3jc5 Citations

Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation.

Nat Struct Mol Biol 23 217-24 (2016)
Related entries: 3jc6, 3jc7

Cited: 96 times
EuropePMC logo PMID: 26854665

Abstract

The CMG helicase is composed of Cdc45, Mcm2-7 and GINS. Here we report the structure of the Saccharomyces cerevisiae CMG, determined by cryo-EM at a resolution of 3.7-4.8 Å. The structure reveals that GINS and Cdc45 scaffold the N tier of the helicase while enabling motion of the AAA+ C tier. CMG exists in two alternating conformations, compact and extended, thus suggesting that the helicase moves like an inchworm. The N-terminal regions of Mcm2-7, braced by Cdc45-GINS, form a rigid platform upon which the AAA+ C domains make longitudinal motions, nodding up and down like an oil-rig pumpjack attached to a stable platform. The Mcm ring is remodeled in CMG relative to the inactive Mcm2-7 double hexamer. The Mcm5 winged-helix domain is inserted into the central channel, thus blocking entry of double-stranded DNA and supporting a steric-exclusion DNA-unwinding model.

Reviews - 3jc5 mentioned but not cited (5)

  1. Mechanisms and regulation of DNA replication initiation in eukaryotes. Parker MW, Botchan MR, Berger JM. Crit. Rev. Biochem. Mol. Biol. 52 107-144 (2017)
  2. Structural insights into Cdc45 function: was there a nuclease at the heart of the ancestral replisome? Pellegrini L. Biophys. Chem. 225 10-14 (2017)
  3. The Eukaryotic CMG Helicase at the Replication Fork: Emerging Architecture Reveals an Unexpected Mechanism. Li H, O'Donnell ME. Bioessays 40 (2018)
  4. Architecture of the Saccharomyces cerevisiae Replisome. Bai L, Yuan Z, Sun J, Georgescu R, O'Donnell ME, Li H. Adv. Exp. Med. Biol. 1042 207-228 (2017)
  5. Cryo-EM of dynamic protein complexes in eukaryotic DNA replication. Sun J, Yuan Z, Bai L, Li H. Protein Sci. 26 40-51 (2017)

Articles - 3jc5 mentioned but not cited (9)

  1. Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation. Yuan Z, Bai L, Sun J, Georgescu R, Liu J, O'Donnell ME, Li H. Nat Struct Mol Biol 23 217-224 (2016)
  2. The mechanism of eukaryotic CMG helicase activation. Douglas ME, Ali FA, Costa A, Diffley JFX. Nature 555 265-268 (2018)
  3. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase. Lõoke M, Maloney MF, Bell SP. Genes Dev. 31 291-305 (2017)
  4. CMG-Pol epsilon dynamics suggests a mechanism for the establishment of leading-strand synthesis in the eukaryotic replisome. Zhou JC, Janska A, Goswami P, Renault L, Abid Ali F, Kotecha A, Diffley JFX, Costa A. Proc. Natl. Acad. Sci. U.S.A. 114 4141-4146 (2017)
  5. DNA unwinding mechanism of a eukaryotic replicative CMG helicase. Yuan Z, Georgescu R, Bai L, Zhang D, Li H, O'Donnell ME. Nat Commun 11 688 (2020)
  6. Critical assessment of coiled-coil predictions based on protein structure data. Simm D, Hatje K, Waack S, Kollmar M. Sci Rep 11 12439 (2021)
  7. New insights into the GINS complex explain the controversy between existing structural models. Carroni M, De March M, Medagli B, Krastanova I, Taylor IA, Amenitsch H, Araki H, Pisani FM, Patwardhan A, Onesti S. Sci Rep 7 40188 (2017)
  8. Ctf4 organizes sister replisomes and Pol α into a replication factory. Yuan Z, Georgescu R, Santos RLA, Zhang D, Bai L, Yao NY, Zhao G, O'Donnell ME, Li H. Elife 8 (2019)
  9. Tissue-Specific Requirement for the GINS Complex During Zebrafish Development. Varga M, Csályi K, Bertyák I, Menyhárd DK, Poole RJ, Cerveny KL, Kövesdi D, Barátki B, Rouse H, Vad Z, Hawkins TA, Stickney HL, Cavodeassi F, Schwarz Q, Young RM, Wilson SW. Front Cell Dev Biol 8 373 (2020)


