DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

Abstract

Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex and an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing,more » with implications for cell cycle control of DNA replication and genome stability.« less

Authors:
 [1];  [2];  [3];  [4];  [4];  [5];  [6];  [3]
  1. Brookhaven National Laboratory (BNL), Upton, NY (United States)
  2. Brookhaven National Laboratory (BNL), Upton, NY (United States); Stony Brook Univ., Stony Brook, NY (United States)
  3. Imperial College Faculty of Medicine, London (United Kingdom). DNA Replication Group
  4. Imperial College Faculty of Medicine, London (United Kingdom). MRC Clinical Sciences Centre
  5. Stony Brook Univ., Stony Brook, NY (United States)
  6. Cold Spring Harbor Lab., NY (United States)
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1165733
Report Number(s):
BNL-107184-2014-JA
Journal ID: ISSN 0890-9369; 400412000
Grant/Contract Number:  
DE-AC02-98CH10886
Resource Type:
Accepted Manuscript
Journal Name:
Genes & Development
Additional Journal Information:
Journal Volume: 28; Journal Issue: 20; Journal ID: ISSN 0890-9369
Publisher:
Cold Springs Harbor Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; origin recognition complex; DNA replication initiation; replicative helicase; prereplication complex; ELECTRON MICROSCOPY

Citation Formats

Sun, Jingchuan, Li, Huilin, Fernandez-Cid, Alejandra, Riera, Alberto, Tognetti, Sivia, Yuan, Zuanning, Stillman, Bruce, and Speck, Christian. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function. United States: N. p., 2014. Web. doi:10.1101/gad.242313.114.
Sun, Jingchuan, Li, Huilin, Fernandez-Cid, Alejandra, Riera, Alberto, Tognetti, Sivia, Yuan, Zuanning, Stillman, Bruce, & Speck, Christian. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function. United States. https://doi.org/10.1101/gad.242313.114
Sun, Jingchuan, Li, Huilin, Fernandez-Cid, Alejandra, Riera, Alberto, Tognetti, Sivia, Yuan, Zuanning, Stillman, Bruce, and Speck, Christian. Wed . "Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function". United States. https://doi.org/10.1101/gad.242313.114. https://www.osti.gov/servlets/purl/1165733.
@article{osti_1165733,
title = {Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function},
author = {Sun, Jingchuan and Li, Huilin and Fernandez-Cid, Alejandra and Riera, Alberto and Tognetti, Sivia and Yuan, Zuanning and Stillman, Bruce and Speck, Christian},
abstractNote = {Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex and an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.},
doi = {10.1101/gad.242313.114},
journal = {Genes & Development},
number = 20,
volume = 28,
place = {United States},
year = {Wed Oct 15 00:00:00 EDT 2014},
month = {Wed Oct 15 00:00:00 EDT 2014}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 74 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Regulating DNA Replication in Bacteria
journal, March 2013


Assembly of a Double Hexameric Helicase
journal, November 2005


In the absence of ATPase activity, pre-RC formation is blocked prior to MCM2-7 hexamer dimerization
journal, February 2013

  • Evrin, C.; Fernandez-Cid, A.; Zech, J.
  • Nucleic Acids Research, Vol. 41, Issue 5
  • DOI: 10.1093/nar/gkt043

Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication
journal, February 2014


Pre-replicative complex assembly with purified proteins
journal, June 2012


Activation of the MCM2-7 Helicase by Association with Cdc45 and GINS Proteins
journal, January 2010


DNA replication: Building the perfect switch
journal, May 2001


The Mcm Complex: Unwinding the Mechanism of a Replicative Helicase
journal, November 2009

  • Bochman, M. L.; Schwacha, A.
  • Microbiology and Molecular Biology Reviews, Vol. 73, Issue 4
  • DOI: 10.1128/mmbr.00019-09

Origin Licensing Requires ATP Binding and Hydrolysis by the MCM Replicative Helicase
journal, September 2014


mcm5/cdc46-bob1 bypasses the requirement for the S phase activator Cdc7p
journal, April 1997

  • Hardy, Christopher F. J.; Dryga, Olga; Seematter, Sara
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 7
  • DOI: 10.1073/pnas.94.7.3151

The Bacterial DnaC Helicase Loader Is a DnaB Ring Breaker
journal, April 2013


Reconstitution of the Mcm2-7p Heterohexamer, Subunit Arrangement, and ATP Site Architecture
journal, December 2002

