Jumonji domain-containing protein
From Proteopedia
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<scene name='59/596434/Cv/10'>Zn coordination site</scene>. | <scene name='59/596434/Cv/10'>Zn coordination site</scene>. | ||
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| + | ==3D structures of jumonji domain-containing protein == | ||
| + | [[Jumonji domain-containing protein 3D structures]] | ||
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</StructureSection> | </StructureSection> | ||
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**[[2ox0]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with dimethyllysine <br /> | **[[2ox0]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with dimethyllysine <br /> | ||
**[[5ly2]], [[5ly1]] – hJmjd2a catalytic domain + Ni + peptide inhibitor <br /> | **[[5ly2]], [[5ly1]] – hJmjd2a catalytic domain + Ni + peptide inhibitor <br /> | ||
| - | **[[5fwe]] – hJmjd2a catalytic domain + Ni + Zn + oxalylglycine + peptide <br /> | + | **[[6hgt]] – hJmjd2a catalytic domain + Zn + oxalylglycine + histone peptide <br /> |
| + | **[[5fwe]], [[6h8p]] – hJmjd2a catalytic domain + Ni + Zn + oxalylglycine + histone peptide <br /> | ||
*Jmjd2a binary complex with other molecules | *Jmjd2a binary complex with other molecules | ||
**[[2oq7]] – hJmjd2a catalytic domain + Ni + oxalylglycine <br /> | **[[2oq7]] – hJmjd2a catalytic domain + Ni + oxalylglycine <br /> | ||
| - | **[[2vd7]], [[2wwj]], [[3njy]], [[3pdq]], [[3rvh]], [[4gd4]], [[4ai9]], [[4bis]] – hJmjd2a catalytic domain + Ni + inhibitor <br /> | + | **[[2vd7]], [[2wwj]], [[3njy]], [[3pdq]], [[3rvh]], [[4gd4]], [[4ai9]], [[4bis]], [[4ura]], [[5fpv]] – hJmjd2a catalytic domain + Ni + inhibitor <br /> |
**[[2gp5]] – hJmjd2a catalytic domain + Fe + α-ketoglutarate <br /> | **[[2gp5]] – hJmjd2a catalytic domain + Fe + α-ketoglutarate <br /> | ||
**[[2ybk]], [[5tvr]] – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative<br /> | **[[2ybk]], [[5tvr]] – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative<br /> | ||
| - | **[[4ura]], [[5fpv]] – hJmjd2a catalytic domain + Ni + inhibitor<br /> | ||
**[[5anq]] – hJmjd2a catalytic domain + Fe + inhibitor<br /> | **[[5anq]] – hJmjd2a catalytic domain + Fe + inhibitor<br /> | ||
**[[5a7n]], [[5a7o]], [[5a7p]], [[5a7q]], [[5a7s]], [[5a7w]], [[5a80]] – hJmjd2a catalytic domain + Mn + inhibitor<br /> | **[[5a7n]], [[5a7o]], [[5a7p]], [[5a7q]], [[5a7s]], [[5a7w]], [[5a80]] – hJmjd2a catalytic domain + Mn + inhibitor<br /> | ||
| - | **[[5f2s]], [[5f2w]], [[5f32]], [[5f37]], [[5f39]], [[5f3c]], [[5f3e]], [[5f3g]], [[5f3i]], [[6cg1]], [[6cg2]], [[5vmp]], [[5vgi]], [[5var]] | + | **[[5f2s]], [[5f2w]], [[5f32]], [[5f37]], [[5f39]], [[5f3c]], [[5f3e]], [[5f3g]], [[5f3i]], [[6cg1]], [[6cg2]], [[5vmp]], [[5vgi]], [[5var]], [[6h4o]], [[6h4p]], [[6h4q]], [[6h4r]], [[6h4s]], [[6h4t]], [[6h4u]], [[6h4v]], [[6h4w]], [[6h4x]], [[6h4y]], [[6h4z]] – hJmjd2a catalytic domain + Zn + inhibitor<br /> |
| + | **[[6g5w]], [[6g5x]] – hJmjd2a catalytic domain + Zn + Ni + inhibitor<br /> | ||
