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The crystal structure of the Thermus aquaticus DnaB helicase monomer.

Bailey S, Eliason WK, Steitz TA
Nucleic Acids Res 35 4728-36 (2007)
Cited: 38 times
EuropePMC logo PMID: 17606462

Abstract

The ring-shaped hexameric DnaB helicase unwinds duplex DNA at the replication fork of eubacteria. We have solved the crystal structure of the full-length Thermus aquaticus DnaB monomer, or possibly dimer, at 2.9 A resolution. DnaB is a highly flexible two domain protein. The C-terminal domain exhibits a RecA-like core fold and contains all the conserved sequence motifs that are characteristic of the DnaB helicase family. The N-terminal domain contains an additional helical hairpin that makes it larger than previously appreciated. Several DnaB mutations that modulate its interaction with primase are found in this hairpin. The similarity in the fold of the DnaB N-terminal domain with that of the C-terminal helicase-binding domain (HBD) of the DnaG primase also includes this hairpin. Comparison of hexameric homology models of DnaB with the structure of the papillomavirus E1 helicase suggests the two helicases may function through different mechanisms despite their sharing a common ancestor.

Reviews - 2q6t mentioned but not cited (1)

  1. Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target. Robinson A, Causer RJ, Dixon NE. Curr Drug Targets 13 352-372 (2012)

Articles - 2q6t mentioned but not cited (6)

  1. Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold. Chatterjee A, Johnson MA, Serrano P, Pedrini B, Joseph JS, Neuman BW, Saikatendu K, Buchmeier MJ, Kuhn P, Wüthrich K. J Virol 83 1823-1836 (2009)
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  4. Structural insight into the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT. Huang YH, Huang CY. Biomed Res Int 2014 195162 (2014)
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Reviews citing this publication (5)

  1. On helicases and other motor proteins. Enemark EJ, Joshua-Tor L. Curr. Opin. Struct. Biol. 18 243-257 (2008)
  2. Mechanisms for initiating cellular DNA replication. Costa A, Hood IV, Berger JM. Annu. Rev. Biochem. 82 25-54 (2013)
  3. Structural Foundations of RNA Silencing by Argonaute. Sheu-Gruttadauria J, MacRae IJ. J. Mol. Biol. 429 2619-2639 (2017)
  4. Replisome Assembly at Bacterial Chromosomes and Iteron Plasmids. Wegrzyn KE, Gross M, Uciechowska U, Konieczny I. Front Mol Biosci 3 39 (2016)
  5. DnaG Primase-A Target for the Development of Novel Antibacterial Agents. Ilic S, Cohen S, Singh M, Tam B, Dayan A, Akabayov B. Antibiotics (Basel) 7 (2018)

Articles citing this publication (26)

