Jumonji domain-containing protein

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. 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. 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. Structural highlights Jmjd2a uses and . An . Water molecules shown as red spheres. .

spinqualitylabelsall models 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). Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

3D structures of jumonji domain-containing protein3D structures of jumonji domain-containing protein

Updated on 01-August-2018

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• Jmjd2a (Lysine-specific demethylase 4A)
  • 2gf7, 2qqr, 5d6w, 5d6x – hJmjd2a double TUDOR domain – human
    
  • 2gp3 – hJmjd2a catalytic domain + Fe
    
  • 5fyc, 5tvs – hJmjd2a catalytic domain + Ni
    
• Jmjd2a binary complex with peptide
  • 2gfa, 5d6y – hJmjd2a double TUDOR domain + peptide with trimethyllysine
    
  • 2qqs – hJmjd2a double TUDOR domain + histone H4 peptide with trimethyllysine
    
  • 2oq6, 2os2 – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine
    
  • 2ot7 – hJmjd2a catalytic domain + Ni + histone H3 peptide with methyllysine
    
  • 2pxj – hJmjd2a catalytic domain + Fe + histone H3 peptide with methyllysine
    
  • 2ox0 – hJmjd2a catalytic domain + Ni + histone H3 peptide with dimethyllysine
    
  • 5ly2, 5ly1 – hJmjd2a catalytic domain + Ni + peptide inhibitor
    
  • 5fwe – hJmjd2a catalytic domain + Ni + Zn + oxalylglycine + peptide
    
• Jmjd2a binary complex with other molecules
  • 2oq7 – hJmjd2a catalytic domain + Ni + oxalylglycine
    
  • 2vd7, 2wwj, 3njy, 3pdq, 3rvh, 4gd4, 4ai9, 4bis – hJmjd2a catalytic domain + Ni + inhibitor
    
  • 2gp5 – hJmjd2a catalytic domain + Fe + α-ketoglutarate
    
  • 2ybk, 5tvr – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative
    
  • 4ura, 5fpv – hJmjd2a catalytic domain + Ni + inhibitor
    
  • 5anq – hJmjd2a catalytic domain + Fe + inhibitor
    
  • 5a7n, 5a7o, 5a7p, 5a7q, 5a7s, 5a7w, 5a80 – hJmjd2a catalytic domain + Mn + inhibitor
    
  • 5f2s, 5f2w, 5f32, 5f37, 5f39, 5f3c, 5f3e, 5f3g, 5f3i, 6cg1, 6cg2, 5vmp, 5vgi, 5var – hJmjd2a catalytic domain + Zn + inhibitor
    
  • 5fy8 – hJmjd2a catalytic domain + Ni + threo-isocitrate
    
  • 5fyi – hJmjd2a catalytic domain + Ni + pyruvate
    
  • 5fyh – hJmjd2a catalytic domain + Mn + fumarate
    
• Jmjd2a ternary complex
  • 2q8c, 2ybp, 2ybs – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + α-ketoglutarate derivative
    
  • 2q8d – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + succinate
    
  • 2q8e, 2p5b – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine
    
  • 4v2v, 4v2w – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylglycine
    
  • 3u4s – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylcysteine
    
• 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 – hJmj1a + inhibitor
    
  • 5k4l, 5ceh – hJmj1a + inhibitor + peptide
    
  • 5c11 – hJmj1a PHD finger domain + H3 peptide
    
  • 5e6h – hJmj1a residues 1-87, 348-588 + Mn + oxoglutarate
    
  • 4tn7 – mJmj1a residues 36-364 + NO + Fe + H3 peptide - mouse
    
  • 4qxh, 4qxb – mJmj1a residues 36-364 + Ni + oxalylglycine
    
  • 4qxc – mJmj1a residues 36-364 + Ni + oxalylglycine + H3 peptide
    
  • 4qx8, 4qx7, 4qwn – mJmj1a residues 36-364 + Ni + oxoglutarate + H3 peptide
    
• Lysine-specific demethylase 5C; KDM5C; JARID1C
  • 5fwj – hLSD5C Jmj domain + inhibitor
    
  • 2jrz – hLSD5C Bright/ARID domain - NMR
    
• lysine-specific demethylase 5D or JARID1D
  • 2yqe – hLSD5D ARID domain - NMR
    
• Jmjd1b (Lysine-specific demethylase 2B; KDM2B)
  • 4o64 – hJmj1b zinc finger domain + Zn
    
