TY  - JOUR
AU  - Genna, Vito
AU  - Carloni, Paolo
AU  - De Vivo, Marco
TI  - A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases
JO  - Journal of the American Chemical Society
VL  - 140
IS  - 9
SN  - 1520-5126
CY  - Washington, DC
PB  - American Chemical Society
M1  - FZJ-2018-01745
SP  - 3312 - 3321
PY  - 2018
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - pmid:29424536
UR  - <Go to ISI:>//WOS:000427203600026
DO  - DOI:10.1021/jacs.7b12446
UR  - https://juser.fz-juelich.de/record/844312
ER  -