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Figure 1.
Figure 1. Closed Conformation of the Ternary Substrate
Complex with an Active-Site Mismatched Nascent Base Pair
(A) Licorice representation of the Pol β backbone of the binary
DNA complex (PDB ID 1BPX; orange) and ternary substrate complex
(green) with an incorrect incoming nucleotide (dAMPCPP; yellow
carbons) with a templating guanine. The catalytic and
DNA-binding subdomains superimposed (gray backbone) with an rmsd
of 0.56 Å (177 Cα). The DNA is omitted for clarity, but
the 5′→3′ direction of the primer entry into the active
site is indicated with a solid arrow. The open and closed
positions of α helix N are shown. The amino-terminal lyase
domain and carboxyl-terminal N subdomain (colored) move in
response to binding an incorrect dNTP. The amino- (N) and
carboxyl-terminal (C) ends are labeled.
(B) Ribbon
representation of the Pol β backbone of the ternary substrate
complex with correct (gray) or incorrect (green) incoming
nucleotides. The polymerase domains with a correct (dA-dUMPNPP;
PDB ID 2FMS) and incorrect (dG-dAMPCPP) nascent base pair were
superimposed with an rmsd of 0.62 Å (314 Cα). The
superimposed structures indicate that α helix N is in a
“closed” position like that observed with a Watson-Crick
nascent base pair. The incoming dAMPCPP of the mismatch
structure is shown (yellow carbons), but the DNA is omitted for
clarity. The amino terminus (N) of the lyase domain is also
indicated.
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