1DK3

REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA

Summary for 1DK3

• Entry DOI: 10.2210/pdb1dk3/pdb
• Related: 1BNO 1BNP
• Descriptor: DNA POLYMERASE BETA (1 entity in total)
• Functional Keywords: dna-binding, deoxyribose 5'-phosphate lyase, nucleotidyltransferase, transferase
• Biological source: Rattus norvegicus (Norway rat)
• Cellular location: Nucleus: P06766
• Total number of polymer chains: 1
• Total formula weight: 9632.30

Authors

Maciejewski, M.W.,Prasad, R.,Liu, D.-J.,Wilson, S.H.,Mullen, G.P. (deposition date: 1999-12-06, release date: 2000-02-14, Last modification date: 2024-05-22)

Primary citation

Maciejewski, M.W.,Liu, D.,Prasad, R.,Wilson, S.H.,Mullen, G.P.
Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity.
J.Mol.Biol., 296:229-253, 2000

PubMed Abstract: Mammalian DNA polymerase beta functions in the base excision DNA repair pathway filling in short patches (1-5 nt) in damaged DNA and removing deoxyribose 5'-phosphate from the 5'-side of damaged DNA. The backbone dynamics and the refined solution structure of the N-terminal domain of beta-Pol have been characterized in order to establish the potential contribution(s) of backbone motion to the DNA binding and deoxyribose 5'-phosphate lyase function of this domain. The N-terminal domain is formed from four helices packed as two antiparallel pairs with a 60 degrees crossing between the pairs. The RMSD of the NMR conformers (residues 13-80) is 0.37 A for the backbone heavy atoms and 0.78 A for all heavy atoms. NMR characterization of the binding site(s) for a ssDNA-5mer, ssDNA-8mer, ssDNA-9mer, and dsDNA-12mer shows a consensus surface for the binding of these various DNA oligomers, that surrounds and includes the deoxyribose 5'-phosphate lyase active site region. Connection segments between helices 1 and 2 and between helices 3 and 4 each contribute to DNA binding. Helix-3-turn-helix-4 forms a helix-hairpin-helix motif. The highly conserved hairpin sequence (LPGVG) displays a significant degree of picosecond time-scale motion within the backbone, that is possibly important for DNA binding at the phosphodiester backbone. An Omega-loop connecting helices 1 and 2 and helix-2 itself display significant exchange contributions (R(ex)) at the backbone amides due to apparent conformational type motion on a millisecond time-scale. This motion is likely important in allowing the Omega-loop and helix-2 to shift toward, and productively interact with, gapped DNA. The deoxyribose 5'-phosphate lyase catalytic residues that include K72 which forms the Schiff's base, Y39 which is postulated to promote proton transfer to the aldehyde, and K35 which assists in phosphate elimination, show highly restricted backbone motion. H34, which apparently participates in detection of the abasic site hole and assists in the opening of the hemiacetal, shows conformational exchange.

PubMed: 10656829
DOI: 10.1006/jmbi.1999.3455

Experimental method

SOLUTION NMR