Assignments of 1H, 15N, and 13C resonances for the backbone and side chains of the N-terminal domain of DNA polymerase beta. Determination of the secondary structure and tertiary contacts

Biochemistry. 1994 Aug 16;33(32):9537-45. doi: 10.1021/bi00198a020.


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)

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • DNA Nucleotidylexotransferase / chemistry
  • DNA Polymerase I / chemistry*
  • DNA Polymerase I / genetics
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Peptide Fragments / chemistry*
  • Peptide Fragments / genetics
  • Protein Structure, Secondary*
  • Protein Structure, Tertiary*
  • Rats
  • Recombinant Proteins / chemistry
  • Sequence Homology, Amino Acid


  • Peptide Fragments
  • Recombinant Proteins
  • DNA polymerase I (2-87)
  • DNA Nucleotidylexotransferase
  • DNA Polymerase I