  • 4c8d, 5fv3 – hJmj1b catalytic domain + Mn + oxalylglycine
    
  • 5fup – hJmj1b catalytic domain + Mn + Zn + oxoglutatate
    
  • 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
    
  • 5jh5 – hJmj1b + S-phase kinase-associated protein + polycomb protein + BCOR-like protein
    
• Jmjd2b (Lysine-specific demethylase 4B)
  • 4lxl – hJmjd2b catalytic domain + Ni + histone H3 peptide with trimethyllysine
    
  • 4uc4 – hJmjd2b tudor domain
    
• Jmjd2c (Lysine-specific demethylase 4C)
  • 2xdp – hJmjd2c tudor domain
    
  • 2xml, 4xdo – hJmjd2c catalytic domain + Ni + oxalylglycine
    
  • 4xdp – hJmjd2c catalytic domain + Fe
    
  • 5fjh, 5fjk – hJmjd2c catalytic domain + Ni + inhibitor
    
  • 5kr7 – hJmjd2c catalytic domain + Fe + Zn + inhibitor
    
• Jmjd2d (Lysine-specific demethylase 4D)
  • 3dxu – hJmjd2d catalytic domain + Fe + oxalylglycine
    
  • 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

• • 4hoo – hJmjd2d catalytic domain (mutant) + Ni
    
  • 4d6q, 5f5a, 5f5c, 5f5i – hJmjd2d catalytic domain + Ni + inhibitor
    
  • 5fp4, 5fp8, 5fp9, 5fpa, 5fpb, 5fp7 – hJmjd2d catalytic domain + Fe + inhibitor
    
  • 4d6r, 4d6s – hJmjd2d catalytic domain + Ni + inhibitor + oxalylglycine
    
  • 4hon – hJmjd2d catalytic domain + Ni + histone H3 peptide with trimethyllysine + α-ketoglutarate
    
• Jmjd3 (Lysine-specific demethylase 6B)
  • 2xxz – hJmjd3 catalytic domain + Ni
    
  • 2xue – hJmjd3 catalytic domain + Fe + α-ketoglutarate
    
  • 4ask – hJmjd3 catalytic and Zinc finger domains + Co + inhibitor
    
  • 4eyu, 4ez4 – mJmjd3 C terminal + Ni + oxalylglycine - mouse
    
  • 4ezh – mJmjd3 C terminal + Ni + histone H3 peptide with trimethyllysine + oxalylglycine
    
  • 5fp3 – hJmjd3 catalytic domain + inhibitor
    
• Jmjd5 (Lysine-specific demethylase 8)
  • 6f4m – hJmjd5 catalytic domain
    
  • 3uyj, 4qu1 – hJmjd5 catalytic domain + Ni + α-ketoglutarate
    
  • 4gjz – hJmjd5 catalytic domain + Co + α-ketoglutarate
    
  • 6f4n – hJmjd5 catalytic domain + Mn + α-ketoglutarate
    
  • 6f4o – hJmjd5 catalytic domain + Mn + succinate
    
  • 4aap – hJmjd5 catalytic domain + Zn + oxalylglycine
    
  • 6avs – hJmjd5 catalytic domain + Zn + NMMA
    
  • 5fbj, 6ax3 – hJmjd5 catalytic domain + Zn + oxoglutarate
    
  • 4gjy – hJmjd5 catalytic domain + Co + oxalylglycine
    
  • 4gaz – hJmjd5 catalytic domain + Ni + oxalylglycine
    
  • 6f4p – hJmjd5 catalytic domain + Mn + oxalylglycine + RPS6
    
  • 6f4q – hJmjd5 catalytic domain (mutant) + Mn + oxalylglycine + RPS6
    
  • 6f4r, 6f4s, 6f4t – hJmjd5 catalytic domain (mutant) + Mn + oxalylglycine + RCCD1
    
• Jmjd6
  • 3ld8 – hJmjd6 catalytic domain + antibody + Fe
    
  • 3ldb – hJmjd6 catalytic domain + antibody + Fe + α-ketoglutarate
    
  • 6fqc – hJmjd6 catalytic domain + polypeptide + Mn
    
• Jmjd7
  • 4qu2 – hJmjd7 catalytic domain + Ni + α-ketoglutarate
    
  • 5nfn – hJmjd7 catalytic domain + Mn + oxoglutarate
    
  • 3u78 – hJmjd7 catalytic domain + Ni + oxoglutarate + inhibitor
    
  • 5nfo – hJmjd7 catalytic domain (mutant) + Mn + oxoglutarate