Reviews citing this publication (23)

  1. Chromosome Duplication in Saccharomyces cerevisiae. Bell SP, Labib K. Genetics 203 1027-1067 (2016)
  2. Unravelling biological macromolecules with cryo-electron microscopy. Fernandez-Leiro R, Scheres SH. Nature 537 339-346 (2016)
  3. Eukaryotic DNA Replication Fork. Burgers PMJ, Kunkel TA. Annu. Rev. Biochem. 86 417-438 (2017)
  4. Mechanisms for initiating cellular DNA replication. Bleichert F, Botchan MR, Berger JM. Science 355 (2017)
  5. From structure to mechanism-understanding initiation of DNA replication. Riera A, Barbon M, Noguchi Y, Reuter LM, Schneider S, Speck C. Genes Dev. 31 1073-1088 (2017)
  6. Mechanisms of hexameric helicases. Fernandez AJ, Berger JM. Crit Rev Biochem Mol Biol 56 621-639 (2021)
  7. Watching cellular machinery in action, one molecule at a time. Monachino E, Spenkelink LM, van Oijen AM. J. Cell Biol. 216 41-51 (2017)
  8. The architecture and function of the chromatin replication machinery. Miller TC, Costa A. Curr. Opin. Struct. Biol. 47 9-16 (2017)
  9. The ring-shaped hexameric helicases that function at DNA replication forks. O'Donnell ME, Li H. Nat. Struct. Mol. Biol. 25 122-130 (2018)
  10. Fundamental Characteristics of AAA+ Protein Family Structure and Function. Miller JM, Enemark EJ. Archaea 2016 9294307 (2016)
  11. A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand DNA cross-links derived from psoralen and abasic sites. Yang Z, Nejad MI, Varela JG, Price NE, Wang Y, Gates KS. DNA Repair (Amst.) 52 1-11 (2017)
  12. Origin DNA Melting-An Essential Process with Divergent Mechanisms. Martinez MP, Jones JM, Bruck I, Kaplan DL. Genes (Basel) 8 (2017)
  13. Effects of radiation damage in studies of protein-DNA complexes by cryo-EM. Mishyna M, Volokh O, Danilova Y, Gerasimova N, Pechnikova E, Sokolova OS. Micron 96 57-64 (2017)
  14. The eukaryotic CMG helicase pumpjack and integration into the replisome. Sun J, Yuan Z, Georgescu R, Li H, O'Donnell M. Nucleus 7 146-154 (2016)
  15. Caught in the act: structural dynamics of replication origin activation and fork progression. Lewis JS, Costa A. Biochem Soc Trans 48 1057-1066 (2020)
  16. Replication of G Quadruplex DNA. Lerner LK, Sale JE. Genes (Basel) 10 (2019)
  17. The Human Replicative Helicase, the CMG Complex, as a Target for Anti-cancer Therapy. Seo YS, Kang YH. Front Mol Biosci 5 26 (2018)
  18. Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication. Martinez MP, Wacker AL, Bruck I, Kaplan DL. Genes (Basel) 8 (2017)
  19. Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage. Guilliam TA. Front Mol Biosci 8 712971 (2021)
  20. History of DNA Helicases. Brosh RM, Matson SW. Genes (Basel) 11 (2020)
  21. Noise in the Machine: Alternative Pathway Sampling is the Rule During DNA Replication. Scherr MJ, Safaric B, Duderstadt KE. Bioessays 40 (2018)
  22. Single-Molecule Insights Into the Dynamics of Replicative Helicases. Spinks RR, Spenkelink LM, Dixon NE, van Oijen AM. Front Mol Biosci 8 741718 (2021)
  23. The Role of MTBP as a Replication Origin Firing Factor. Zaffar E, Ferreira P, Sanchez-Pulido L, Boos D. Biology (Basel) 11 827 (2022)

Articles citing this publication (59)

