%0 Journal Article
%A Genna, Vito
%A Carloni, Paolo
%A De Vivo, Marco
%T A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases
%J Journal of the American Chemical Society
%V 140
%N 9
%@ 1520-5126
%C Washington, DC
%I American Chemical Society
%M FZJ-2018-01745
%P 3312 - 3321
%D 2018
%X Polymerases (Pols) synthesize the double-stranded nucleic acids in the Watson–Crick (W–C) conformation, which is critical for DNA and RNA functioning. Yet, the molecular basis to catalyze the W–C base pairing during Pol-mediated nucleic acids biosynthesis remains unclear. Here, through bioinformatics analyses on a large data set of Pol/DNA structures, we first describe the conserved presence of one positively charged residue (Lys or Arg), which is similarly located near the enzymatic two-metal active site, always interacting directly with the incoming substrate (d)NTP. Incidentally, we noted that some Pol/DNA structures showing the alternative Hoogsteen base pairing were often solved with this specific residue either mutated, displaced, or missing. We then used quantum and classical simulations coupled to free-energy calculations to illustrate how, in human DNA Pol-η, the conserved Arg61 favors W–C base pairing through defined interactions with the incoming nucleotide. Taken together, these structural observations and computational results suggest a structural framework in which this specific residue is critical for stabilizing the incoming (d)NTP nucleotide and base pairing during Pol-mediated nucleic acid biosynthesis. These results may benefit enzyme engineering for nucleic acid processing and encourage new drug discovery strategies to modulate Pols function.
%F PUB:(DE-HGF)16
%9 Journal Article
%$ pmid:29424536
%U <Go to ISI:>//WOS:000427203600026
%R 10.1021/jacs.7b12446
%U https://juser.fz-juelich.de/record/844312