Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics.
Formamidopyrimidine-DNA glycosylase (Fpg) identifies and removes 8-oxoguanine from DNA. All of the X-ray structures of Fpg complexed to an abasic site containing DNA exhibit a common disordered region present in the C-terminal domain of the enzyme. However, this region is believed to be involved in the damaged base binding site when the initial protein/DNA complex is formed. The dynamic behavior of the disordered polypeptide (named Loop) in relation to the supposed scenario for the DNA repair mechanism was investigated by molecular dynamics on different models, derived from the X-ray structure of Lactococcus lactis Fpg bound to an abasic site analog-containing DNA and of Bacillus stearothermophilus Fpg bound to 8-oxoG. This study shows that the presence of the damaged base influences the dynamics of the whole enzyme and that the Loop location is dependent on the presence and on the conformation of the 8-oxoG in its binding site. In addition, from our results, the conformation of the 8-oxoG seems to be favored in syn in the L. lactis models, in agreement with the available X-ray structure from B. stearothermophilus Fpg and with a possible catalytic role of the flexibility of the Loop region.
Amara
Patricia
P
Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel Commissariat à l'énergie Atomique/Centre National de la Recherche Scientifique/Université Joseph Fourier, 38027 Grenoble 1, France. amara@ibs.fr
Serre
Laurence
L
Castaing
Bertrand
B
Thomas
Aline
A
D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004260:DNA Repair; D043382:DNA-Formamidopyrimidine Glycosylase / Q000737:chemistry*; D001411:Geobacillus stearothermophilus / Q000201:enzymology*; D013294:Lactococcus lactis / Q000201:enzymology*; D008956:Models, Chemical; D017434:Protein Structure, Tertiary
D001426:Bacterial Proteins; D004247:DNA; D043382:DNA-Formamidopyrimidine Glycosylase