Figure 2.
Figure 2. Dpo4 in complex with matched and mismatched primer
termini. (a) An overall view of different Dpo4 -DNA
complexes: the type I structure determined by Yang and
colleagues, and the structures reported here of Dpo4 bound to a
mismatched (G T)
and the matched (A-T) primer template. Dpo4 in each complex is
colored by palm (blue), fingers (yellow) and thumb (orange)
domains, as well as PAD (green). The terminal base pair of the
DNA in each complex is red. (b) Close-up view of the
template-primer terminus in each complex, highlighting the
terminal base pair (red), the incoming nucleotide, the active
site residues (Asp7, Asp105 and Glu106) coordinating a metal ion
(yellow ball, refined as Ca^2+), residues (Tyr48, Arg51 and
Lys159) bonding to the di- or triphosphate moiety of the
incoming nucleotide, as well as residues (Val32, Ala42 and
Gly58) from the fingers domain that impinge on the templating
base. Also in red is the C3' atom at the primer terminus. The
figure was generated with MolMol32 and PovRay
(http://www.povray.org). (c) 2F [o] - F [c] electron density for
a portion of the primer and the incoming nucleotide in the G
T
complex. The map was computed with the terminal guanine (ddG)
and the incoming nucleotide (ddCTP) omitted (and followed by
simulated annealing). The terminal guanine inverts to form a
reverse wobble. Also in red is the hypothetical position for the
guanine in a standard wobble configuration (which is completely
out of density).
T)
and the matched (A-T) primer template. Dpo4 in each complex is
colored by palm (blue), fingers (yellow) and thumb (orange)
domains, as well as PAD (green). The terminal base pair of the
DNA in each complex is red. (b) Close-up view of the
template-primer terminus in each complex, highlighting the
terminal base pair (red), the incoming nucleotide, the active
site residues (Asp7, Asp105 and Glu106) coordinating a metal ion
(yellow ball, refined as Ca^2+), residues (Tyr48, Arg51 and
Lys159) bonding to the di- or triphosphate moiety of the
incoming nucleotide, as well as residues (Val32, Ala42 and
Gly58) from the fingers domain that impinge on the templating
base. Also in red is the C3' atom at the primer terminus. The
figure was generated with MolMol32 and PovRay
(http://www.povray.org). (c) 2F [o] - F [c] electron density for
a portion of the primer and the incoming nucleotide in the G