Abstract
Crystal structures of various DNA polymerases show a common structural topology that resembles a right hand and has distinct finger, palm and thumb subdomains. Early models of the Klenow fragment (KF) of Escherichia coli polymerase I showed DNA entering a large cleft that faces the palm subdomain where the catalytic site is situated [1, 2]. However, subsequent resolution of the structures of HIV-1 reverse transcriptase, KF and polymerase β (pol β) bound to DNA [3–5]yielded conflicting data that suggested a different orientation for DNA bound to pol β compared with DNA bound to other polymerases. The debate, on the correct orientation of the template–primer DNA, that followed failed to reach a consensus. Using an alternative superposition scheme, we now provide convincing evidence for a common DNA-binding mode that is applicable to all polymerases, including pol β.
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