Jumonji domain-containing protein: Difference between revisions

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</StructureSection>
</StructureSection>


==3D structures of jumonji domain-containing protein ==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#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]], [[5tvs]] – 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 />
**[[5ly2]], [[5ly1]] – hJmjd2a catalytic domain + Ni + peptide inhibitor <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
**[[2oq7]] – hJmjd2a catalytic domain + Ni + oxalylglycine <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 />
**[[2ybk]], [[5tvr]] – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative<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]], [[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 />
**[[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 />
*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]], [[6dq4]], [[6dq5]], [[6dq6]], [[6dq7]], [[6dq8]], [[6dq9]], [[6dqa]], [[6dqb]], [[6dqc]], [[6dqd]], [[6dqe]], [[6dqf]] – hJmj1a + inhibitor <br />
**[[5k4l]], [[5ceh]] – hJmj1a + inhibitor + peptide<br />
**[[5c11]] – hJmj1a PHD finger domain +  H3 peptide<br />
**[[5e6h]] – hJmj1a residues 1-87, 348-588 + Mn + oxoglutarate<br />
**[[4tn7]] – mJmj1a residues 36-364 + NO + Fe + H3 peptide - mouse <br />
**[[4qxh]], [[4qxb]] – mJmj1a residues 36-364 + Ni + oxalylglycine  <br />
**[[4qxc]] – mJmj1a residues 36-364 + Ni + oxalylglycine + H3 peptide <br />
**[[4qx8]], [[4qx7]], [[4qwn]] – mJmj1a residues 36-364 + Ni + oxoglutarate + H3 peptide <br />
* Lysine-specific demethylase 5B; KDM5B
**[[6h50]], [[6h51]], [[6h52]], [[6ein]], [[6eiu]], [[6eiy]], [[6ej0]], [[6ej1]], [[6ek6]] – hLSD5B Jmj domain + inhibitor + Zn + Mn<br />
* Lysine-specific demethylase 5C; KDM5C; JARID1C
**[[5fwj]] – hLSD5C Jmj domain + inhibitor<br />
**[[2jrz]] – hLSD5C Bright/ARID domain - NMR<br />
*lysine-specific demethylase 5D or JARID1D
**[[2yqe]] – hLSD5D ARID domain - NMR<br />
* Lysine-specific demethylase REF6 or Jmjd12
**[[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)
**[[4o64]] – hJmj1b zinc finger domain + Zn <br />
**[[4c8d]], [[5fv3]] – hJmj1b catalytic domain + Mn + oxalylglycine <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 />
**[[6bva]] – hJmj1b + S-phase kinase-associated protein + polyubiquitin <br />
**[[5jh5]] – hJmj1b + S-phase kinase-associated protein + polycomb protein + BCOR-like protein <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 />
**[[5kr7]] – hJmjd2c catalytic domain + Fe + Zn + inhibitor<br />
*Jmjd2d (Lysine-specific demethylase 4D)
**[[3dxu]] – hJmjd2d catalytic domain + Fe + oxalylglycine <br />
**[[3dxt]], [[5pnw]], [[5pnv]], [[5pnu]], [[5pns]], [[5pnr]], [[5pnq]], [[5pnp]], [[5pno]], [[5pnn]], [[5pnm]], [[5pnl]], [[5pnk]], [[5pnj]], [[5pni]], [[5pnh]], [[5png]], [[5pnf]], [[5pne]], [[5pnd]], [[5pnc]], [[5pnb]], [[5pna]], [[5pn9]], [[5pn8]], [[5pn7]], [[5pn6]], [[5pn5]], [[5pn4]], [[5pn3]], [[5pn2]], [[5pn1]], [[5pn0]], [[5pmz]], [[5pmy]], [[5pmx]], [[5pmw]], [[5pmv]], [[5pmu]], [[5pmt]], [[5pms]], [[5pmr]], [[5pmq]], [[5pmp]], [[5pmo]], [[5pmn]], [[5pmm]], [[5pml]], [[5pmk]], [[5pmj]], [[5pmi]], [[5pmh]], [[5pmj]], [[5pmi]], [[5pmh]], [[5pmg]], [[5pmf]], [[5pme]], [[5pmd]], [[5pmc]], [[5pmb]], [[5pma]], [[5pm9]], [[5pm8]], [[5pm7]], [[5pm6]], [[5pm5]], [[5pm4]], [[5pm3]], [[5pm2]], [[5pm1]], [[5pm0]], [[5plz]], [[5ply]], [[5plx]], [[5plw]], [[5plv]], [[5plu]], [[5plt]], [[5pls]], [[5plr]], [[5plq]], [[5plp]], [[5plo]], [[5pln]], [[5plm]], [[5pll]], [[5plk]], [[5plj]], [[5pli]], [[5plh]], [[5plg]], [[5plf]], [[5ple]], [[5pld]], [[5plc]], [[5plb]], [[5pla]], [[5pl9]], [[5pl8]], [[5pl7]], [[5pl6]], [[5pl5]], [[5pl4]], [[5pl3]], [[5pl2]], [[5pl1]], [[5pl0]], [[5pkz]], [[5pky]], [[5pkx]], [[5pkw]], [[5pkv]], [[5pku]], [[5pkt]], [[5pks]], [[5pkr]], [[5pkq]], [[5pkp]], [[5pko]], [[5pkn]], [[5pkm]], [[5pkl]], [[5pkk]], [[5pkj]], [[5pki]], [[5pkh]], [[5pkg]], [[5pkf]], [[5pke]], [[5pkd]], [[5pkc]], [[5pkb]], [[