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Mammalian DNA polymerase beta (pol beta) is a small (39 kDa) DNA gap-filling
enzyme that comprises an amino-terminal 8-kDa domain and a carboxy-terminal
31-kDa domain. In the work reported here, crystal structures of human pol beta
complexed with blunt-ended segments of DNA show that, although the crystals
belong to a different space group, the DNA is nevertheless bound in the pol beta
binding channel in the same way as the DNA in previously reported structures of
rat pol beta complexed with a template-primer and ddCTP [Pelletier, H., Sawaya,
M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) Science 264, 1891-1903].
The 8-kDa domain is in one of three previously observed positions relative to
the 31-kDa domain, suggesting that the 8-kDa domain may assume only a small
number of stable conformations. The thumb subdomain is in a more open position
in the human pol beta-DNA binary complex than it is in the rat pol
beta-DNA-ddCTP ternary complex, and a closing thumb upon nucleotide binding
could represent the rate-limiting conformational change that has been observed
in pre-steady-state kinetic studies. Intermolecular contacts between the DNA and
the 8-kDa domain of a symmetry-related pol beta molecule reveal a plausible
binding site on the 8-kDa domain for the downstream oligonucleotide of a
gapped-DNA substrate; in addition to a lysine-rich binding pocket that
accommodates a 5'-PO4 end group, the 8-kDa domain also contains a newly
discovered helix-hairpin-helix (HhH) motif that binds to DNA in the same way as
does a structurally and sequentially homologous HhH motif in the 31-kDa domain.
DNA binding by both HhH motifs is facilitated by a metal ion. In that HhH motifs
have been identified in other DNA repair enzymes and DNA polymerases, the
HhH-DNA interactions observed in pol beta may be applicable to a broad range of
DNA binding proteins. The sequence similarity between the HhH motif of
endonuclease III from Escherichia coli and the HhH motif of the 8-kDa domain of
pol beta is particularly striking in that all of the conserved residues are
clustered in one short sequence segment, LPGVGXK, where LPGV corresponds to a
type II beta-turn (the hairpin turn), and GXK corresponds to a part of the HhH
motif that is proposed to be critical for DNA binding and catalysis for both
enzymes. These results suggest that endonuclease III and the 8-kDa domain of pol
beta may employ a similar mode of DNA binding and may have similar catalytic
mechanisms for their respective DNA lyase activities. A model for productive
binding of pol beta to a gapped-DNA substrate requires a 90 degrees bend in the
single-stranded template, which could enhance nucleotide selectivity during DNA
repair or replication.
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