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the structure, which are near the hinges or domain boundaries and which should affect the
motional characteristics.
DNA polymerase β
HAG hinges: 88-89,263-264
The base excision repair pathway responds to oxidative or alkylation damage to DNA,
removing on the order of 10,000 lesions per cell per day and is one of several DNA repair
processes necessary for the survival of eukaryotic cells. This process begins with
recognition of the damaged site by a specific glycosylase, which then removes the
offending base. An apurimic/apyrimidimic exonuclease removes the backbone sugar-
phosphate backbone. DNA polymerase β (pol β) then fills in the resulting gap and DNA
ligase completes the repair by healing the nicked backbone.
Structurally, Pol β resembles a hand, with so-named fingers, palm, and thumb
subdomains. Four metal ion binding sites exist. Two are in helix-hairpin-helix motifs
away from the active site and associate directly with the DNA backbone, while the other
two are involved in catalysis. It has a hinge between the catalytic (palm) domain
(residues 149-262) and the C-terminal (thumb) domain (residues 263-338), both of which
form part of a large active site cleft. The hinge region consists of a stretch of
hydrophobic residues which appear to play a role in substrate recognition, since
mutations of residue 260 result in an inaccurate polymerase.
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