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DNA polymerase beta consists of an N-terminal single-stranded DNA binding domain
and a C-terminal catalytic domain separable by mild proteolysis [Kumar et al.
(1990) J. Biol. Chem. 265, 2124-2131]. The N-terminal domain participates in
template and gapped DNA recognition and contributes significantly to catalysis.
The secondary structure and tertiary contacts within the cloned N-terminal
domain (residues 2-87) of mammalian DNA polymerase beta have been determined
using multidimensional NMR. Assignments of backbone 1H, 15N, and 13C resonances
and side chain 1H and 13C resonances have been obtained from double- and
triple-resonance 3D NMR experiments. The 13C-edited TOCSY experiment has allowed
nearly complete assignments of 1H and 13C resonances within side chains. The
13C-edited NOESY experiment has been used for determination of medium- and
long-range NOEs and a determination of tertiary contacts. The N-terminal domain
is found to consist of four helices, helix-1 (15-26), helix-2 (36-47), helix-3
(56-61), and helix-4 (69-78), which on the basis of long-range NOEs are tightly
packed of form a hydrophobic core. The remainder of the domain consists of two
turns (48-51 and 62-65), an omega-type loop (27-35), and extended structure. The
aromatic side chains of Y36, Y39, Y49, and F76 display tertiary contacts
indicative of at least partial hydrophobic packing. The S30 and H34 residues
which cross-link to single-stranded DNA [Prasad et al. (1993) J. Biol. Chem.
268, 15906-15911] are contained within the K27-K35 loop.(ABSTRACT TRUNCATED AT
250 WORDS)
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