  1. Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation. Georgescu R, Yuan Z, Bai L, de Luna Almeida Santos R, Sun J, Zhang D, Yurieva O, Li H, O'Donnell ME. Proc. Natl. Acad. Sci. U.S.A. 114 E697-E706 (2017)
  2. Mutations in CDC45, Encoding an Essential Component of the Pre-initiation Complex, Cause Meier-Gorlin Syndrome and Craniosynostosis. Fenwick AL, Kliszczak M, Cooper F, Murray J, Sanchez-Pulido L, Twigg SR, Goriely A, McGowan SJ, Miller KA, Taylor IB, Logan C, WGS500 Consortium, Bozdogan S, Danda S, Dixon J, Elsayed SM, Elsobky E, Gardham A, Hoffer MJ, Koopmans M, McDonald-McGinn DM, Santen GW, Savarirayan R, de Silva D, Vanakker O, Wall SA, Wilson LC, Yuregir OO, Zackai EH, Ponting CP, Jackson AP, Wilkie AO, Niedzwiedz W, Bicknell LS. Am. J. Hum. Genet. 99 125-138 (2016)
  3. Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H. Nat. Struct. Mol. Biol. 24 316-324 (2017)
  4. Open-ringed structure of the Cdt1-Mcm2-7 complex as a precursor of the MCM double hexamer. Zhai Y, Cheng E, Wu H, Li N, Yung PY, Gao N, Tye BK. Nat. Struct. Mol. Biol. 24 300-308 (2017)
  5. Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model. Noguchi Y, Yuan Z, Bai L, Schneider S, Zhao G, Stillman B, Speck C, Li H. Proc. Natl. Acad. Sci. U.S.A. 114 E9529-E9538 (2017)
  6. Archaeal orthologs of Cdc45 and GINS form a stable complex that stimulates the helicase activity of MCM. Xu Y, Gristwood T, Hodgson B, Trinidad JC, Albers SV, Bell SD. Proc. Natl. Acad. Sci. U.S.A. 113 13390-13395 (2016)
  7. Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase. Wasserman MR, Schauer GD, O'Donnell ME, Liu S. Cell 178 600-611.e16 (2019)
  8. Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. Oyama T, Ishino S, Shirai T, Yamagami T, Nagata M, Ogino H, Kusunoki M, Ishino Y. Nucleic Acids Res. 44 9505-9517 (2016)
  9. Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. Baretić D, Jenkyn-Bedford M, Aria V, Cannone G, Skehel M, Yeeles JTP. Mol Cell 78 926-940.e13 (2020)
  10. Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative. Mir-Sanchis I, Roman CA, Misiura A, Pigli YZ, Boyle-Vavra S, Rice PA. Nat. Struct. Mol. Biol. 23 891-898 (2016)
  11. Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA. Xu N, You Y, Liu C, Balasov M, Lun LT, Geng Y, Fung CP, Miao H, Tian H, Choy TT, Shi X, Fan Z, Zhou B, Akhmetova K, Din RU, Yang H, Hao Q, Qian P, Chesnokov I, Zhu G. Nucleic Acids Res 48 11146-11161 (2020)
  12. Action of CMG with strand-specific DNA blocks supports an internal unwinding mode for the eukaryotic replicative helicase. Langston L, O'Donnell M. Elife 6 (2017)
  13. Cryo-EM structure of a licensed DNA replication origin. Abid Ali F, Douglas ME, Locke J, Pye VE, Nans A, Diffley JFX, Costa A. Nat Commun 8 2241 (2017)
  14. Cdt1 stabilizes an open MCM ring for helicase loading. Frigola J, He J, Kinkelin K, Pye VE, Renault L, Douglas ME, Remus D, Cherepanov P, Costa A, Diffley JFX. Nat Commun 8 15720 (2017)
  15. Human DDK rescues stalled forks and counteracts checkpoint inhibition at unfired origins to complete DNA replication. Jones MJK, Gelot C, Munk S, Koren A, Kawasoe Y, George KA, Santos RE, Olsen JV, McCarroll SA, Frattini MG, Takahashi TS, Jallepalli PV. Mol Cell 81 426-441.e8 (2021)
  16. EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps. Zhou N, Wang H, Wang J. Sci Rep 7 2664 (2017)
  17. Bacterial and Eukaryotic Replisome Machines. Yao N, O'Donnell M. JSM Biochem Mol Biol 3 (2016)
  18. Cdc45-induced loading of human RPA onto single-stranded DNA. Szambowska A, Tessmer I, Prus P, Schlott B, Pospiech H, Grosse F. Nucleic Acids Res. 45 3217-3230 (2017)
