Figure 1.
Figure 1. Positioning of the cis-syn thymine dimer in the T7 DNA
polymerase. (a) CPD-3'a complex, in which the CPD is rotated
by 90°
and lying outside of the polymerase active site. The fingers
domain is in an open conformation. (b) CPD-5'b complex, in which
the CPD is in the polymerase active site and it base-pairs with
the 3' base of the primer strand and the incoming nucleotide.
The fingers domain is in a closed conformation. (c) CPD-5'a
complex, in which the DNA slides back by one base pair and the
CPD curves back into the major grove of the duplex DNA. The
fingers domain is in an open conformation. The protein is shown
as surface representation. The DNA and nucleotide are
ball-and-stick models in which the backbone of the primer strand
is red and that of the template is light purple. The 5' base of
the cis-syn thymine dimer is magenta and the 3' base is light
magenta. The carbon atoms in the incoming nucleotide in b are
green and the Mg2+ ions are gold spheres. For clarity, the thumb
subdomain and the processivity factor E. coli thioredoxin were
removed from Figures 1,2,3.
The above figure is reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2004,
11,
784-790)
copyright 2004.
90°
and lying outside of the polymerase active site. The fingers
domain is in an open conformation. (b) CPD-5'b complex, in which
the CPD is in the polymerase active site and it base-pairs with
the 3' base of the primer strand and the incoming nucleotide.
The fingers domain is in a closed conformation. (c) CPD-5'a
complex, in which the DNA slides back by one base pair and the
CPD curves back into the major grove of the duplex DNA. The
fingers domain is in an open conformation. The protein is shown
as surface representation. The DNA and nucleotide are
ball-and-stick models in which the backbone of the primer strand
is red and that of the template is light purple. The 5' base of
the cis-syn thymine dimer is magenta and the 3' base is light
magenta. The carbon atoms in the incoming nucleotide in b are
green and the Mg2+ ions are gold spheres. For clarity, the thumb
subdomain and the processivity factor E. coli thioredoxin were
removed from Figures 1,2,3.