2d) or '''KDM4D''' catalyze the demethylation of trimethylated histone H3 at lysine residues 27 producing the dimethylated form<ref>PMID:22308433</ref>. <br />
*'''Jumonji domain-containing protein 3''' (Jmjd3) or '''KDM6B''' and '''Jumonji domain-containing protein 2d''' (Jmjd2d) or '''KDM4D''' catalyze the demethylation of trimethylated histone H3 at lysine residues 27 producing the dimethylated form<ref>PMID:22308433</ref>. <br />
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== Structural highlights ==
== Structural highlights ==
Jmjd2a uses 9 residues for interaction with the methylated peptide and 4 residues are involved with binding to the peptide's trimethyllysine moiety. An O2 molecule is recruited into the catalytic center<ref>PMID:17567753</ref>.
Jmjd2a uses <scene name='59/596434/Cv/7'>9 residues for interaction with the methylated peptide</scene> and <scene name='59/596434/Cv/8'>4 residues are involved with binding to the peptide's trimethyllysine moiety</scene>. An <scene name='59/596434/Cv/9'>O2 molecules are recruited into the catalytic center</scene><ref>PMID:17567753</ref>. Water molecules shown as red spheres.
</StructureSection>
 
<scene name='59/596434/Cv/10'>Zn coordination site</scene>.


==3D structures of jumonji domain-containing protein ==
==3D structures of jumonji domain-containing protein ==
[[Jumonji domain-containing protein 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>
{{#tree:id=OrganizedByTopic|openlevels=0|
 
*Jmjd2a (Lysine-specific demethylase 4A)
 
**[[2gf7]], [[2qqr]], [[5d6w]], [[5d6x]] – hJmjd2a double TUDOR domain – human <br />
**[[2gp3]] – hJmjd2a catalytic domain + Fe<br />
**[[5fyc]] – hJmjd2a catalytic domain + Ni<br />
 
*Jmjd2a binary complex with peptide
 
**[[2gfa]], [[5d6y]] – hJmjd2a double TUDOR domain + peptide with trimethyllysine<br />
**[[2qqs]] – hJmjd2a double TUDOR domain + histone H4 peptide with trimethyllysine<br />
**[[2oq6]], [[2os2]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine <br />
**[[2ot7]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with methyllysine <br />
**[[2pxj]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with methyllysine <br />
**[[2ox0]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with dimethyllysine <br />
 
*Jmjd2a binary complex with other molecules
 
**[[2oq7]] – hJmjd2a catalytic domain + Ni + oxalylglycine <br />
**[[2vd7]], [[2wwj]], [[3njy]], [[3pdq]], [[3rvh]], [[4gd4]], [[4ai9]], [[4bis]] – hJmjd2a catalytic domain + Ni + inhibitor <br />
**[[2gp5]] – hJmjd2a catalytic domain + Fe + α-ketoglutarate <br />
**[[2ybk]] – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative<br />
**[[4ura]], [[5fpv]] – hJmjd2a catalytic domain + Ni + inhibitor<br />
**[[5anq]] – hJmjd2a catalytic domain + Fe + inhibitor<br />
**[[5a7n]], [[5a7o]], [[5a7p]], [[5a7q]], [[5a7s]], [[5a7w]], [[5a80]] – hJmjd2a catalytic domain + Mn + inhibitor<br />
**[[5f2s]], [[5f2w]], [[5f32]], [[5f37]], [[5f39]], [[5f3c]], [[5f3e]], [[5f3g]], [[5f3i]]  – hJmjd2a catalytic domain + Zn + inhibitor<br />
**[[5fy8]]  – hJmjd2a catalytic domain + Ni + threo-isocitrate<br />
**[[5fyi]]  – hJmjd2a catalytic domain + Ni + pyruvate<br />
**[[5fyh]]  – hJmjd2a catalytic domain + Mn + fumarate<br />
 
*Jmjd2a ternary complex
 
**[[2q8c]], [[2ybp]], [[2ybs]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + α-ketoglutarate derivative<br />
**[[2q8d]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + succinate <br />
**[[2q8e]], [[2p5b]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine <br />
**[[4v2v]], [[4v2w]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylglycine <br />
**[[3u4s]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylcysteine <br />
 
*Jmjd1b (Lysine-specific demethylase 3B)
 
**[[4c8d]] – hJmj1b catalytic domain + Mn + oxalylglycine <br />
 
*Jmjd2b (Lysine-specific demethylase 4B)
 
**[[4lxl]] – hJmjd2b catalytic domain + Ni + histone H3 peptide with trimethyllysine <br />
**[[4uc4]] – hJmjd2b tudor domain  <br />
 
*Jmjd2c (Lysine-specific demethylase 4C)
 
**[[2xdp]] – hJmjd2c tudor domain  <br />
**[[2xml]], [[4xdo]] – hJmjd2c catalytic domain + Ni + oxalylglycine <br />
**[[4xdp]] – hJmjd2c catalytic domain + Fe <br />
**[[5fjh]], [[5fjk]] – hJmjd2c catalytic domain + Ni + inhibitor<br />
 
*Jmjd2d (Lysine-specific demethylase 4D)
 
**[[3dxu]] – hJmjd2d catalytic domain + Fe + oxalylglycine <br />
**[[3dxt]] – hJmjd2d catalytic domain + Zn<br />
**[[4hoo]] – hJmjd2d catalytic domain (mutant) + Ni<br />
**[[4d6q]], [[5f5a]], [[5f5c]], [[5f5i]] – hJmjd2d catalytic domain + Ni + inhibitor<br />
**[[5fp4]], [[5fp8]], [[5fp9]], [[5fpa]], [[5fpb]] – hJmjd2d catalytic domain + Fe + inhibitor<br />
**[[4d6r]], [[4d6s]] – hJmjd2d catalytic domain + Ni + inhibitor + oxalylglycine <br />
**[[4hon]] – hJmjd2d catalytic domain + Ni + histone H3 peptide with trimethyllysine + α-ketoglutarate <br />
 
*Jmjd3 (Lysine-specific demethylase 6B)
 
**[[2xxz]] – hJmjd3 catalytic domain + Ni <br />
**[[2xue]] – hJmjd3 catalytic domain + Fe + α-ketoglutarate <br />
**[[4ask]] – hJmjd3 catalytic and Zinc finger domains + Co + inhibitor <br />
**[[4eyu]], [[4ez4]] – mJmjd3 C terminal + Ni + oxalylglycine - mouse <br />
**[[4ezh]] – mJmjd3 C terminal + Ni + histone H3 peptide with trimethyllysine + oxalylglycine <br />
 
*Jmjd5 (Lysine-specific demethylase 8)
 
**[[3uyj]], [[4qu1]] – hJmjd5 catalytic domain + Ni + α-ketoglutarate <br />
**[[4gjz]] – hJmjd5 catalytic domain + Co + α-ketoglutarate <br />
**[[4aap]] – hJmjd5 catalytic domain + Zn + oxalylglycine <br/ > **[[4gjy]] – hJmjd5 catalytic domain + Co + oxalylglycine <br />
**[[4gaz]] – hJmjd5 catalytic domain + Ni + oxalylglycine <br />
 
*Jmjd6
 
**[[3ld8]] – hJmjd6 catalytic domain + antibody + Fe <br />
**[[3ldb]] – hJmjd6 catalytic domain + antibody + Fe + α-ketoglutarate <br />
 
*Jmjd7
 
**[[4qu2]] – hJmjd7 catalytic domain + Ni + α-ketoglutarate <br />


}}
== 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, Jaime Prilusky, Alexander Berchansky, Joel L. Sussman
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