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PDBsum entry 1skr
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Transferase/electron transport/DNA
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PDB id
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1skr
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Nucleotide insertion opposite a cis-Syn thymine dimer by a replicative DNA polymerase from bacteriophage t7.
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Authors
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Y.Li,
S.Dutta,
S.Doublié,
H.M.Bdour,
J.S.Taylor,
T.Ellenberger.
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Ref.
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Nat Struct Mol Biol, 2004,
11,
784-790.
[DOI no: ]
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PubMed id
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Abstract
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Ultraviolet-induced DNA damage poses a lethal block to replication. To
understand the structural basis for this, we determined crystal structures of a
replicative DNA polymerase from bacteriophage T7 in complex with nucleotide
substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer
(CPD). When the 3' thymine is the templating base, the CPD is rotated out of the
polymerase active site and the fingers subdomain adopts an open orientation.
When the 5' thymine is the templating base, the CPD lies within the polymerase
active site where it base-pairs with the incoming nucleotide and the 3' base of
the primer, while the fingers are in a closed conformation. These structures
reveal the basis for the strong block of DNA replication that is caused by this
photolesion.
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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.
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Figure 4.
Figure 4. The cis-syn thymine dimer base pairs with ddATP in the
closed CPD-5'b complex. (a) View from the major groove side
of the duplex DNA. (b) The view in a has been rotated by 90°
along an axis (straight arrow). The 3' T of the CPD forms a
normal Watson-Crick base pair with the 3' base of the primer. A
twisted base pair is formed between the 5' T and the incoming
ddATP. The view in b shows the distorted stacking of the 5' T
base pair with that of the 3' T. The nucleic acids are in
ball-and-stick representation with the same color scheme used in
Figure 1.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2004,
11,
784-790)
copyright 2004.
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