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Figure 4.
Figure 4. Conformations of the Synthetase Site in
Rel[Seq]1–385 and a Superposition with pol β(A) The
synthetase-ON conformation (monomer 1). Coloring is according to
Figure 1; individual structural elements are labeled in red. The
nucleophilic O3′ of GDP is marked. The final 2mFo-DFc
electron density map, shown for GDP (blue mesh), is contoured at
1.0 σ. Selected H-bonds are shown as gray dashed lines. The
catalytic loop (α13/β4) harboring Asp264 is stabilized in a
3[10]-helical conformation through multiple van der Waals
interactions (represented by black double-arrow dashed lines)
with loop α11/α12 and the first two turns of α12 (labeled t1,
t2). Chain traces extending from loops α11/α12, β3/α13, and
α13/β4 are not visible due to image slab restrictions.(B) The
synthetase-OFF conformation (monomer 2). The α11/α12 loop and
the first two turns of α12 are disordered; the resulting
elimination of van der Waals contacts to the catalytic loop
(α13/β4) leads to (1), partial refolding of the latter into an
N-terminal extension of β4, and (2), disorder of residues
254–261 including the remaining residues of the catalytic loop
and the C terminus of α13.(C) Representative electron density
in the synthetase site of monomer 1. GDP is highlighted in
orange. The final 2mFo-DFc electron density map (1.0 σ) is
overlaid as blue mesh.(D) Stereographic superposition between
the synthetase site of Rel[Seq]1–385 (monomer 1) and the
active site of pol β in the (pol β)·(gapped
DNA)·(ddCTP) complex. The latter complex is rendered in
gray shading with the exception of the primer 3′-terminal
nucleotide (orange), ddCTP (cyan), and the two Mg^2+ ions (dark
blue). Rel[Seq]1–385 and its GDP ligand are colored according
to (A). The putative catalytic carboxylates of Rel[Seq], Asp264
and Glu323, are N terminally frameshifted by two residues
relative to their pol β counterparts (indicated by black
arrows).
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