Jumonji domain-containing protein

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<StructureSection load='2p5b' size='450' 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) (PDB code [[2p5b]]).' scene='59/596434/Cv/1'>
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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'>
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SEE ALSO [[Lysine-specific histone demethylase]]
== Function ==
== Function ==
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*'''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 />
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*'''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 ==
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Jmjd2a uses <scene name='59/596434/Cv/2'>9 residues for interaction with the methylated peptide</scene> 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>.
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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.
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</StructureSection>
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<scene name='59/596434/Cv/10'>Zn coordination site</scene>.
==3D structures of jumonji domain-containing protein ==
==3D structures of jumonji domain-containing protein ==
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[[Jumonji domain-containing protein 3D structures]]
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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</StructureSection>
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*Jmjd2a (Lysine-specific demethylase 4A)
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**[[2gf7]], [[2qqr]], [[5d6w]], [[5d6x]] – hJmjd2a double TUDOR domain – human <br />
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**[[2gp3]] – hJmjd2a catalytic domain + Fe<br />
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**[[5fyc]] – hJmjd2a catalytic domain + Ni<br />
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*Jmjd2a binary complex with peptide
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**[[2gfa]], [[5d6y]] – hJmjd2a double TUDOR domain + peptide with trimethyllysine<br />
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**[[2qqs]] – hJmjd2a double TUDOR domain + histone H4 peptide with trimethyllysine<br />
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**[[2oq6]], [[2os2]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine <br />
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**[[2ot7]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with methyllysine <br />
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**[[2pxj]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with methyllysine <br />
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**[[2ox0]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with dimethyllysine <br />
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*Jmjd2a binary complex with other molecules
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**[[2oq7]] – hJmjd2a catalytic domain + Ni + oxalylglycine <br />
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**[[2vd7]], [[2wwj]], [[3njy]], [[3pdq]], [[3rvh]], [[4gd4]], [[4ai9]], [[4bis]] – hJmjd2a catalytic domain + Ni + inhibitor <br />
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**[[2gp5]] – hJmjd2a catalytic domain + Fe + α-ketoglutarate <br />
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**[[2ybk]] – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative<br />
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**[[4ura]], [[5fpv]] – hJmjd2a catalytic domain + Ni + inhibitor<br />
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**[[5anq]] – hJmjd2a catalytic domain + Fe + inhibitor<br />
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**[[5a7n]], [[5a7o]], [[5a7p]], [[5a7q]], [[5a7s]], [[5a7w]], [[5a80]] – hJmjd2a catalytic domain + Mn + inhibitor<br />
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**[[5f2s]], [[5f2w]], [[5f32]], [[5f37]], [[5f39]], [[5f3c]], [[5f3e]], [[5f3g]], [[5f3i]] – hJmjd2a catalytic domain + Zn + inhibitor<br />
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**[[5fy8]] – hJmjd2a catalytic domain + Ni + threo-isocitrate<br />
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**[[5fyi]] – hJmjd2a catalytic domain + Ni + pyruvate<br />
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**[[5fyh]] – hJmjd2a catalytic domain + Mn + fumarate<br />
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*Jmjd2a ternary complex
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**[[2q8c]], [[2ybp]], [[2ybs]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + α-ketoglutarate derivative<br />
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**[[2q8d]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + succinate <br />
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**[[2q8e]], [[2p5b]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine <br />
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**[[4v2v]], [[4v2w]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylglycine <br />
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**[[3u4s]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylcysteine <br />
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*Jmjd1b (Lysine-specific demethylase 3B)
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**[[4c8d]] – hJmj1b catalytic domain + Mn + oxalylglycine <br />
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*Jmjd2b (Lysine-specific demethylase 4B)
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**[[4lxl]] – hJmjd2b catalytic domain + Ni + histone H3 peptide with trimethyllysine <br />
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**[[4uc4]] – hJmjd2b tudor domain <br />
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*Jmjd2c (Lysine-specific demethylase 4C)
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**[[2xdp]] – hJmjd2c tudor domain <br />
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**[[2xml]], [[4xdo]] – hJmjd2c catalytic domain + Ni + oxalylglycine <br />
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**[[4xdp]] – hJmjd2c catalytic domain + Fe <br />
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**[[5fjh]], [[5fjk]] – hJmjd2c catalytic domain + Ni + inhibitor<br />
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*Jmjd2d (Lysine-specific demethylase 4D)
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**[[3dxu]] – hJmjd2d catalytic domain + Fe + oxalylglycine <br />
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**[[3dxt]] – hJmjd2d catalytic domain + Zn<br />
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**[[4hoo]] – hJmjd2d catalytic domain (mutant) + Ni<br />
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**[[4d6q]], [[5f5a]], [[5f5c]], [[5f5i]] – hJmjd2d catalytic domain + Ni + inhibitor<br />
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**[[5fp4]], [[5fp8]], [[5fp9]], [[5fpa]], [[5fpb]] – hJmjd2d catalytic domain + Fe + inhibitor<br />
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**[[4d6r]], [[4d6s]] – hJmjd2d catalytic domain + Ni + inhibitor + oxalylglycine <br />
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**[[4hon]] – hJmjd2d catalytic domain + Ni + histone H3 peptide with trimethyllysine + α-ketoglutarate <br />
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*Jmjd3 (Lysine-specific demethylase 6B)
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**[[2xxz]] – hJmjd3 catalytic domain + Ni <br />
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**[[2xue]] – hJmjd3 catalytic domain + Fe + α-ketoglutarate <br />
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**[[4ask]] – hJmjd3 catalytic and Zinc finger domains + Co + inhibitor <br />
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**[[4eyu]], [[4ez4]] – mJmjd3 C terminal + Ni + oxalylglycine - mouse <br />
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**[[4ezh]] – mJmjd3 C terminal + Ni + histone H3 peptide with trimethyllysine + oxalylglycine <br />
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*Jmjd5 (Lysine-specific demethylase 8)
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**[[3uyj]], [[4qu1]] – hJmjd5 catalytic domain + Ni + α-ketoglutarate <br />
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**[[4gjz]] – hJmjd5 catalytic domain + Co + α-ketoglutarate <br />
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**[[4aap]] – hJmjd5 catalytic domain + Zn + oxalylglycine <br/ > **[[4gjy]] – hJmjd5 catalytic domain + Co + oxalylglycine <br />
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**[[4gaz]] – hJmjd5 catalytic domain + Ni + oxalylglycine <br />
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*Jmjd6
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**[[3ld8]] – hJmjd6 catalytic domain + antibody + Fe <br />
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**[[3ldb]] – hJmjd6 catalytic domain + antibody + Fe + α-ketoglutarate <br />
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*Jmjd7
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**[[4qu2]] – hJmjd7 catalytic domain + Ni + α-ketoglutarate <br />
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}}
 
