Figure 1.
Figure 1: Replication of a CPD by Dpo4 in solution and crystals.
a, Extension of two primers (13 nucleotides each) paired with
undamaged or CPD-containing 18-nucleotide templates used in the
crystallization studies (TT-1, TT-2). Reactions were carried out
with 10 nM DNA substrate, 10 nM Dpo4 and 100 M
dATP at 37 °C for 2, 5, 10 or 20 min. b, Inhibition of primer
extension by ddATP. P indicates primer strand, and U and D
indicate undamaged and CPD-containing template, respectively.
The reactions took place for 30 min at 22 °C or 37 °C as
indicated. c, The active site of TT-1, where the 3' thymine of
the CPD (orange) is base-paired with ddATP (yellow). The
conserved residues interacting with ddATP and catalytic
carboxylates are highlighted. Tyr 10, which immobilizes the
finger domain by wedging between the palm and finger domains, is
shown in red. d, Replication at the 3' T of the CPD. The CPD and
the replicating and preceding base pairs of TT-1 are shown with
the F[o] - F[c] omit electron densities. e, Active site of TT-2,
where the 5' thymine of the CPD is base-paired with ddATP, f,
The replicating and two preceding base pairs of the TT-2 are
shown with the F[o] - F[c] omit electron densities. g, Stereo
view of the TT-1 (blue) and TT-2 (pink) active-site
superposition. The three catalytic carboxylates, two Ca^2+ ions,
the 3' nucleotide of the primer strand, and the incoming
nucleotide are shown in the ball-and-stick model.
M
dATP at 37 °C for 2, 5, 10 or 20 min. b, Inhibition of primer
extension by ddATP. P indicates primer strand, and U and D
indicate undamaged and CPD-containing template, respectively.
The reactions took place for 30 min at 22 °C or 37 °C as
indicated. c, The active site of TT-1, where the 3' thymine of
the CPD (orange) is base-paired with ddATP (yellow). The
conserved residues interacting with ddATP and catalytic
carboxylates are highlighted. Tyr 10, which immobilizes the
finger domain by wedging between the palm and finger domains, is
shown in red. d, Replication at the 3' T of the CPD. The CPD and
the replicating and preceding base pairs of TT-1 are shown with
the F[o] - F[c] omit electron densities. e, Active site of TT-2,
where the 5' thymine of the CPD is base-paired with ddATP, f,
The replicating and two preceding base pairs of the TT-2 are
shown with the F[o] - F[c] omit electron densities. g, Stereo
view of the TT-1 (blue) and TT-2 (pink) active-site
superposition. The three catalytic carboxylates, two Ca^2+ ions,
the 3' nucleotide of the primer strand, and the incoming
nucleotide are shown in the ball-and-stick model.