Abstract
Single stranded DNA binding proteins (SSBs) are present in all known cellular organisms and are critical for DNA replication, recombination and repair. The SSB from the hyperthermophilic crenarchaeote Sulfolobus solfataricus (SsoSSB) has an unusual domain structure with a single DNA-binding oligonucleotide binding (OB) fold coupled to a flexible C-terminal tail. This ‘simple’ domain organisation differs significantly from other known SSBs, such as human replication protein A (RPA). However, it is conserved in another important human SSB, hSSB1, which we have recently discovered and shown to be essential in the DNA damage response. In this study we report the solution-state backbone and side-chain chemical shift assignments of the OB domain of SsoSSB. In addition, using the recently determined crystal structure, we have utilized NMR to reveal the DNA-binding interface of SsoSSB. These data will allow us to elucidate the structural basis of DNA-binding and shed light onto the molecular mechanism by which these ‘simple’ SSBs interact with single-stranded DNA.
Similar content being viewed by others
References
Ayed A, Mulder FA, Yi GS, Lu Y, Kay LE, Arrowsmith CH (2001) Latent and active p53 are identical in conformation. Nat Struct Biol 8(9):756–760
Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L (1997) Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385(6612):176–181
Bochkarev A, Bochkareva E, Frappier L, Edwards AM (1999) The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding. EMBO J 18(16):4498–4504
Cai M, Huang Y, Sakaguchi K, Clore GM, Gronenborn AM, Craigie R (1998) An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli. J Biomol NMR 11(1):97–102
Cubeddu L, White MF (2005) DNA damage detection by an archaeal single-stranded DNA-binding protein. J Mol Biol 353(3):507–516
Flynn RL, Zou L (2010) Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians. Crit Rev Biochem Mol Biol 45(4):266–275
Iftode C, Daniely Y, Borowiec JA (1999) Replication protein A (RPA): the eukaryotic SSB. Crit Rev Biochem Mol Biol 34(3):141–180
Kerr ID, Wadsworth RI, Cubeddu L, Blankenfeldt W, Naismith JH, White MF (2003) Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J 22(11):2561–2570
Lohman TM, Ferrari ME (1994) Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu Rev Biochem 63:527–570
Meyer RR, Laine PS (1990) The single-stranded DNA-binding protein of Escherichia coli. Microbiol Rev 54(4):342–380
Murzin AG (1993) OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J 12(3):861–867
Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 93(19):10268–10273
Newport JW, Lonberg N, Kowalczykowski SC, von Hippel PH (1981) Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. II. Specificity of binding to DNA and RNA. J Mol Biol 145(1):105–121
Raghunathan S, Kozlov AG, Lohman TM, Waksman G (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat Struct Biol 7(8):648–652
Richard DJ, Bell SD, White MF (2004) Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase. Nucleic Acids Res 32(3):1065–1074
Richard DJ, Bolderson E, Cubeddu L, Wadsworth RI, Savage K, Sharma GG, Nicolette ML, Tsvetanov S, McIlwraith MJ, Pandita RK, Takeda S, Hay RT, Gautier J, West SC, Paull TT, Pandita TK, White MF, Khanna KK (2008) Single-stranded DNA-binding protein hSSB1 is critical for genomic stability. Nature 453(7195):677–681
Richard DJ, Bolderson E, Khanna KK (2009) Multiple human single-stranded DNA binding proteins function in genome maintenance: structural, biochemical and functional analysis. Crit Rev Biochem Mol Biol 44(2–3):98–116
Shi H, Zhang Y, Zhang G, Guo J, Zhang X, Song H, Lv J, Gao J, Wang Y, Chen L (2013) Systematic functional comparative analysis of four single-stranded DNA-binding proteins and their affection on viral RNA metabolism. PLoS One 8(1):e55076
Suck D (1997) Common fold, common function, common origin? Nat Struct Biol 4(3):161–165
Sun S, Shamoo Y (2003) Biochemical characterization of interactions between DNA polymerase and single-stranded DNA-binding protein in bacteriophage RB69. J Biol Chem 278(6):3876–3881
Wadsworth RI, White MF (2001) Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res 29(4):914–920
Wold MS (1997) Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem 66:61–92
Acknowledgments
This work was supported by the National Health and Medical Council of Australia (NHMRC) [632610 to L.C.].
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
About this article
Cite this article
Gamsjaeger, R., Kariawasam, R., Touma, C. et al. Backbone and side-chain 1H, 13C and 15N resonance assignments of the OB domain of the single stranded DNA binding protein from Sulfolobus solfataricus and chemical shift mapping of the DNA-binding interface. Biomol NMR Assign 8, 243–246 (2014). https://doi.org/10.1007/s12104-013-9492-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12104-013-9492-4