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

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).

Drag the structure with the mouse to rotate

References

  1. ↑ Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, Hagman J, Hansen K, Shi Y, Zhang G. Structural insights into histone demethylation by JMJD2 family members. Cell. 2006 May 19;125(4):691-702. Epub 2006 May 4. PMID:16677698 doi:http://dx.doi.org/10.1016/j.cell.2006.04.024
  2. ↑ Canovas S, Cibelli JB, Ross PJ. Jumonji domain-containing protein 3 regulates histone 3 lysine 27 methylation during bovine preimplantation development. Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2400-5. doi:, 10.1073/pnas.1119112109. Epub 2012 Jan 30. PMID:22308433 doi:http://dx.doi.org/10.1073/pnas.1119112109
  3. ↑ Lawrence P, Rai D, Conderino JS, Uddowla S, Rieder E. Role of Jumonji C-domain containing protein 6 (JMJD6) in infectivity of foot-and-mouth disease virus. Virology. 2016 Feb 18;492:38-52. doi: 10.1016/j.virol.2016.02.005. PMID:26896934 doi:http://dx.doi.org/10.1016/j.virol.2016.02.005
  4. ↑ Chen Z, Zang J, Kappler J, Hong X, Crawford F, Wang Q, Lan F, Jiang C, Whetstine J, Dai S, Hansen K, Shi Y, Zhang G. Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):10818-23. Epub 2007 Jun 13. PMID:17567753

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