Abstract
Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase, bypasses a wide range of DNA lesions in vitro and in vivo. In this paper, we report the backbone chemical shift assignments of the full length Dpo4 in its binary complex with a 14/14-mer DNA substrate. Upon DNA binding, several β-stranded regions in the isolated catalytic core and little finger/linker fragments of Dpo4 become more structured. This work serves as a foundation for our ongoing investigation of conformational dynamics of Dpo4 and future determination of the first solution structures of a DNA polymerase and its binary and ternary complexes.
Similar content being viewed by others
References
Boudsocq F, Iwai S et al (2001) Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta. Nucleic Acids Res 29(22):4607–4616
Boudsocq F, Kokoska RJ et al (2004) Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication. J Biol Chem 279(31):32932–32940
Brown JA, Newmister SA et al (2008) Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase. Nucleic Acids Res 36(12):3867–3878
Delaglio F, Grzesiek S et al (1995) Nmrpipe—a multidimensional spectral processing system based on unix pipes. J Biomol NMR 6(3):277–293
Doublie S, Tabor S et al (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391(6664):251–258
Eoff RL, Sanchez-Ponce R et al (2009) Conformational changes during nucleotide selection by Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem 284(31):21090–21099
Fiala KA, Suo Z (2007) Sloppy bypass of an abasic lesion catalyzed by a Y-family DNA polymerase. J Biol Chem 282(11):8199–8206
Fiala KA, Abdel-Gawad W et al (2004) Pre-steady-state kinetic studies of the fidelity and mechanism of polymerization catalyzed by truncated human DNA polymerase lambda. Biochemistry 43(21):6751–6762
Fiala KA, Brown JA et al (2007a) Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase. J Mol Biol 365(3):590–602
Fiala KA, Hypes CD et al (2007b) Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase. J Biol Chem 282(11):8188–8198
Franklin MC, Wang J et al (2001) Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105(5):657–667
Gaur V, Vyas R et al (2014) Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res 42(15):9984–9995
Johnson BA, Blevins RA (1994) NMRView: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614
Johnson SJ, Taylor JS et al (2003) Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc Natl Acad Sci USA 100(7):3895–3900
Li Y, Korolev S et al (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J 17(24):7514–7525
Ling H, Boudsocq F et al (2001) Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107(1):91–102
Ling H, Boudsocq F et al (2003) Replication of a cis-syn thymine dimer at atomic resolution. Nature 424(6952):1083–1087
Ling H, Boudsocq F et al (2004a) Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts. Mol Cell 13(5):751–762
Ling H, Sayer JM et al (2004b) Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase. Proc Natl Acad Sci USA 101(8):2265–2269
Loria JP, Rance M et al (1999) Transverse-relaxation-optimized (TROSY) gradient-enhanced triple-resonance NMR spectroscopy. J Magn Reson 141(1):180–184
Ma D, Fowler JD et al (2010) Backbone assignment of the catalytic core of a Y-family DNA polymerase. Biomol NMR Assign 4(2):207–209
Ma D, Fowler JD et al (2011) Backbone assignment of the little finger domain of a Y-family DNA polymerase. Biomol NMR Assign 5(2):195–198
Maxwell BA, Suo Z (2012) Kinetic basis for the differing response to an oxidative lesion by a replicative and a lesion bypass DNA polymerase from Solfolobus solfataricus. Biochemistry 51:3485–3496
Maxwell BA, Suo Z (2014) Recent insight into the kinetic mechanisms and conformational dynamics of Y-Family DNA polymerases. Biochemistry 53(17):2804–2814
Maxwell BA, Xu C et al (2012) DNA lesion alters global conformational dynamics of Y-family DNA polymerase during catalysis. J Biol Chem 287(16):13040–13047
Ohmori H, Friedberg EC et al (2001) The Y-family of DNA polymerases. Mol Cell 8(1):7–8
Pelletier H, Sawaya MR et al (1996) Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity. Biochemistry 35(39):12742–12761
Raper AT, Gadkari VV et al (2016) Single-molecule investigation of response to oxidative DNA damage by a Y-family DNA polymerase. Biochemistry 55(14):2187–2196
Rechkoblit O, Malinina L et al (2006) Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. PLoS Biol 4(1):e11
Salzmann M, Wider G et al (1999) TROSY-type triple-resonance experiments of sequential NMR assignments of large protein. J Am Chem Soc 121:844–848
Shen Y, Delaglio F et al (2009) TALOS + : a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44(4):213–223
Sherrer SM, Brown JA et al (2009) mechanistic studies of the bypass of a bulky single-base lesion catalyzed by a Y-family DNA polymerase. J Biol Chem 284(10):6379–6388
Sherrer SM, Maxwell BA et al (2012a) Identification of an unfolding intermediate for a DNA lesion bypass polymerase. Chem Res Toxicol 25(7):1531–1540
Sherrer SM, Taggart DJ et al (2012b) Quantitative analysis of the mutagenic potential of 1-aminopyrene-DNA adduct bypass catalyzed by Y-family DNA polymerases. Mutat Res 737(1–2):25–33
Vyas R, Efthimiopoulos G et al (2015) Mechanistic basis for the bypass of a bulky DNA adduct catalyzed by a Y-family DNA polymerase. J Am Chem Soc 137(37):12131–12142
Wong JH, Fiala KA et al (2008) Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4. J Mol Biol 379(2):317–330
Xu C, Maxwell BA et al (2009) Global conformational dynamics of a Y-family DNA polymerase during catalysis. PLoS Biol 7(10):e1000225
Acknowledgments
This work was supported by the National Institute of Health Grant R21ES024585 to both Z.S. and Z.W.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Lee, E., Fowler, J.D., Suo, Z. et al. Backbone assignment of the binary complex of the full length Sulfolobus solfataricus DNA polymerase IV and DNA. Biomol NMR Assign 11, 39–43 (2017). https://doi.org/10.1007/s12104-016-9717-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12104-016-9717-4