Crystal structure of the C. thermophilum condensin Smc2 ATPase head (crystal from I)

Summary The condensin protein complex plays a key role in the structural organization of genomes. How the ATPase activity of its SMC subunits drives large-scale changes in chromosome topology has remained unknown. Here we reconstruct, at near-atomic resolution, the sequence of events that take place during the condensin ATPase cycle. We show that ATP binding induces a conformational switch in the Smc4 head domain that releases its hitherto undescribed interaction with the Ycs4 HEAT-repeat subunit and promotes its engagement with the Smc2 head into an asymmetric heterodimer. SMC head dimerization subsequently enables nucleotide binding at the second active site and disengages the Brn1 kleisin subunit from the Smc2 coiled coil to open the condensin ring. These large-scale transitions in the condensin architecture lay out a mechanistic path for its ability to extrude DNA helices into large loop structures.

[1]  K. Nasmyth,et al.  A folded conformation of MukBEF and cohesin , 2018, bioRxiv.

[2]  C. Haering,et al.  Towards a Unified Model of SMC Complex Function , 2018, Current Biology.

[3]  M. Tyers,et al.  Condensin ATPase motifs contribute differentially to the maintenance of chromosome morphology and genome stability , 2018, PLoS biology.

[4]  F. Uhlmann,et al.  Cell-Cycle Regulation of Dynamic Chromosome Association of the Condensin Complex , 2018, Cell reports.

[5]  Cees Dekker,et al.  Real-time imaging of DNA loop extrusion by condensin , 2018, Science.

[6]  D. Sherratt,et al.  MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin , 2018, eLife.

[7]  Shveta Bisht,et al.  Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes , 2017, Cell.

[8]  B. Oh,et al.  Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization , 2017, Molecular cell.

[9]  S. Gruber Shaping chromosomes by DNA capture and release: gating the SMC rings. , 2017, Current opinion in cell biology.

[10]  Cees Dekker,et al.  The condensin complex is a mechanochemical motor that translocates along DNA , 2017, Science.

[11]  T. Hirano,et al.  Overall Shapes of the SMC-ScpAB Complex Are Determined by Balance between Constraint and Relaxation of Its Structural Parts. , 2017, Structure.

[12]  Z. Otwinowski,et al.  Crystal structure of the cohesin loader Scc2 and insight into cohesinopathy , 2016, Proceedings of the National Academy of Sciences.

[13]  E. Nora,et al.  CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation. , 2016, Annual review of genomics and human genetics.

[14]  K. Hopfner Invited review: Architectures and mechanisms of ATP binding cassette proteins , 2016, Biopolymers.

[15]  Itay Mayrose,et al.  ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..

[16]  Liisa Holm,et al.  Dali server update , 2016, Nucleic Acids Res..

[17]  Hongtao Yu,et al.  Structural Basis and IP6 Requirement for Pds5-Dependent Cohesin Dynamics. , 2016, Molecular cell.

[18]  F. Uhlmann SMC complexes: from DNA to chromosomes , 2016, Nature Reviews Molecular Cell Biology.

[19]  T. Hirano,et al.  Condensin-Based Chromosome Organization from Bacteria to Vertebrates , 2016, Cell.

[20]  K. Nasmyth,et al.  Cohesin Releases DNA through Asymmetric ATPase-Driven Ring Opening , 2016, Molecular cell.

[21]  K. Nasmyth,et al.  Releasing Activity Disengages Cohesin’s Smc3/Scc1 Interface in a Process Blocked by Acetylation , 2016, Molecular cell.

[22]  Anton Goloborodko,et al.  Compaction and segregation of sister chromatids via active loop extrusion , 2016, bioRxiv.

[23]  F. Uhlmann,et al.  DNA Entry into and Exit out of the Cohesin Ring by an Interlocking Gate Mechanism , 2015, Cell.

[24]  D. Nurizzo,et al.  MASSIF-1: a beamline dedicated to the fully automatic characterization and data collection from crystals of biological macromolecules , 2015, Journal of synchrotron radiation.

[25]  G. Drewes,et al.  Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry , 2015, Nature Protocols.

[26]  Olof Svensson,et al.  Fully automatic characterization and data collection from crystals of biological macromolecules , 2015, Acta crystallographica. Section D, Biological crystallography.

[27]  B. Oh,et al.  SMC condensin entraps chromosomal DNA by an ATP hydrolysis dependent loading mechanism in Bacillus subtilis , 2015, eLife.

[28]  Adam Round,et al.  The status of the macromolecular crystallography beamlines at the European Synchrotron Radiation Facility , 2015 .

[29]  Tetsuya J. Kobayashi,et al.  Balancing acts of two HEAT subunits of condensin I support dynamic assembly of chromosome axes. , 2015, Developmental cell.

[30]  Ruedi Aebersold,et al.  Characterization of a DNA exit gate in the human cohesin ring , 2014, Science.

[31]  Kim Nasmyth,et al.  Closing the cohesin ring: Structure and function of its Smc3-kleisin interface , 2014, Science.

[32]  Q. Qu,et al.  Structure of cohesin subcomplex pinpoints direct shugoshin–Wapl antagonism in centromeric cohesion , 2014, Nature Structural &Molecular Biology.

[33]  M. Beck,et al.  Association of condensin with chromosomes depends on DNA binding by its HEAT-repeat subunits , 2014, Nature Structural &Molecular Biology.

[34]  Philip R. Evans,et al.  How good are my data and what is the resolution? , 2013, Acta crystallographica. Section D, Biological crystallography.