  19. DDK regulates replication initiation by controlling the multiplicity of Cdc45-GINS binding to Mcm2-7. De Jesús-Kim L, Friedman LJ, Lõoke M, Ramsoomair CK, Gelles J, Bell SP. Elife 10 e65471 (2021)
  20. DNA melting initiates the RAG catalytic pathway. Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H. Nat. Struct. Mol. Biol. 25 732-742 (2018)
  21. The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis. Nagata M, Ishino S, Yamagami T, Ogino H, Simons JR, Kanai T, Atomi H, Ishino Y. Nucleic Acids Res. 45 10693-10705 (2017)
  22. The RecJ2 protein in the thermophilic archaeon Thermoplasma acidophilum is a 3'-5' exonuclease that associates with a DNA replication complex. Ogino H, Ishino S, Kohda D, Ishino Y. J. Biol. Chem. 292 7921-7931 (2017)
  23. DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase. Graham BW, Tao Y, Dodge KL, Thaxton CT, Olaso D, Young NL, Marshall AG, Trakselis MA. J. Biol. Chem. 291 12467-12480 (2016)
  24. In Vitro Reconstitution Defines the Minimal Requirements for Cdc48-Dependent Disassembly of the CMG Helicase in Budding Yeast. Mukherjee PP, Labib KPM. Cell Rep 28 2777-2783.e4 (2019)
  25. Mcm10 has potent strand-annealing activity and limits translocase-mediated fork regression. Mayle R, Langston L, Molloy KR, Zhang D, Chait BT, O'Donnell ME. Proc. Natl. Acad. Sci. U.S.A. 116 798-803 (2019)
  26. Pre-initiation complex assembly functions as a molecular switch that splits the Mcm2-7 double hexamer. Miyazawa-Onami M, Araki H, Tanaka S. EMBO Rep. 18 1752-1761 (2017)
  27. Structure of a human replisome shows the organisation and interactions of a DNA replication machine. Jones ML, Baris Y, Taylor MRG, Yeeles JTP. EMBO J 40 e108819 (2021)
  28. The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer. Saleh A, Noguchi Y, Aramayo R, Ivanova ME, Stevens KM, Montoya A, Sunidhi S, Carranza NL, Skwark MJ, Speck C. Nat Commun 13 2915 (2022)
  29. CryoEM structures of human CMG-ATPγS-DNA and CMG-AND-1 complexes. Rzechorzek NJ, Hardwick SW, Jatikusumo VA, Chirgadze DY, Pellegrini L. Nucleic Acids Res 48 6980-6995 (2020)
  30. Multistep mechanism of G-quadruplex resolution during DNA replication. Sato K, Martin-Pintado N, Post H, Altelaar M, Knipscheer P. Sci Adv 7 eabf8653 (2021)
  31. Possible function of the second RecJ-like protein in stalled replication fork repair by interacting with Hef. Nagata M, Ishino S, Yamagami T, Simons JR, Kanai T, Atomi H, Ishino Y. Sci Rep 7 16949 (2017)
  32. The intra-S phase checkpoint directly regulates replication elongation to preserve the integrity of stalled replisomes. Liu Y, Wang L, Xu X, Yuan Y, Zhang B, Li Z, Xie Y, Yan R, Zheng Z, Ji J, Murray JM, Carr AM, Kong D. Proc Natl Acad Sci U S A 118 e2019183118 (2021)
  33. Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea. Yi GS, Song Y, Wang WW, Chen JN, Deng W, Cao W, Wang FP, Xiao X, Liu XP. Genes (Basel) 8 (2017)
  34. High expression of PSF1 promotes drug resistance and cell cycle transit in leukemia cells. Hsieh HY, Jia W, Jin ZC, Kidoya H, Takakura N. Cancer Sci 111 2400-2412 (2020)
  35. Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome. Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A. Nat Commun 9 5061 (2018)
  36. Activity, substrate preference and structure of the HsMCM8/9 helicase. McKinzey DR, Li C, Gao Y, Trakselis MA. Nucleic Acids Res 51 7330-7341 (2023)
  37. Amidst multiple binding orientations on fork DNA, Saccharolobus MCM helicase proceeds N-first for unwinding. Perera HM, Trakselis MA. Elife 8 (2019)
