PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 12927538-4 2003 Moreover, Pol beta can efficiently incorporate rCTP opposite G in the absence of dCTP and, to a lesser extent, rATP opposite T in the absence of dATP and rGTP opposite C in the absence of dGTP. 2'-deoxycytidine 5'-triphosphate 81-85 DNA polymerase beta Homo sapiens 10-18 16173754-2 2005 We report, using path sampling simulations and a reaction network model, strikingly different transition states in DNA polymerase beta"s conformational closing for correct dCTP versus incorrect dATP incoming nucleotide opposite a template G. The cascade of transition states leads to differing active-site assembly processes toward the "two-metal-ion catalysis" geometry. 2'-deoxycytidine 5'-triphosphate 172-176 DNA polymerase beta Homo sapiens 115-134 15656594-3 2005 FAP-dCTP is an efficient substrate of mammalian DNA polymerase beta in the reaction of primer elongation displaying substrate properties as an analogue of dCTP and dTTP. 2'-deoxycytidine 5'-triphosphate 4-8 DNA polymerase beta Homo sapiens 48-67 15507687-3 2004 Anchors for our study are available in crystallographic structures of the DNA pol-beta in "open" (polymerase bound to gapped DNA) and "closed" (polymerase bound to gapped DNA and substrate, dCTP) forms; these different states have long been used to deduce that a large-scale conformational change may help the polymerase choose the correct nucleotide, and hence monitor DNA synthesis fidelity, through an "induced-fit" mechanism. 2'-deoxycytidine 5'-triphosphate 190-194 DNA polymerase beta Homo sapiens 78-86 12388548-5 2002 pol beta mostly incorporates the correct dATP opposite the 3"-terminus of both CPD and the (6-4) photoproduct but can also misinsert dCTP at a frequency of 32 and 26%, respectively. 2'-deoxycytidine 5'-triphosphate 133-137 DNA polymerase beta Homo sapiens 0-8 8702991-1 1996 The dNTP binding pocket of human immunodeficiency virus type 1 reverse transcriptase (RT) and DNA polymerase beta (beta-pol) were labeled using a photoreactive analog of dCTP, exo-N-[beta-(p-azidotetrafluorobenzamido)-ethyl]-deoxycytidine-5"- triphosphate (FABdCTP). 2'-deoxycytidine 5'-triphosphate 170-174 DNA polymerase beta Homo sapiens 94-113 10653647-3 2000 For wild-type pol beta, there is a 2:1 preference for incorporation of dCTP over dATP opposite 8-oxodG using a 5"-phosphorylated 4-base gap substrate. 2'-deoxycytidine 5'-triphosphate 71-75 DNA polymerase beta Homo sapiens 14-22 19120024-11 2008 Modified on heterocyclic base photoreactive analogs of dCTP and dUTP showed substrate specificity for DNA polymerase beta. 2'-deoxycytidine 5'-triphosphate 55-59 DNA polymerase beta Homo sapiens 102-121 24966350-4 2014 Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2"-fluoro-m7dG (Fm7dG), by human DNA polymerase beta (polbeta) and solved three X-ray structures of polbeta in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. 2'-deoxycytidine 5'-triphosphate 51-55 DNA polymerase beta Homo sapiens 143-162 24694247-1 2014 Human DNA polymerase beta (polbeta) inserts, albeit slowly, T opposite the carcinogenic lesion O6-methylguanine (O6MeG) ~30-fold more frequently than C. To gain insight into this promutagenic process, we solved four ternary structures of polbeta with an incoming dCTP or dTTP analogue base-paired with O6MeG in the presence of active-site Mg(2+) or Mn(2+). 2'-deoxycytidine 5'-triphosphate 263-267 DNA polymerase beta Homo sapiens 6-25 22178760-6 2012 The DNA base excision repair enzyme DNA polymerase (pol) beta is presented with gap-filling synthesis opposite 8-oxoG during repair and has similar insertion efficiencies for dCTP and dATP. 2'-deoxycytidine 5'-triphosphate 175-179 DNA polymerase beta Homo sapiens 40-61 17293403-0 2007 Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. 2'-deoxycytidine 5'-triphosphate 90-94 DNA polymerase beta Homo sapiens 114-133 17320292-3 2007 Oligonucleotides carrying photoreactive "damages" were prepared using the multi-stage protocol including one-nucleotide gap filling by DNA polymerase beta using photoreactive dCTP or dUTP analogues followed by ligation of the resulting nick. 2'-deoxycytidine 5'-triphosphate 175-179 DNA polymerase beta Homo sapiens 135-154 17293403-1 2007 To elucidate how human DNA polymerase beta (pol beta) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical step with dATP and dCTP opposite an 8-oxoG template started from partially open complexes of pol beta. 2'-deoxycytidine 5'-triphosphate 78-82 DNA polymerase beta Homo sapiens 23-42 17293403-1 2007 To elucidate how human DNA polymerase beta (pol beta) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical step with dATP and dCTP opposite an 8-oxoG template started from partially open complexes of pol beta. 2'-deoxycytidine 5'-triphosphate 78-82 DNA polymerase beta Homo sapiens 44-52 17293403-1 2007 To elucidate how human DNA polymerase beta (pol beta) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical step with dATP and dCTP opposite an 8-oxoG template started from partially open complexes of pol beta. 2'-deoxycytidine 5'-triphosphate 215-219 DNA polymerase beta Homo sapiens 23-42 17293403-1 2007 To elucidate how human DNA polymerase beta (pol beta) discriminates dATP from dCTP when processing 8-oxoguanine (8-oxoG), we analyze a series of dynamics simulations before and after the chemical step with dATP and dCTP opposite an 8-oxoG template started from partially open complexes of pol beta. 2'-deoxycytidine 5'-triphosphate 215-219 DNA polymerase beta Homo sapiens 44-52 17293403-2 2007 Analyses reveal that the thumb closing of pol beta before chemistry is hampered when the incorrect nucleotide dATP is bound opposite 8-oxoG; the unfavorable interaction between active-site residue Tyr(271) and dATP that causes an anti to syn change in the 8-oxoG (syn):dATP complex explains this slow motion, in contrast to the 8-oxoG (anti):dCTP system. 2'-deoxycytidine 5'-triphosphate 342-346 DNA polymerase beta Homo sapiens 42-50 17293403-4 2007 Together with reference studies with a nonlesioned G template, we propose that 8-oxoG leads to lower efficiency in pol beta"s incorporation of dCTP compared with G by affecting the requisite active-site geometry for the chemical reaction before chemistry. 2'-deoxycytidine 5'-triphosphate 143-147 DNA polymerase beta Homo sapiens 115-123 17286973-0 2007 DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. 2'-deoxycytidine 5'-triphosphate 60-64 DNA polymerase beta Homo sapiens 0-19 17286973-1 2007 Ternary complexes of wild type or mutant form of human DNA polymerase beta (pol beta) bound to DNA and dCTP substrates were studied by molecular dynamics (MD) simulations. 2'-deoxycytidine 5'-triphosphate 103-107 DNA polymerase beta Homo sapiens 55-74 17286973-1 2007 Ternary complexes of wild type or mutant form of human DNA polymerase beta (pol beta) bound to DNA and dCTP substrates were studied by molecular dynamics (MD) simulations. 2'-deoxycytidine 5'-triphosphate 103-107 DNA polymerase beta Homo sapiens 76-84 17286973-4 2007 The correlation coefficients show that the strength of the H-bond between dCTP and Asn279 is a strong predictor of the mutation-induced changes in the catalytic efficiency of pol beta. 2'-deoxycytidine 5'-triphosphate 74-78 DNA polymerase beta Homo sapiens 175-183 17313689-2 2007 To interpret in atomic and energetic detail how pol beta processes 8-oxoG, we apply transition path sampling to delineate closing pathways of pol beta 8-oxoG complexes with dCTP and dATP incoming nucleotides and compare the results to those of the nonlesioned G:dCTP and G:dATPanalogues. 2'-deoxycytidine 5'-triphosphate 173-177 DNA polymerase beta Homo sapiens 48-56 17313689-2 2007 To interpret in atomic and energetic detail how pol beta processes 8-oxoG, we apply transition path sampling to delineate closing pathways of pol beta 8-oxoG complexes with dCTP and dATP incoming nucleotides and compare the results to those of the nonlesioned G:dCTP and G:dATPanalogues. 2'-deoxycytidine 5'-triphosphate 173-177 DNA polymerase beta Homo sapiens 142-150 17313689-2 2007 To interpret in atomic and energetic detail how pol beta processes 8-oxoG, we apply transition path sampling to delineate closing pathways of pol beta 8-oxoG complexes with dCTP and dATP incoming nucleotides and compare the results to those of the nonlesioned G:dCTP and G:dATPanalogues. 2'-deoxycytidine 5'-triphosphate 262-266 DNA polymerase beta Homo sapiens 48-56 17313689-2 2007 To interpret in atomic and energetic detail how pol beta processes 8-oxoG, we apply transition path sampling to delineate closing pathways of pol beta 8-oxoG complexes with dCTP and dATP incoming nucleotides and compare the results to those of the nonlesioned G:dCTP and G:dATPanalogues. 2'-deoxycytidine 5'-triphosphate 262-266 DNA polymerase beta Homo sapiens 142-150 17313689-7 2007 CONCLUSION: These results suggest that the lower insertion efficiency (larger Km) for dATP compared to dCTP opposite 8-oxoG is caused by a less stable closed-form of pol beta, destabilized by unfavorable interactions between Tyr271 and the mispair. 2'-deoxycytidine 5'-triphosphate 103-107 DNA polymerase beta Homo sapiens 166-174