Structure of lithocholic acid binding to the N-terminal 8-kDa domain of DNA polymerase beta.
The purpose of this study was to investigate the molecular action of lithocholic acid (LCA), known as a selective inhibitor of DNA polymerase beta (pol beta). The 39-kDa pol beta was separated proteolytically into two fragments of the template-primer binding domain (8 kDa) and the catalytic domain (31 kDa). LCA bound tightly to the 8-kDa fragment but not to the 31-kDa fragment. We examined the structural interaction with the 8-kDa domain using LCA. On (1)H-(15)N HMQC NMR analysis of pol beta with LCA, the 8-kDa domain bound to LCA as a 1:1 complex with a dissociation constant (K(D)) of 1.56 mM. The chemical shifts were observed only in residues mainly in helix-3, helix-4, and the 79-87 turn of the same face. No significant shifts were observed for helix-1, helix-2, and other loops of the 8-kDa domain. This region was composed mainly of three amino acid residues (Lys60, Leu77, and Thr79) of pol beta on the LCA interaction interface. The inhibition mechanism and the structure-function relationship between pol beta and LCA is discussed.
Mizushina
Y
Y
Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
Ohkubo
T
T
Sugawara
F
F
Sakaguchi
K
K
D000818:Animals; D001667:Binding, Competitive; D002384:Catalysis; D003198:Computer Simulation; D019951:DNA Polymerase beta / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D004789:Enzyme Activation; D008095:Lithocholic Acid / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008970:Molecular Weight; D019906:Nuclear Magnetic Resonance, Biomolecular; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D010449:Peptide Mapping; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D051381:Rats; D013329:Structure-Activity Relationship
D010446:Peptide Fragments; D008095:Lithocholic Acid; D019951:DNA Polymerase beta