|
Figure 4.
Figure 4. Classification of the PHD Finger Family
Sequence features of structurally characterized three distinct
subclasses of the PHD finger family with respect to ligand
binding specificity, i.e., H3K4me0 (group I), H3K4me3 (group
II), and nonhistone binding (group III). The recognition of
H3K4me3 takes place by embracement of the trimethyl groups by
characteristically positioned aromatic cage residues, whereas
that of K4me0 is due to an ion pair formed with a distinct
N-terminal Asp residue. The characteristic histone-peptide
interacting positions are in red, and the Zn-chelating residues
(the first and second tetrads are connected by regular and
dotted lines, respectively) and conserved C-terminal aromatic
residue characteristic of the entire PHD family are in green. In
either of the H3 interacting PHD fingers, H3R2 often interacts
with Asp/Glu (blue). These “red” and “blue” positions
are absent in KAP1-PHD finger (bottom) indicated by ↑ that
binds the adjacent bromodomain's Z[A] helix by patch of nonpolar
residues (yellow). Topology diagrams (bottom; based on Aravind
et al. [2006]), not drawn to scale, highlight these features for
clarity. The domain boundaries and gi numbers are indicated in
the alignments. The secondary structural elements of the
AIRE-PHD1 are indicated above the sequence. The black ↑
indicates position where similar interactions involving protein
side chain is observed in AIRE and BHC80 PHD fingers. The
sequence of AIRE-PHD2 is shown below the alignment to show its
grouping with group III as non-H3 binder.
|
