Jumonji domain-containing protein: Difference between revisions

← Older edit Newer edit →

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

@@ Line 1: / Line 1: @@
-<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='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=''>
 == 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''' 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 />
-'''Jumonji domain-containing protein 5''' (Jmjd5) or '''KDM8''' and '''Jumonji domain-containing protein 6''' (Jmjd6) function as histone demethylase and as a protein hydroxylase.<br />
+*'''Jumonji domain-containing protein 5''' (Jmjd5) or '''KDM8''' and '''Jumonji domain-containing protein 6''' (Jmjd6) function as histone demethylase and as a protein hydroxylase.<br />
 == Disease ==
@@ Line 14: / Line 14: @@
 </StructureSection>
-==3D structures of jumonji domain-containing protein 2A==
+==3D structures of jumonji domain-containing protein ==
 Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
 {{#tree:id=OrganizedByTopic|openlevels=0|
-*Jmjd2a
+*Jmjd2a (Lysine-specific demethylase 4A)
-**[[2gf7]], [[2qqr]] – hJmjd2a double TUDOR domain – human <br />
+**[[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]] – hJmjd2a double TUDOR domain + peptide with trimethyllysine<br />
+**[[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 />
@@ Line 39: / Line 40: @@
 **[[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
@@ Line 44: / Line 52: @@
 **[[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 />
-**[[2q8c]], [[2p5b]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine <br />
+**[[2q8e]], [[2p5b]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine <br />
-**[[2q8c]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylcysteine <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/>
 [[Category:Topic Page]]