5pka]], [[5pk9]], [[5pk8]], [[5pk7]], [[5pk6]], [[5pk5]], [[5pk4]], [[5pk3]], [[5pk2]], [[5pk1]], [[5pk0]], [[5pjz]], [[5pjy]], [[5pjx]], [[5pjw]], [[5pjv]], [[5pju]], [[5pjt]], [[5pjs]], [[5pjr]], [[5pjq]], [[5pjp]], [[5pjo]], [[5pjn]], [[5pjm]], [[5pjl]], [[5pjk]], [[5pjj]], [[5pji]], [[5pjh]], [[5pjg]], [[5pjf]], [[5pje]], [[5pjd]], [[5pjc]], [[5pjb]], [[5pja]], [[5pj9]], [[5pj8]], [[5pj7]], [[5pj6]], [[5pj5]], [[5pj4]], [[5pj3]], [[5pj2]], [[5pj1]], [[5pj0]], [[5piz]], [[5piy]], [[5pix]], [[5piw]], [[5piv]], [[5piu]], [[5pit]], [[5pis]], [[5pir]], [[5piq]], [[5pip]], [[5pio]], [[5pin]], [[5pim]], [[5pil]], [[5pik]], [[5pij]], [[5pii]], [[5pih]], [[5pig]], [[5pif]], [[5pie]], [[5pid]], [[5pic]], [[5pib]], [[5pia]], [[5pi9]], [[5pi8]], [[5pi7]], [[5pi6]], [[5pi5]], [[5pi4]], [[5pi3]], [[5pi2]], [[5pi1]], [[5pi0]], [[5phz]], [[5phy]], [[5phx]], [[5phw]], [[5phv]], [[5phu]], [[5pht]], [[5phs]], [[5phr]], [[5phq]], [[5php]], [[5pho]], [[5phn]], [[5phm]], [[5phl]], [[5phk]], [[5phj]], [[5phi]], [[5phh]], [[5phg]], [[5phf]], [[5phe]], [[5phd]], [[5phc]], [[5phb]], [[5pha]], [[5ph9]], [[5ph8]], [[5ph7]], [[5ph6]], [[5ph5]], [[5ph4]], [[5ph3]], [[5ph2]], [[5ph1]], [[5ph0]],
[[5pka]], [[5pk9]], [[5pk8]], [[5pk7]], [[5pk6]], [[5pk5]], [[5pk4]], [[5pk3]], [[5pk2]], [[5pk1]], [[5pk0]], [[5plj]], [[5pli]], [[5plh]], [[5plg]] – hJmjd2d catalytic domain + Zn<br />
**[[4hoo]] – hJmjd2d catalytic domain (mutant) + Ni<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 />
**[[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 />
**[[6f6d]], [[5oy3]] – hJmjd3 catalytic domain + Fe + Zn + α-ketoglutarate + histone peptide<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 />
**[[5fp3]] – hJmjd3 catalytic domain + inhibitor<br />
*Jmjd5 (Lysine-specific demethylase 8)
**[[6f4m]] – hJmjd5 catalytic domain  <br />
**[[3uyj]], [[4qu1]] – hJmjd5 catalytic domain + Ni + α-ketoglutarate <br />
**[[4gjz]] – hJmjd5 catalytic domain + Co + α-ketoglutarate <br />
**[[6f4n]] – hJmjd5 catalytic domain + Mn + α-ketoglutarate <br />
**[[6f4o]] – hJmjd5 catalytic domain + Mn + succinate <br />
**[[4aap]] – hJmjd5 catalytic domain + Zn + oxalylglycine <br/ >
**[[6avs]] – hJmjd5 catalytic domain + Zn + NMMA <br/ >
**[[5fbj]], [[6ax3]] – hJmjd5 catalytic domain + Zn + oxoglutarate <br/ >
**[[4gjy]] – hJmjd5 catalytic domain + Co + oxalylglycine <br />
**[[4gaz]] – hJmjd5 catalytic domain + Ni + oxalylglycine <br />
**[[6f4p]] – hJmjd5 catalytic domain + Mn + oxalylglycine + RPS6<br />
**[[6f4q]] – hJmjd5 catalytic domain (mutant) + Mn + oxalylglycine + RPS6<br />
**[[6f4r]], [[6f4s]], [[6f4t]] – hJmjd5 catalytic domain (mutant) + Mn + oxalylglycine + RCCD1<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 />
**[[5nfn]] – hJmjd7 catalytic domain + Mn + oxoglutarate <br/ >
**[[3u78]] – hJmjd7 catalytic domain + Ni + oxoglutarate + inhibitor<br/ >
**[[5nfo]] – hJmjd7 catalytic domain (mutant) + Mn + oxoglutarate <br/ >
}}
== References ==
== References ==
<references/>
<references/>


[[Category:Topic Page]]
[[Category:Topic Page]]

Latest revision as of 11:45, 8 September 2019

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[1].
  • 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.
  • 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[2].
  • Jumonji domain-containing protein 5 (Jmjd5) or KDM8 and Jumonji domain-containing protein 6 (Jmjd6) function as histone demethylase and as a protein hydroxylase.

Disease

Jmjd6 serves as a receptor allowing the foot-and-mouth virus to infect cells[3].

Structural highlights

Jmjd2a uses and . An [4]. Water molecules shown as red spheres.

.

3D structures of jumonji domain-containing protein

Jumonji domain-containing protein 3D structures


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

ReferencesReferences

  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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Michal Harel, Jaime Prilusky, Alexander Berchansky, Joel L. Sussman
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