**[[5fy8]] – hJmjd2a catalytic domain + Ni + threo-isocitrate<br /> | **[[5fy8]] – hJmjd2a catalytic domain + Ni + threo-isocitrate<br /> | ||
**[[5fyi]] – hJmjd2a catalytic domain + Ni + pyruvate<br /> | **[[5fyi]] – hJmjd2a catalytic domain + Ni + pyruvate<br /> | ||
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*Jmjd1a (Lysine-specific demethylase 5A; KDM5A) | *Jmjd1a (Lysine-specific demethylase 5A; KDM5A) | ||
| - | **[[5v9p]], [[5v9t]], [[5iwf]], [[5iw0]], [[5ivy]], [[5ivv]], [[5ivj]], [[5ivf]], [[5ive]], [[5ivc]], [[5ivb]], [[5isl]], [[6bh5]], [[6bh4]], [[6bh3]], [[6bh2]], [[6bh1]], [[6bh0]], [[6bgz]], [[6bgy]], [[6bgx]], [[6bgw]], [[6bgv]], [[6bgu]] | + | **[[5v9p]], [[5v9t]], [[5iwf]], [[5iw0]], [[5ivy]], [[5ivv]], [[5ivj]], [[5ivf]], [[5ive]], [[5ivc]], [[5ivb]], [[5isl]], [[6bh5]], [[6bh4]], [[6bh3]], [[6bh2]], [[6bh1]], [[6bh0]], [[6bgz]], [[6bgy]], [[6bgx]], [[6bgw]], [[6bgv]], [[6bgu]], [[6dq4]], [[6dq5]], [[6dq6]], [[6dq7]], [[6dq8]], [[6dq9]], [[6dqa]], [[6dqb]], [[6dqc]], [[6dqd]], [[6dqe]], [[6dqf]] – hJmj1a + inhibitor <br /> |
**[[5k4l]], [[5ceh]] – hJmj1a + inhibitor + peptide<br /> | **[[5k4l]], [[5ceh]] – hJmj1a + inhibitor + peptide<br /> | ||
**[[5c11]] – hJmj1a PHD finger domain + H3 peptide<br /> | **[[5c11]] – hJmj1a PHD finger domain + H3 peptide<br /> | ||
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**[[4qxc]] – mJmj1a residues 36-364 + Ni + oxalylglycine + H3 peptide <br /> | **[[4qxc]] – mJmj1a residues 36-364 + Ni + oxalylglycine + H3 peptide <br /> | ||
**[[4qx8]], [[4qx7]], [[4qwn]] – mJmj1a residues 36-364 + Ni + oxoglutarate + H3 peptide <br /> | **[[4qx8]], [[4qx7]], [[4qwn]] – mJmj1a residues 36-364 + Ni + oxoglutarate + H3 peptide <br /> | ||
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| + | * Lysine-specific demethylase 5B; KDM5B | ||
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| + | **[[6h50]], [[6h51]], [[6h52]], [[6ein]], [[6eiu]], [[6eiy]], [[6ej0]], [[6ej1]], [[6ek6]] – hLSD5B Jmj domain + inhibitor + Zn + Mn<br /> | ||
* Lysine-specific demethylase 5C; KDM5C; JARID1C | * Lysine-specific demethylase 5C; KDM5C; JARID1C | ||
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**[[2yqe]] – hLSD5D ARID domain - NMR<br /> | **[[2yqe]] – hLSD5D ARID domain - NMR<br /> | ||
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| + | * Lysine-specific demethylase REF6 or Jmjd12 | ||
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| + | **[[6jnl]], [[6jnm]], [[6jnn]] – AtREF6 + DNA + AMP derivative – ''Arabidopsis thaliana''<br /> | ||
| + | **[[6a58]], [[6a59]] – AtREF6 Ig g-1 chain + Zn<br /> | ||
| + | **[[6a57]] – AtREF6 + DNA + Zn<br /> | ||
*Jmjd1b (Lysine-specific demethylase 2B; KDM2B) | *Jmjd1b (Lysine-specific demethylase 2B; KDM2B) | ||
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**[[5fup]] – hJmj1b catalytic domain + Mn + Zn + oxoglutatate <br /> | **[[5fup]] – hJmj1b catalytic domain + Mn + Zn + oxoglutatate <br /> | ||