  • Davey, Megan J.; Indiani, Chiara; O'Donnell, Mike
  • Journal of Biological Chemistry, Vol. 278, Issue 7
  • DOI: 10.1074/jbc.m210511200

ATPase-dependent quality control of DNA replication origin licensing
journal, March 2013

  • Frigola, Jordi; Remus, Dirk; Mehanna, Amina
  • Nature, Vol. 495, Issue 7441
  • DOI: 10.1038/nature11920

Strength in numbers: preventing rereplication via multiple mechanisms in eukaryotic cells
journal, March 2007


The Bacterial DnaC Helicase Loader Is a DnaB Ring Breaker
journal, April 2013


DNA Replication in Eukaryotic Cells
journal, June 2002


ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex
journal, May 1992

  • Bell, Stephen P.; Stillman, Bruce
  • Nature, Vol. 357, Issue 6374
  • DOI: 10.1038/357128a0

The Mcm2-7 Complex Has In Vitro Helicase Activity
journal, July 2008


The Saccharomyces cerevisiae Mcm6/2 and Mcm5/3 ATPase active sites contribute to the function of the putative Mcm2-7 ‘gate’
journal, May 2010

  • Bochman, Matthew L.; Schwacha, Anthony
  • Nucleic Acids Research, Vol. 38, Issue 18
  • DOI: 10.1093/nar/gkq422

Crystal structure of a near-full-length archaeal MCM: Functional insights for an AAA+ hexameric helicase
journal, December 2008

  • Brewster, A. S.; Wang, G.; Yu, X.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 51
  • DOI: 10.1073/pnas.0808037105

Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2 7 loading
journal, November 2007

  • Chen, S.; de Vries, M. A.; Bell, S. P.
  • Genes & Development, Vol. 21, Issue 22
  • DOI: 10.1101/gad.1596807

A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase
journal, February 2000

  • Chong, J. P. J.; Hayashi, M. K.; Simon, M. N.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 4
  • DOI: 10.1073/pnas.030539597

The structural basis for MCM2–7 helicase activation by GINS and Cdc45
journal, March 2011

  • Costa, Alessandro; Ilves, Ivar; Tamberg, Nele
  • Nature Structural & Molecular Biology, Vol. 18, Issue 4
  • DOI: 10.1038/nsmb.2004

DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome
journal, August 2014


Origin Licensing Requires ATP Binding and Hydrolysis by the MCM Replicative Helicase
journal, September 2014


A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication
journal, November 2009

  • Evrin, C.; Clarke, P.; Zech, J.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 48
  • DOI: 10.1073/pnas.0911500106

In the absence of ATPase activity, pre-RC formation is blocked prior to MCM2-7 hexamer dimerization
journal, February 2013

  • Evrin, C.; Fernandez-Cid, A.; Zech, J.
  • Nucleic Acids Research, Vol. 41, Issue 5
  • DOI: 10.1093/nar/gkt043

The ORC/Cdc6/MCM2-7 complex facilitates MCM2-7 dimerization during prereplicative complex formation
journal, November 2013

  • Evrin, Cecile; Fernández-Cid, Alejandra; Riera, Alberto
  • Nucleic Acids Research, Vol. 42, Issue 4
  • DOI: 10.1093/nar/gkt1148

An ORC/Cdc6/MCM2-7 Complex Is Formed in a Multistep Reaction to Serve as a Platform for MCM Double-Hexamer Assembly
journal, May 2013


The structure and function of MCM from archaeal M. Thermoautotrophicum
journal, January 2003

  • Fletcher, Ryan J.; Bishop, Brooke E.; Leon, Ronald P.
  • Nature Structural & Molecular Biology, Vol. 10, Issue 3
  • DOI: 10.1038/nsb893

Incorporation into the prereplicative complex activates the Mcm2-7 helicase for Cdc7-Dbf4 phosphorylation
journal, March 2009

  • Francis, L. I.; Randell, J. C. W.; Takara, T. J.
  • Genes & Development, Vol. 23, Issue 5
  • DOI: 10.1101/gad.1759609

ATPase-dependent quality control of DNA replication origin licensing
journal, March 2013

  • Frigola, Jordi; Remus, Dirk; Mehanna, Amina
  • Nature, Vol. 495, Issue 7441
  • DOI: 10.1038/nature11920

Selective Bypass of a Lagging Strand Roadblock by the Eukaryotic Replicative DNA Helicase
journal, September 2011


mcm5/cdc46-bob1 bypasses the requirement for the S phase activator Cdc7p
journal, April 1997

