Jumonji domain-containing protein: Difference between revisions

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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+<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'>
-<StructureSection load='2p5b' size='340' side='right' caption='Structure of human Jumonji domain-containing protein 2A catalytic domain complex with Fe+2 ion and histone H3 peptide with trimethyllysine (PDB code [[2p5b]]).' scene=''>
+SEE ALSO [[Lysine-specific histone demethylase]]
 == Function ==
+*'''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 2A''' (Jmjd2a) catalyzes the demethylation of trimethylated histone at lysine residues 9 and 36 producing the dimethylated form.  Jmjd2a domains contain: N-terminal, catalytic core (residues 1-350), 2 TUDOR domains (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.
+*'''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 5''' (Jmjd5) or '''KDM8''' and '''Jumonji domain-containing protein 6''' (Jmjd6) function as histone demethylase and as a protein hydroxylase.<br />
 == Disease ==
+Jmjd6 serves as a receptor allowing the foot-and-mouth virus to infect cells<ref>PMID:26896934</ref>.
-== Relevance ==
 == Structural highlights ==
+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.
-==3D structures of jumonji domain-containing protein 2A==
+<scene name='59/596434/Cv/10'>Zn coordination site</scene>.
-Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-[[2gf7]], [[2qqr]] – hJmjd2a double TUDOR domain – human <br />
-[[2gp3]] – hJmjd2a catalytic domain + Fe<br />
-===Jmjd2a binary complex with peptide===
-[[2gfa]] – 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 />
-[[2p5b]] – hJmjd2a catalytic domain + Fe + 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 />
-===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 />
-[[2q8c]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine <br />
-[[2q8c]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylcysteine <br />
+==3D structures of jumonji domain-containing protein ==
+[[Jumonji domain-containing protein 3D structures]]
+</StructureSection>
 == References ==