  38. Anatomy of a twin DNA replication factory. Li H, Yao NY, O'Donnell ME. Biochem Soc Trans 48 2769-2778 (2020)
  39. CMG helicase activity on G4-containing DNA templates. Batra S, Devbhandari S, Remus D. Methods Enzymol 672 233-260 (2022)
  40. CMG helicase can use ATPγS to unwind DNA: Implications for the rate-limiting step in the reaction mechanism. Yao NY, Zhang D, Yurieva O, O'Donnell ME. Proc Natl Acad Sci U S A 119 e2119580119 (2022)
  41. Crystal Structure of Entamoeba histolytica Cdc45 Suggests a Conformational Switch that May Regulate DNA Replication. Kurniawan F, Shi K, Kurahashi K, Bielinsky AK, Aihara H. iScience 3 102-109 (2018)
  42. DNA replication protein Cdc45 directly interacts with PCNA via its PIP box in Leishmania donovani and the Cdc45 PIP box is essential for cell survival. Yadav A, Sharma V, Pal J, Gulati P, Goel M, Chandra U, Bansal N, Saha S. PLoS Pathog 16 e1008190 (2020)
  43. DNA translocation mechanism of the MCM complex and implications for replication initiation. Meagher M, Epling LB, Enemark EJ. Nat Commun 10 3117 (2019)
  44. Defects in the GINS complex increase the instability of repetitive sequences via a recombination-dependent mechanism. Jedrychowska M, Denkiewicz-Kruk M, Alabrudzinska M, Skoneczna A, Jonczyk P, Dmowski M, Fijalkowska IJ. PLoS Genet. 15 e1008494 (2019)
  45. Dpb11 may function with RPA and DNA to initiate DNA replication. Bruck I, Dhingra N, Martinez MP, Kaplan DL. PLoS ONE 12 e0177147 (2017)
  46. Human CST suppresses origin licensing and promotes AND-1/Ctf4 chromatin association. Wang Y, Brady KS, Caiello BP, Ackerson SM, Stewart JA. Life Sci Alliance 2 (2019)
  47. Human NOC3 is essential for DNA replication licensing in human cells. Cheung MH, Amin A, Wu R, Qin Y, Zou L, Yu Z, Liang C. Cell Cycle 18 605-620 (2019)
  48. Initiation-specific alleles of the Cdc45 helicase-activating protein. Rios-Morales RY, Chan SH, Bell SP. PLoS ONE 14 e0214426 (2019)
  49. Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome. Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A. Cell Rep 28 2673-2688.e8 (2019)
  50. Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance. Yuan Z, Li H. Biochem J 477 3499-3525 (2020)
  51. Multiple roles of Pol epsilon in eukaryotic chromosome replication. Cvetkovic MA, Ortega E, Bellelli R, Costa A. Biochem Soc Trans 50 309-320 (2022)
  52. Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility. Qiao C, Debiasi-Anders G, Mir-Sanchis I. Nucleic Acids Res 50 8349-8362 (2022)
  53. Structural and mechanistic insights into the MCM8/9 helicase complex. Weng Z, Zheng J, Zhou Y, Lu Z, Wu Y, Xu D, Li H, Liang H, Liu Y. Elife 12 RP87468 (2023)
  54. Structure of a dimer of the Sulfolobus solfataricus MCM N-terminal domain reveals a potential role in MCM ring opening. Meagher M, Spence MN, Enemark EJ. Acta Crystallogr F Struct Biol Commun 77 177-186 (2021)
  55. Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y. Nat Commun 14 5849 (2023)
  56. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Grabarczyk DB. Subcell Biochem 99 83-107 (2022)
  57. The absence of the catalytic domains of Saccharomyces cerevisiae DNA polymerase ϵ strongly reduces DNA replication fidelity. Garbacz MA, Cox PB, Sharma S, Lujan SA, Chabes A, Kunkel TA. Nucleic Acids Res. 47 3986-3995 (2019)
  58. The mechanism of DNA unwinding by the eukaryotic replicative helicase. Burnham DR, Kose HB, Hoyle RB, Yardimci H. Nat Commun 10 2159 (2019)
  59. Two Distinct Modes of DNA Binding by an MCM Helicase Enable DNA Translocation. Meagher M, Myasnikov A, Enemark EJ. Int J Mol Sci 23 14678 (2022)