**[[5lwb]], [[5lw9]], [[5fzm]], [[5fzl]], [[5fzk]], [[5fzi]], [[5fzh]], [[5fzg]], [[5fzf]], [[5fze]], [[5fzd]], [[5fzc]], [[5fzb]], [[5fza]], [[5fz9]], [[5fz8]], [[5fz7]], [[5fz6]], [[5fz4]], [[5fz3]], [[5fz1]], [[5fz0]], [[5fyz]], [[5fyy]], [[5fyv]], [[5fyu]], [[5fyt]], [[5fyb]], [[5fy9]], [[5fy5]], [[5fy4]], [[5fun]], [[5fpu]], [[5fpl]], [[5a3w]], [[5a3t]], [[5a3p]], [[5a3n]] – hJmj1b catalytic domain + Mn + Zn + inhibitor <br /> | **[[5lwb]], [[5lw9]], [[5fzm]], [[5fzl]], [[5fzk]], [[5fzi]], [[5fzh]], [[5fzg]], [[5fzf]], [[5fze]], [[5fzd]], [[5fzc]], [[5fzb]], [[5fza]], [[5fz9]], [[5fz8]], [[5fz7]], [[5fz6]], [[5fz4]], [[5fz3]], [[5fz1]], [[5fz0]], [[5fyz]], [[5fyy]], [[5fyv]], [[5fyu]], [[5fyt]], [[5fyb]], [[5fy9]], [[5fy5]], [[5fy4]], [[5fun]], [[5fpu]], [[5fpl]], [[5a3w]], [[5a3t]], [[5a3p]], [[5a3n]] – hJmj1b catalytic domain + Mn + Zn + inhibitor <br /> | ||
| + | **[[6bva]] – hJmj1b + S-phase kinase-associated protein + polyubiquitin <br /> | ||
**[[5jh5]] – hJmj1b + S-phase kinase-associated protein + polycomb protein + BCOR-like protein <br /> | **[[5jh5]] – hJmj1b + S-phase kinase-associated protein + polycomb protein + BCOR-like protein <br /> | ||
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**[[4hoo]] – hJmjd2d catalytic domain (mutant) + Ni<br /> | **[[4hoo]] – hJmjd2d catalytic domain (mutant) + Ni<br /> | ||
**[[4d6q]], [[5f5a]], [[5f5c]], [[5f5i]] – hJmjd2d catalytic domain + Ni + inhibitor<br /> | **[[4d6q]], [[5f5a]], [[5f5c]], [[5f5i]] – hJmjd2d catalytic domain + Ni + inhibitor<br /> | ||
| + | **[[6ete]], [[6etg]], [[6ets]], [[6ett]], [[6etu]], [[6etv]], [[6etw]] – hJmjd2d catalytic domain + Ni + Zn + inhibitor<br /> | ||
**[[5fp4]], [[5fp8]], [[5fp9]], [[5fpa]], [[5fpb]], [[5fp7]] – hJmjd2d catalytic domain + Fe + inhibitor<br /> | **[[5fp4]], [[5fp8]], [[5fp9]], [[5fpa]], [[5fpb]], [[5fp7]] – hJmjd2d catalytic domain + Fe + inhibitor<br /> | ||
**[[4d6r]], [[4d6s]] – hJmjd2d catalytic domain + Ni + inhibitor + oxalylglycine <br /> | **[[4d6r]], [[4d6s]] – hJmjd2d catalytic domain + Ni + inhibitor + oxalylglycine <br /> | ||
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**[[2xxz]] – hJmjd3 catalytic domain + Ni <br /> | **[[2xxz]] – hJmjd3 catalytic domain + Ni <br /> | ||
**[[2xue]] – hJmjd3 catalytic domain + Fe + α-ketoglutarate <br /> | **[[2xue]] – hJmjd3 catalytic domain + Fe + α-ketoglutarate <br /> | ||
| + | **[[6f6d]], [[5oy3]] – hJmjd3 catalytic domain + Fe + Zn + α-ketoglutarate + histone peptide<br /> | ||
**[[4ask]] – hJmjd3 catalytic and Zinc finger domains + Co + inhibitor <br /> | **[[4ask]] – hJmjd3 catalytic and Zinc finger domains + Co + inhibitor <br /> | ||
**[[4eyu]], [[4ez4]] – mJmjd3 C terminal + Ni + oxalylglycine - mouse <br /> | **[[4eyu]], [[4ez4]] – mJmjd3 C terminal + Ni + oxalylglycine - mouse <br /> | ||
Revision as of 08:44, 8 September 2019
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3D structures of jumonji domain-containing protein
Updated on 08-September-2019
5pka, 5pk9, 5pk8, 5pk7, 5pk6, 5pk5, 5pk4, 5pk3, 5pk2, 5pk1, 5pk0, 5plj, 5pli, 5plh, 5plg – hJmjd2d catalytic domain + Zn
References
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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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