  1. Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase. Bailey S, Eliason WK, Steitz TA. Science 318 459-463 (2007)
  2. The hexameric helicase DnaB adopts a nonplanar conformation during translocation. Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA. Cell 151 267-277 (2012)
  3. The bacterial DnaC helicase loader is a DnaB ring breaker. Arias-Palomo E, O'Shea VL, Hood IV, Berger JM. Cell 153 438-448 (2013)
  4. The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA. Lo YH, Tsai KL, Sun YJ, Chen WT, Huang CY, Hsiao CD. Nucleic Acids Res. 37 804-814 (2009)
  5. Primase directs the release of DnaC from DnaB. Makowska-Grzyska M, Kaguni JM. Mol. Cell 37 90-101 (2010)
  6. Hexameric ring structure of the N-terminal domain of Mycobacterium tuberculosis DnaB helicase. Biswas T, Tsodikov OV. FEBS J. 275 3064-3071 (2008)
  7. Architecture of a dodecameric bacterial replicative helicase. Stelter M, Gutsche I, Kapp U, Bazin A, Bajic G, Goret G, Jamin M, Timmins J, Terradot L. Structure 20 554-564 (2012)
  8. Three-dimensional structure of N-terminal domain of DnaB helicase and helicase-primase interactions in Helicobacter pylori. Kashav T, Nitharwal R, Abdulrehman SA, Gabdoulkhakov A, Saenger W, Dhar SK, Gourinath S. PLoS ONE 4 e7515 (2009)
  9. Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, Berger JM. Mol. Cell 52 844-854 (2013)
  10. Structure of a helicase-helicase loader complex reveals insights into the mechanism of bacterial primosome assembly. Liu B, Eliason WK, Steitz TA. Nat Commun 4 2495 (2013)
  11. Structure and primase-mediated activation of a bacterial dodecameric replicative helicase. Bazin A, Cherrier MV, Gutsche I, Timmins J, Terradot L. Nucleic Acids Res. 43 8564-8576 (2015)
  12. Transcription leads to pervasive replisome instability in bacteria. Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Elife 6 (2017)
  13. DnaC traps DnaB as an open ring and remodels the domain that binds primase. Chodavarapu S, Jones AD, Feig M, Kaguni JM. Nucleic Acids Res. 44 210-220 (2016)
  14. DNA binding activity of Helicobacter pylori DnaB helicase: the role of the N-terminal domain in modulating DNA binding activities. Nitharwal RG, Verma V, Subbarao N, Dasgupta S, Choudhury NR, Dhar SK. FEBS J. 279 234-250 (2012)
  15. Characterization of physical interaction between replication initiator protein DnaA and replicative helicase from Mycobacterium tuberculosis H37Rv. Xie Y, He ZG. Biochemistry Mosc. 74 1320-1327 (2009)
  16. Molecular basis for recognition of nucleoside triphosphate by gene 4 helicase of bacteriophage T7. Lee SJ, Richardson CC. J. Biol. Chem. 285 31462-31471 (2010)
  17. Monitoring ssDNA Binding to the DnaB Helicase from Helicobacter pylori by Solid-State NMR Spectroscopy. Wiegand T, Cadalbert R, Gardiennet C, Timmins J, Terradot L, Böckmann A, Meier BH. Angew. Chem. Int. Ed. Engl. 55 14164-14168 (2016)
  18. Variability and conservation of structural domains in divide-and-conquer approaches. Wiegand T, Gardiennet C, Cadalbert R, Lacabanne D, Kunert B, Terradot L, Böckmann A, Meier BH. J. Biomol. NMR 65 79-86 (2016)
  19. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication. Hood IV, Berger JM. Elife 5 (2016)
  20. Analysis of the roles of NrdR and DnaB from Streptococcus pyogenes in response to host defense. Zhang Y, Okada R, Isaka M, Tatsuno I, Isobe K, Hasegawa T. APMIS 123 252-259 (2015)
  21. Bacterial DnaB helicase interacts with the excluded strand to regulate unwinding. Carney SM, Gomathinayagam S, Leuba SH, Trakselis MA. J. Biol. Chem. 292 19001-19012 (2017)
  22. Replisome Dynamics during Chromosome Duplication. Kurth I, O'Donnell M. EcoSal Plus 3 (2009)
  23. The Caulobacter crescentus DciA promotes chromosome replication through topological loading of the DnaB replicative helicase at replication forks. Ozaki S, Wang D, Wakasugi Y, Itani N, Katayama T. Nucleic Acids Res 50 12896-12912 (2022)
  24. DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells. Williams ND, Landajuela A, Kasula RK, Zhou W, Powell JT, Xi Z, Isaacs FJ, Berro J, Toomre D, Karatekin E, Lin C. Nano Lett 20 8890-8896 (2020)
  25. Mechanisms of opening and closing of the bacterial replicative helicase. Chase J, Catalano A, Noble AJ, Eng ET, Olinares PD, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. Elife 7 (2018)
  26. Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase. Marsin S, Adam Y, Cargemel C, Andreani J, Baconnais S, Legrand P, Li de la Sierra-Gallay I, Humbert A, Aumont-Nicaise M, Velours C, Ochsenbein F, Durand D, Le Cam E, Walbott H, Possoz C, Quevillon-Cheruel S, Ferat JL. Nucleic Acids Res 49 6569-6586 (2021)


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