Table 1 Comparison of residues binding to metal centre in JmjC-KDMs
Name
Synonyms
Substrate
a
PDB (ligand)
Fe(II) metal-binding
residues
KDM2A FBXL11,
JHDM1A
H3K36me2/1
4QX7 (2OG, Ni(II),
H3K36me2)
b
H212
D214
H284
KDM2B
c
FBXL10,
JHDM1B
H3K36me2/1
–
H211
D213
H283
KDM3A
c
JMJD1A,
JHDM2A
H3K9me2/1
–
H1120 D1122 H1175
KDM3B JMJD1B,
JHDM2B
H3K9me2/1
4C8D (2OG, Mn(II)) H1560 D1562 H1689
JMJD1C KDM3C,
JHDM2C
5FZO (Mn(II))
H2336 E2338 H2466
KDM4A JMJD2A,
JHDM3A
H3K9me3/2,
H3K36me3/2
5TVR (2OG, Ni(II))
H188
E190
H276
KDM4B JMJD2B,
JHDM3B
H3K9me3/2,
H3K36me3/2
4LXL (24PDCA, Ni
(II), H3K9me3)
H189
E191
H277
KDM4C JMJD2C,
JHDM3C
H3K9me3/2
4XDO (2OG, Fe(II))
H190
E192
H278
KDM4D JMJD2D,
JHDM3D
H3K9me3/2
4HON (2OG, Ni(II),
H3K9me3)
H192
E194
H280
KDM5A JARID1A,
RBP2
H3K4me3/2
5IVB (2OG, Mn(II))
H483
E485
H571
KDM5B JARID1B,
PLU1
H3K4me3/2
5FUP (2OG, Mn(II))
H499
E501
H587
KDM5C JARID1C,
SMCX
H3K4me3/2
5FWJ (4, Mn(II))
H514
E516
H602
KDM5D
c
JARID1D,
SMCY
H3K4me3/2
H514
E516
H602
KDM6A UTX
H3K27me3/
me2
3AVR (2OG, Ni(II),
H3K27me3)
H1146 E1148 H1226
KDM6B JMJD3
H3K27me3/
me2
2XUE (2OG, Fe(II))
H1390 E1392 H1470
KDM6C UTY
3ZLI (2OG, Fe(II))
H1014 E1016 H1094
KDM7A KIAA1718,
JHDM1D
H3K9me2/1,
H3K27me2/1
3KVA (2OG, Fe(II))
H282
D284
H354
KDM7B PHF8,
JHDM1F
H3K9me2/1
3KV4 (2OG, Ni(II),
H3K4me3K9me2)
H247
D249
H319
PHF2
KDM7C,
JHDM1E
3PU8 (2OG, Fe(II))
H249
D251
Y321
The crystal structures of human JmjC-KDMs reveal three residues that coordinate the active site
Fe(II)
a Independently verified consensus assignment in vitro and in cells. Other putative substrates have
been identified in vitro. Ligands are Ni(II) and NOG unless otherwise stated. All PDBs are from
Homo sapiens except where indicated
b
Mus musculus
c Where the metal-chelating residues are identified from sequence alignments [1]. Note that the
KDM nomenclature is not used when histone demethylase activity has not been independently
verified. PDB is a representative from the protein when more than one structure is available
224
M. Wright et al.