Mode analysis of a fatty acid molecule binding to the N-terminal 8-kDa domain of DNA polymerase beta. A 1:1 complex and binding surface.
We reported previously that long-chain fatty acids are potent inhibitors of mammalian DNA polymerase beta. At present, based on information available from the NMR structure of the N-terminal 8-kDa domain, we examined the structural interaction with the 8-kDa domain using two species, C(18)-linoleic acid (LA) or C(24)-nervonic acid (NA). In the 8-kDa domain with LA or NA, the structure that forms the interaction interface included helix-1, helix-2, helix-4, the three turns (residues 1-13, 48-51, and 79-87) and residues adjacent to an Omega-type loop connecting helix-1 and helix-2 of the same face. No significant shifts were observed for any of the residues on the opposite side of the 8-kDa domain. The NA interaction interface on the amino acid residues of the 8-kDa domain fragment was mostly the same as that of LA, except that the shifted cross-peaks of Leu-11 and Thr-79 were significantly changed between LA and NA. The 8-kDa domain bound to LA or NA as a 1:1 complex with a dissociation constant (K(D)) of 1.02 or 2.64 mM, respectively.
Mizushina
Y
Y
Department of Applied Biological Science, Science University of Tokyo, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
Ohkubo
T
T
Date
T
T
Yamaguchi
T
T
Saneyoshi
M
M
Sugawara
F
F
Sakaguchi
K
K
D000818:Animals; D001665:Binding Sites; D002942:Circular Dichroism; D019951:DNA Polymerase beta / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli; D005227:Fatty Acids / Q000737:chemistry* / Q000378:metabolism; D051381:Rats
D005227:Fatty Acids; D019951:DNA Polymerase beta