A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4).
Primer extension studies have shown that the Y-family DNA polymerase IV (Dpo4) from Sulfolobus solfataricus P2 can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) [F. Boudsocq, S. Iwai, F. Hanaoka and R. Woodgate (2001) Nucleic Acids Res., 29, 4607-4616]. Our goal is to elucidate on a structural level how AAF-dG can be harbored in the Dpo4 active site opposite an incoming dCTP, using molecular modeling and molecular dynamics simulations, since AAF-dG prefers the syn glycosidic torsion. Both anti and syn conformations of the templating AAF-dG in a Dpo4 ternary complex were investigated. All four dNTPs were studied. We found that an anti glycosidic torsion with C1'-exo deoxyribose conformation allows AAF-dG to be Watson-Crick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting. The AAF is situated in the Dpo4 major groove open pocket with fluorenyl rings 3'- and acetyl 5'-directed along the modified strand, irrespective of dNTP. With AAF-dG syn, the fluorenyl rings are in the small minor groove pocket and the active site region is highly distorted. The anti-AAF-dG conformation with C1'-exo sugar pucker can explain the preferential incorporation of dC by Dpo4. Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed.
Wang
Lihua
L
Biology Department, New York University, New York, NY 10003, USA.
Broyde
Suse
S
D015073:2-Acetylaminofluorene / Q000031:analogs & derivatives* / Q000737:chemistry; D020029:Base Pairing; D001665:Binding Sites; D018736:DNA Adducts / Q000737:chemistry*; D019951:DNA Polymerase beta / Q000737:chemistry*; D004261:DNA Replication; D003838:Deoxyadenine Nucleotides / Q000737:chemistry; D003845:Deoxycytosine Nucleotides / Q000737:chemistry; D003849:Deoxyguanosine / Q000031:analogs & derivatives* / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D048229:Sulfolobus solfataricus / Q000201:enzymology*
D018736:DNA Adducts; D003838:Deoxyadenine Nucleotides; D003845:Deoxycytosine Nucleotides; C024107:2'-deoxycytidine 5'-triphosphate; C018776:N-(deoxyguanosin-8-yl)acetylaminofluorene; D015073:2-Acetylaminofluorene; D019951:DNA Polymerase beta; D003849:Deoxyguanosine; C026600:2'-deoxyadenosine triphosphate