[35]  O. Stemmann,et al.  Prophase pathway‐dependent removal of cohesin from human chromosomes requires opening of the Smc3–Scc1 gate , 2013, The EMBO journal.

[36]  B. Oh,et al.  An asymmetric SMC–kleisin bridge in prokaryotic condensin , 2013, Nature Structural &Molecular Biology.

[37]  A. M. George,et al.  Mechanism of the ABC transporter ATPase domains: catalytic models and the biochemical and biophysical record , 2013, Critical reviews in biochemistry and molecular biology.

[38]  K. Nasmyth,et al.  Cohesin’s DNA Exit Gate Is Distinct from Its Entrance Gate and Is Regulated by Acetylation , 2012, Cell.

[39]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[40]  Gordon A Leonard,et al.  ID29: a high-intensity highly automated ESRF beamline for macromolecular crystallography experiments exploiting anomalous scattering. , 2012, Journal of synchrotron radiation.

[41]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[42]  Randy J. Read,et al.  Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum , 2012, Acta crystallographica. Section D, Biological crystallography.

[43]  Hongtao Yu,et al.  The Smc complexes in DNA damage response , 2012, Cell & Bioscience.

[44]  Ian Stokes-Rees,et al.  A grid-enabled web service for low-resolution crystal structure refinement , 2012, Acta crystallographica. Section D, Biological crystallography.

[45]  C. Haering,et al.  Condensin structures chromosomal DNA through topological links , 2011, Nature Structural &Molecular Biology.

[46]  Philip R. Evans,et al.  An introduction to data reduction: space-group determination, scaling and intensity statistics , 2011, Acta crystallographica. Section D, Biological crystallography.

[47]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[48]  A. Wood,et al.  Condensin and cohesin complexity: the expanding repertoire of functions , 2010, Nature Reviews Genetics.

[49]  R. Durbin,et al.  Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes , 2010, Nature.

[50]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[51]  Michael Levitt,et al.  Super-resolution biomolecular crystallography with low-resolution data , 2010, Nature.

[52]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[53]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[54]  A. Bax,et al.  TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts , 2009, Journal of biomolecular NMR.

[55]  D. D'Amours,et al.  Polo kinase regulates mitotic chromosome condensation by hyperactivation of condensin DNA supercoiling activity. , 2009, Molecular cell.

[56]  Rachelle Gaudet,et al.  The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter , 2009, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[57]  Keehyoung Joo,et al.  Structural Studies of a Bacterial Condensin Complex Reveal ATP-Dependent Disruption of Intersubunit Interactions , 2009, Cell.

[58]  J. Rappsilber,et al.  Explorer Molecular and Genetic Analysis of Condensin Function in Vertebrate Cells , 2017 .

[59]  K. Nasmyth,et al.  The cohesin ring concatenates sister DNA molecules , 2008, Nature.

[60]  Randy J. Read,et al.  Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard , 2007 .

[61]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[62]  A. Brunger Version 1.2 of the Crystallography and NMR system , 2007, Nature Protocols.

[63]  S. Hahn,et al.  The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex , 2007, Nature Structural &Molecular Biology.

[64]  T. Hirano,et al.  Reconstitution and subunit geometry of human condensin complexes , 2007, The EMBO journal.

[65]  Airlie J. McCoy,et al.  Solving structures of protein complexes by molecular replacement with Phaser , 2006, Acta crystallographica. Section D, Biological crystallography.

[66]  Christiane Schaffitzel,et al.  Protein complex expression by using multigene baculoviral vectors , 2006, Nature Methods.

[67]  Christophe Romier,et al.  Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies. , 2006, Acta crystallographica. Section D, Biological crystallography.

[68]  Kim Nasmyth,et al.  Structure and stability of cohesin's Smc1-kleisin interaction. , 2004, Molecular cell.

[69]  K. Nasmyth,et al.  ATP Hydrolysis Is Required for Cohesin's Association with Chromosomes , 2003, Current Biology.

[70]  F. Uhlmann,et al.  A Model for ATP Hydrolysis-Dependent Binding of Cohesin to DNA , 2003, Current Biology.

[71]  Michael Nilges,et al.  ARIA: automated NOE assignment and NMR structure calculation , 2003, Bioinform..

[72]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[73]  D. Koshland,et al.  In vivo dissection of the chromosome condensation machinery , 2002, The Journal of cell biology.

[74]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[75]  K Wüthrich,et al.  TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[76]  R. Riek,et al.  Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[77]  J. Thornton,et al.  AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR , 1996, Journal of biomolecular NMR.

[78]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[79]  Bruce A. Johnson,et al.  NMR View: A computer program for the visualization and analysis of NMR data , 1994, Journal of biomolecular NMR.

[80]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[81]  K. Gull,et al.  Definition of individual components within the cytoskeleton of Trypanosoma brucei by a library of monoclonal antibodies. , 1989, Journal of cell science.

[82]  D. Smith,et al.  Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. , 1988, Gene.

[83]  Sevinç Ercan,et al.  Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation. , 2018, Trends in genetics : TIG.

[84]  Eric Blanc,et al.  Automated structure solution with autoSHARP. , 2007, Methods in molecular biology.

[85]  P. Evans,et al.  Scaling and assessment of data quality. , 2006, Acta crystallographica. Section D, Biological crystallography.

[86]  K. Nasmyth THE GENOME : Joining , Resolving , and Separating Sister Chromatids During Mitosis and Meiosis , 2006 .

[87]  S. Doublié [29] Preparation of selenomethionyl proteins for phase determination. , 1997, Methods in enzymology.