  • Hardy, Christopher F. J.; Dryga, Olga; Seematter, Sara
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 7
  • DOI: 10.1073/pnas.94.7.3151

Eukaryotic Origin-Dependent DNA Replication In Vitro Reveals Sequential Action of DDK and S-CDK Kinases
journal, July 2011


Activation of the MCM2-7 Helicase by Association with Cdc45 and GINS Proteins
journal, January 2010


Multiple Functions for Mcm2–7 ATPase Motifs during Replication Initiation
journal, September 2014


Coordinate Binding of ATP and Origin DNA Regulates the ATPase Activity of the Origin Recognition Complex
journal, February 1997


Building a double hexamer of DNA helicase at eukaryotic replication origins
journal, December 2011


Mcm2 is a target of regulation by Cdc7–Dbf4 during the initiation of DNA synthesis
journal, December 1997

  • Lei, Ming; Kawasaki, Yasuo; Young, Michael R.
  • Genes & Development, Vol. 11, Issue 24
  • DOI: 10.1101/gad.11.24.3365

ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote
journal, July 2012

  • Lyubimov, Artem Y.; Costa, Alessandro; Bleichert, Franziska
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 30
  • DOI: 10.1073/pnas.1209406109

Pre-replicative complex assembly with purified proteins
journal, June 2012


Prereplicative complexes assembled in vitro support origin-dependent and independent DNA replication
journal, February 2014


UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

The Initiation Step of Eukaryotic DNA Replication
book, December 2009


Dbf4 and Cdc7 Proteins Promote DNA Replication through Interactions with Distinct Mcm2–7 Protein Subunits
journal, May 2013

  • Ramer, Matthew D.; Suman, Evelyin S.; Richter, Hagen
  • Journal of Biological Chemistry, Vol. 288, Issue 21
  • DOI: 10.1074/jbc.M112.392910

Sequential ATP Hydrolysis by Cdc6 and ORC Directs Loading of the Mcm2-7 Helicase
journal, January 2006


Mec1 Is One of Multiple Kinases that Prime the Mcm2-7 Helicase for Phosphorylation by Cdc7
journal, November 2010


Eukaryotic DNA replication control: Lock and load, then fire
journal, December 2009


Concerted Loading of Mcm2–7 Double Hexamers around DNA during DNA Replication Origin Licensing
journal, November 2009


A unique DNA entry gate serves for regulated loading of the eukaryotic replicative helicase MCM2–7 onto DNA
journal, August 2014

  • Samel, Stefan A.; Fernández-Cid, Alejandra; Sun, Jingchuan
  • Genes & Development, Vol. 28, Issue 15
  • DOI: 10.1101/gad.242404.114

Assembly of a Double Hexameric Helicase
journal, November 2005


Cdc7-Dbf4 Phosphorylates MCM Proteins via a Docking Site-Mediated Mechanism to Promote S Phase Progression
journal, October 2006


The Dbf4–Cdc7 kinase promotes S phase by alleviating an inhibitory activity in Mcm4
journal, January 2010


Regulating DNA Replication in Eukarya
journal, July 2013

  • Siddiqui, K.; On, K. F.; Diffley, J. F. X.
  • Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 9
  • DOI: 10.1101/cshperspect.a012930

Regulating DNA Replication in Bacteria
journal, March 2013


ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA
journal, October 2005

  • Speck, Christian; Chen, Zhiqiang; Li, Huilin
  • Nature Structural & Molecular Biology, Vol. 12, Issue 11
  • DOI: 10.1038/nsmb1002

Cdc6-Induced Conformational Changes in ORC Bound to Origin DNA Revealed by Cryo-Electron Microscopy
journal, March 2012


Cryo-EM structure of a helicase loading intermediate containing ORC–Cdc6–Cdt1–MCM2-7 bound to DNA
journal, July 2013

  • Sun, Jingchuan; Evrin, Cecile; Samel, Stefan A.
  • Nature Structural & Molecular Biology, Vol. 20, Issue 8
  • DOI: 10.1038/nsmb.2629

Multiple Cdt1 molecules act at each origin to load replication-competent Mcm2-7 helicases: Cdt1 influences Mcm2-7 helicase activation
journal, November 2011


Helicase Activation and Establishment of Replication Forks at Chromosomal Origins of Replication
journal, July 2013


EMAN2: An extensible image processing suite for electron microscopy
journal, January 2007

  • Tang, Guang; Peng, Liwei; Baldwin, Philip R.
  • Journal of Structural Biology, Vol. 157, Issue 1
  • DOI: 10.1016/j.jsb.2006.05.009

Dynamics of Pre-replicative Complex Assembly
journal, March 2010

  • Tsakraklides, Vasiliki; Bell, Stephen P.
  • Journal of Biological Chemistry, Vol. 285, Issue 13
  • DOI: 10.1074/jbc.M109.072504

The Eukaryotic Mcm2-7 Replicative Helicase
book, January 2012


Structure and function of the AAA+ nucleotide binding pocket
journal, January 2012

  • Wendler, Petra; Ciniawsky, Susanne; Kock, Malte
  • Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1823, Issue 1
  • DOI: 10.1016/j.bbamcr.2011.06.014

Prereplication-complex formation: a molecular double take?
journal, January 2014

  • Yardimci, Hasan; Walter, Johannes C.
  • Nature Structural & Molecular Biology, Vol. 21, Issue 1
  • DOI: 10.1038/nsmb.2738

Works referencing / citing this record:

From structure to mechanism—understanding initiation of DNA replication
journal, June 2017

  • Riera, Alberto; Barbon, Marta; Noguchi, Yasunori
  • Genes & Development, Vol. 31, Issue 11
  • DOI: 10.1101/gad.298232.117

Recruitment of Mcm10 to Sites of Replication Initiation Requires Direct Binding to the Minichromosome Maintenance (MCM) Complex
journal, March 2016

  • Douglas, Max E.; Diffley, John F. X.
  • Journal of Biological Chemistry, Vol. 291, Issue 11
  • DOI: 10.1074/jbc.m115.707802

DNA translocation mechanism of the MCM complex and implications for replication initiation
journal, July 2019


The eukaryotic CMG helicase pumpjack and integration into the replisome
journal, March 2016


Chromosome Duplication in Saccharomyces cerevisiae
journal, July 2016


Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model
journal, October 2017

  • Noguchi, Yasunori; Yuan, Zuanning; Bai, Lin
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 45
  • DOI: 10.1073/pnas.1712537114

Utilizing Biotinylated Proteins Expressed in Yeast to Visualize DNA–Protein Interactions at the Single-Molecule Level
journal, October 2017


Eukaryotic replication origins: Strength in flexibility
journal, May 2016


Replication landscape of the human genome
journal, January 2016

  • Petryk, Nataliya; Kahli, Malik; d'Aubenton-Carafa, Yves
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms10208

The Temporal Regulation of S Phase Proteins During G1
book, January 2017


Overexpression of minichromosome maintenance protein 10 in medulloblastoma and its clinical implications
journal, June 2017

  • Senfter, Daniel; Erkan, Erdogan Pekcan; Özer, Erdener
  • Pediatric Blood & Cancer, Vol. 64, Issue 12
  • DOI: 10.1002/pbc.26670

Structural basis of Mcm2–7 replicative helicase loading by ORC–Cdc6 and Cdt1
journal, February 2017

  • Yuan, Zuanning; Riera, Alberto; Bai, Lin
  • Nature Structural & Molecular Biology, Vol. 24, Issue 3
  • DOI: 10.1038/nsmb.3372

Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis
journal, December 2016

  • Pauzaite, Tekle; Thacker, Urvi; Tollitt, James
  • Biomolecules, Vol. 7, Issue 4
  • DOI: 10.3390/biom7010001

The architecture of a eukaryotic replisome
journal, November 2015

  • Sun, Jingchuan; Shi, Yi; Georgescu, Roxana E.
  • Nature Structural & Molecular Biology, Vol. 22, Issue 12
  • DOI: 10.1038/nsmb.3113

Structure of the active form of human origin recognition complex and its ATPase motor module
journal, January 2017


Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA
journal, January 2019


Structural basis of Mcm2–7 replicative helicase loading by ORC–Cdc6 and Cdt1
journal, February 2017

  • Yuan, Zuanning; Riera, Alberto; Bai, Lin
  • Nature Structural & Molecular Biology, Vol. 24, Issue 3
  • DOI: 10.1038/nsmb.3372

Replication landscape of the human genome
journal, January 2016

  • Petryk, Nataliya; Kahli, Malik; d'Aubenton-Carafa, Yves
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms10208

Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model
journal, October 2017

  • Noguchi, Yasunori; Yuan, Zuanning; Bai, Lin
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 45
  • DOI: 10.1073/pnas.1712537114

The eukaryotic CMG helicase pumpjack and integration into the replisome
journal, March 2016


DNA translocation mechanism of the MCM complex and implications for replication initiation
journal, July 2019


Human RIF 1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation
journal, January 2017