Jumonji domain-containing protein

Function 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. 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 9 residues for interaction with the methylated peptide and 4 residues are involved with binding to the peptide's trimethyllysine moiety. An O2 molecule is recruited into the catalytic center.

spinqualitylabelsall models 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 and wheat) (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 protein 2A3D structures of jumonji domain-containing protein 2A

Updated on 05-April-2016

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• Jmjd2a
  • 2gf7, 2qqr – hJmjd2a double TUDOR domain – human
    
  • 2gp3 – hJmjd2a catalytic domain + Fe
    
• Jmjd2a binary complex with peptide
  • 2gfa – 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
    
• 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 – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative
    
• 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
    
  • 2q8c, 2p5b – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine
    
  • 2q8c – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylcysteine