scholarly journals Folding of cohesin’s coiled coil is important for Scc2/4-induced association with chromosomes

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Naomi J Petela ◽  
Andres Gonzalez Llamazares ◽  
Sarah Dixon ◽  
Bin Hu ◽  
Byung-Gil Lee ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Entire Length ◽  
Mutant Phenotype ◽  
Physiological Importance ◽  
Sister Chromatids ◽  
Dna Loop ◽  
Smc Proteins

Cohesin’s association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being ‘clamped’ by Scc2 and ATP-dependent engagement of cohesin’s Smc1 and Smc3 head domains. Scc2’s replacement by Pds5 abrogates cohesin’s ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1’s ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin’s coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1’s hinge that alters how Scc2 and Pds5 interact with Smc1’s hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin’s hinge, which in turn requires coiled coil folding.

scholarly journals Topological in vitro loading of the budding yeast cohesin ring onto DNA

2018 ◽  
Vol 1 (5) ◽  
pp. e201800143 ◽  
Author(s):  
Masashi Minamino ◽  
Torahiko L Higashi ◽  
Céline Bouchoux ◽  
Frank Uhlmann
Keyword(s):  
Chromosome Segregation ◽  
Genome Organization ◽  
Atp Hydrolysis ◽  
Budding Yeast ◽  
Reaction Step ◽  
Subsequent Reaction ◽  
Transition State Analog ◽  
Sister Chromatids

The ring-shaped chromosomal cohesin complex holds sister chromatids together by topological embrace, a prerequisite for accurate chromosome segregation. Cohesin plays additional roles in genome organization, transcriptional regulation, and DNA repair. The cohesin ring includes an ABC family ATPase, but the molecular mechanism by which the ATPase contributes to cohesin function is not yet understood. In this study, we have purified budding yeast cohesin, as well as its Scc2–Scc4 cohesin loader complex, and biochemically reconstituted ATP-dependent topological cohesin loading onto DNA. Our results reproduce previous observations obtained using fission yeast cohesin, thereby establishing conserved aspects of cohesin behavior. Unexpectedly, we find that nonhydrolyzable ATP ground state mimetics ADP·BeF2, ADP·BeF3−, and ADP·AlFx, but not a hydrolysis transition state analog ADP·VO43−, support cohesin loading. The energy from nucleotide binding is sufficient to drive the DNA entry reaction into the cohesin ring. ATP hydrolysis, believed to be essential for in vivo cohesin loading, must serve a subsequent reaction step. These results provide molecular insights into cohesin function and open new experimental opportunities that the budding yeast model affords.

scholarly journals In Vivo Bypass of Chaperone by Extended Coiled-Coil Motif in T4 Tail Fiber

2004 ◽  
Vol 186 (24) ◽  
pp. 8363-8369 ◽  
Author(s):  
Yun Qu ◽  
Paul Hyman ◽  
Timothy Harrah ◽  
Edward Goldberg
Keyword(s):  
Bacteriophage T4 ◽  
Coiled Coil ◽  
Critical Factor ◽  
Coiled Coils ◽  
Temperature Sensitive ◽  
Tail Fiber ◽  
Type Gene ◽  
In Vivo Screen

ABSTRACT The distal-half tail fiber of bacteriophage T4 is made of three gene products: trimeric gp36 and gp37 and monomeric gp35. Chaperone P38 is normally required for folding gp37 peptides into a P37 trimer; however, a temperature-sensitive mutation in T4 (ts3813) that suppresses this requirement at 30°C but not at 42°C was found in gene 37 (R. J. Bishop and W. B. Wood, Virology 72:244-254, 1976). Sequencing of the temperature-sensitive mutant revealed a 21-bp duplication of wild-type gene 37 inserted into its C-terminal portion (S. Hashemolhosseini et al., J. Mol. Biol. 241:524-533, 1994). We noticed that the 21-amino-acid segment encompassing this duplication in the ts3813 mutant has a sequence typical of a coiled coil and hypothesized that its extension would relieve the temperature sensitivity of the ts3813 mutation. To test our hypothesis, we crossed the T4 ts3813 mutant with a plasmid encoding an engineered pentaheptad coiled coil. Each of the six mutants that we examined retained two amber mutations in gene 38 and had a different coiled-coil sequence varying from three to five heptads. While the sequences varied, all maintained the heptad-repeating coiled-coil motif and produced plaques at up to 50°C. This finding strongly suggests that the coiled-coil motif is a critical factor in the folding of gp37. The presence of a terminal coiled-coil-like sequence in the tail fiber genes of 17 additional T-even phages implies the conservation of this mechanism. The increased melting temperature should be useful for “clamps” to initiate the folding of trimeric β-helices in vitro and as an in vivo screen to identify, sequence, and characterize trimeric coiled coils.

scholarly journals Coiled-Coil Trigger Motifs in the 1B and 2B Rod Domain Segments Are Required for the Stability of Keratin Intermediate Filaments

2000 ◽  
Vol 11 (10) ◽  
pp. 3539-3558 ◽  
Author(s):  
Kenneth C. Wu ◽  
Janine T. Bryan ◽  
Maria I. Morasso ◽  
Shyh-Ing Jang ◽  
Jeung-Hoon Lee ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Coiled Coils ◽  
Detectable Effect ◽  
Keratin 5 ◽  
Molecular Stability ◽  
Potential Trigger ◽  
Helical Proteins ◽  
The Stability

Many α-helical proteins that form two-chain coiled coils possess a 13-residue trigger motif that seems to be required for the stability of the coiled coil. However, as currently defined, the motif is absent from intermediate filament (IF) protein chains, which nevertheless form segmented two-chain coiled coils. In the present work, we have searched for and identified two regions in IF chains that are essential for the stability necessary for the formation of coiled-coil molecules and thus may function as trigger motifs. We made a series of point substitutions with the keratin 5/keratin 14 IF system. Combinations of the wild-type and mutant chains were assembled in vitro and in vivo, and the stabilities of two-chain (one-molecule) and two-molecule assemblies were examined with use of a urea disassembly assay. Our new data document that there is a region located between residues 100 and 113 of the 2B rod domain segment that is absolutely required for molecular stability and IF assembly. This potential trigger motif differs slightly from the consensus in having an Asp residue at position 4 (instead of a Glu) and a Thr residue at position 9 (instead of a charged residue), but there is an absolute requirement for a Glu residue at position 6. Because these 13 residues are highly conserved, it seems possible that this motif functions in all IF chains. Likewise, by testing keratin IF with substitutions in both chains, we identified a second potential trigger motif between residues 79 and 91 of the 1B rod domain segment, which may also be conserved in all IF chains. However, we were unable to find a trigger motif in the 1A rod domain segment. In addition, many other point substitutions had little detectable effect on IF assembly, except for the conserved Lys-23 residue of the 2B rod domain segment. Cross-linking and modeling studies revealed that Lys-23 may lie very close to Glu-106 when two molecules are aligned in the A22 mode. Thus, the Glu-106 residue may have a dual role in IF structure: it may participate in trigger formation to afford special stability to the two-chain coiled-coil molecule, and it may participate in stabilization of the two-molecule hierarchical stage of IF structure.

scholarly journals Structural and Functional Analysis of Essential pre-mRNA Splicing Factor Prp19p

2005 ◽  
Vol 25 (1) ◽  
pp. 451-460 ◽  
Author(s):  
Melanie D. Ohi ◽  
Craig W. Vander Kooi ◽  
Joshua A. Rosenberg ◽  
Liping Ren ◽  
Justin P. Hirsch ◽  
...  
Keyword(s):  
Functional Data ◽  
Coiled Coil ◽  
Single Copy ◽  
Coiled Coils ◽  
Binding Partner ◽  
Central Stalk ◽  
Interaction Surface

ABSTRACT U-box-containing Prp19p is an integral component of the Prp19p-associated complex (the nineteen complex, or NTC) that is essential for activation of the spliceosome. Prp19p makes numerous protein-protein contacts with other NTC components and is required for NTC stability. Here we show that Prp19p forms a tetramer in vitro and in vivo and we map the domain required for its oligomerization to a central tetrameric coiled-coil. Biochemical and in vivo analyses are consistent with Prp19p tetramerization providing an interaction surface for a single copy of its binding partner, Cef1p. Electron microscopy showed that the isolated Prp19p tetramer is an elongated particle consisting of four globular WD40 domains held together by a central stalk consisting of four N-terminal U-boxes and four coiled-coils. These structural and functional data provide a basis for understanding the role of Prp19p as a key architectural component of the NTC.

scholarly journals The preprophase band-associated kinesin-14 OsKCH2 is a processive minus-end-directed microtubule motor

2017 ◽  
Author(s):  
Kuo-Fu Tseng ◽  
Pan Wang ◽  
Yuh-Ru Julie Lee ◽  
Joel Bowen ◽  
Allison M. Gicking ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Preprophase Band ◽  
Cytoplasmic Dynein ◽  
Coiled Coils ◽  
Land Plants ◽  
Actin Binding ◽  
Actin Binding Domain ◽  
Microtubule Motor

AbstractIn animals and fungi, cytoplasmic dynein is a processive motor that plays dominant roles in various intracellular processes. In contrast, land plants lack cytoplasmic dynein but contain many minus-end-directed kinesin-14s. No plant kinesin-14 is known to produce processive motility as a homodimer. OsKCH2 is a plant-specific kinesin-14 with an N-terminal actin-binding domain and a central motor domain flanked by two predicted coiled-coils (CC1 and CC2). Here, we show that OsKCH2 specifically decorates preprophase band microtubules in vivo and transports actin filaments along microtubules in vitro. Importantly, OsKCH2 exhibits processive minus-end-directed motility on single microtubules as individual homodimers. We find that CC1 but not CC2 forms the coiled-coil for OsKCH2 dimerization. Instead, CC2 functions to enable OsKCH2 processivity by enhancing its binding to microtubules. Collectively, these results show that land plants have evolved unconventional kinesin-14 homodimers with inherent minus-end-directed processivity that may function to compensate for the loss of cytoplasmic dynein.

scholarly journals Acyl Carrier Protein is essential for MukBEF action in Escherichia coli chromosome organization-segregation

2021 ◽  
Author(s):  
Josh Prince ◽  
Jani Bolla ◽  
Gemma Fisher ◽  
Jarno Makela ◽  
Majorie Fournier ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acyl Carrier Protein ◽  
Coiled Coil ◽  
Acid Synthesis ◽  
Chromosome Organization ◽  
Carrier Protein ◽  
Accessory Proteins ◽  
Structural Maintenance Of Chromosomes ◽  
Smc Proteins

Abstract Structural Maintenance of Chromosomes (SMC) complexes contribute ubiquitously to chromosome organization-segregation. SMC proteins have a conserved architecture, with a dimerization hinge and an ATPase head domain separated by a long antiparallel intramolecular coiled-coil. Dimeric SMC proteins interact with essential accessory proteins, kleisins that bridge the two subunits of an SMC dimer, and HAWK/KITE accessory proteins that interact with kleisins. The ATPase activity of the Escherichia coli SMC protein, MukB, is essential for in vivo function and is regulated by interactions with its dimeric kleisin, MukF, and KITE, MukE. Here we demonstrate that, in addition, MukB interacts with Acyl Carrier Protein (AcpP) that has essential functions in fatty acid synthesis. We characterize the AcpP interaction site at the joint of the MukB coiled-coil and show that the interaction is essential for MukB ATPase and for MukBEF function in vivo. Therefore, AcpP is an essential co-factor for MukBEF action in chromosome organization-segregation.

scholarly journals Extrinsic conditions influence the self-association and structure of IF1, the regulatory protein of mitochondrial ATP synthase

2019 ◽  
Vol 116 (21) ◽  
pp. 10354-10359 ◽  
Author(s):  
Vytaute Boreikaite ◽  
Basile I. M. Wicky ◽  
Ian N. Watt ◽  
Jane Clarke ◽  
John E. Walker
Keyword(s):  
Atp Synthase ◽  
Atp Hydrolysis ◽  
Regulatory Protein ◽  
Coiled Coil ◽  
The Self ◽  
Intrinsically Disordered ◽  
Mitochondrial Atp Synthase ◽  
Self Association ◽  
Α Helix

The endogenous inhibitor of ATP synthase in mitochondria, called IF1, conserves cellular energy when the proton-motive force collapses by inhibiting ATP hydrolysis. Around neutrality, the 84-amino-acid bovine IF1 is thought to self-assemble into active dimers and, under alkaline conditions, into inactive tetramers and higher oligomers. Dimerization is mediated by formation of an antiparallel α-helical coiled-coil involving residues 44–84. The inhibitory region of each monomer from residues 1–46 is largely α-helical in crystals, but disordered in solution. The formation of the inhibited enzyme complex requires the hydrolysis of two ATP molecules, and in the complex the disordered region from residues 8–13 is extended and is followed by an α-helix from residues 14–18 and a longer α-helix from residue 21, which continues unbroken into the coiled-coil region. From residues 21–46, the long α-helix binds to other α-helices in the C-terminal region of predominantly one of the β-subunits in the most closed of the three catalytic interfaces. The definition of the factors that influence the self-association of IF1 is a key to understanding the regulation of its inhibitory properties. Therefore, we investigated the influence of pH and salt-types on the self-association of bovine IF1 and the folding of its unfolded region. We identified the equilibrium between dimers and tetramers as a potential central factor in the in vivo modulation of the inhibitory activity and suggest that the intrinsically disordered region makes its inhibitory potency exquisitely sensitive and responsive to physiological changes that influence the capability of mitochondria to make ATP.

scholarly journals Condensin and cohesin display different arm conformations with characteristic hinge angles

2002 ◽  
Vol 156 (3) ◽  
pp. 419-424 ◽  
Author(s):  
David E. Anderson ◽  
Ana Losada ◽  
Harold P. Erickson ◽  
Tatsuya Hirano
Keyword(s):  
Catalytic Domain ◽  
Protein Complexes ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Structure Characteristic ◽  
Catalytic Domains ◽  
Open Conformation ◽  
Chromatid Cohesion ◽  
Structural Maintenance Of Chromosomes ◽  
Smc Proteins

Structural maintenance of chromosomes (SMC) proteins play central roles in higher-order chromosome dynamics from bacteria to humans. In eukaryotes, two different SMC protein complexes, condensin and cohesin, regulate chromosome condensation and sister chromatid cohesion, respectively. Each of the complexes consists of a heterodimeric pair of SMC subunits and two or three non-SMC subunits. Previous studies have shown that a bacterial SMC homodimer has a symmetrical structure in which two long coiled-coil arms are connected by a flexible hinge. A catalytic domain with DNA- and ATP-binding activities is located at the distal end of each arm. We report here the visualization of vertebrate condensin and cohesin by electron microscopy. Both complexes display the two-armed structure characteristic of SMC proteins, but their conformations are remarkably different. The hinge of condensin is closed and the coiled-coil arms are placed close together. In contrast, the hinge of cohesin is wide open and the coiled-coils are spread apart from each other. The non-SMC subunits of both condensin and cohesin form a globular complex bound to the catalytic domains of the SMC heterodimers. We propose that the “closed” conformation of condensin and the “open” conformation of cohesin are important structural properties that contribute to their specialized biochemical and physiological functions.

scholarly journals The topology of DNA entrapment by cohesin rings

2018 ◽  
Author(s):  
Christophe Chapard ◽  
Robert Jones ◽  
Till van Oepen ◽  
Johanna C Scheinost ◽  
Kim Nasmyth
Keyword(s):  
Atp Hydrolysis ◽  
S Phase ◽  
Coiled Coils ◽  
Pairwise Interactions

SummaryCohesin entraps sister DNAs within tripartite rings created by pairwise interactions between Smc1,Smc3, and Scc1. Because the ATPase heads of Smc1 and Smc3 can interact with each other, cohesin rings in fact have the potential to form a variety of sub-compartments. Using in vivo cysteine crosslinking,we show that when Smc1 and Smc3 ATPases are engaged in the presence of ATP (E heads)cohesin rings generate a “SMC (S) compartment” between hinge and E heads and a “kleisin (K)compartment” between E heads and their associated kleisin subunit. Upon ATP hydrolysis, cohesin’s heads associate with each other in a very different mode, in which their signature motifs and their coiled coils are closely juxtaposed (J heads), creating alternative S and K compartments. We show that all four sub-compartments exist in vivo, that acetylation of Smc3 during S phase is accompanied by an increase in the ratio of J to E heads, and that sister DNAs are entrapped in J-K but not E-K compartments or in either type of S compartment.

scholarly journals The Symmetrical Structure of Structural Maintenance of Chromosomes (SMC) and MukB Proteins: Long, Antiparallel Coiled Coils, Folded at a Flexible Hinge

1998 ◽  
Vol 142 (6) ◽  
pp. 1595-1604 ◽  
Author(s):  
Thomas E. Melby ◽  
Charles N. Ciampaglio ◽  
Gina Briscoe ◽  
Harold P. Erickson
Keyword(s):  
Escherichia Coli ◽  
Coiled Coil ◽  
Biomechanical Properties ◽  
Coiled Coils ◽  
Symmetrical Structure ◽  
Terminal Domain ◽  
Symmetrical Molecule ◽  
Almost All ◽  
Structural Maintenance Of Chromosomes ◽  
Smc Proteins

Structural maintenance of chromosomes (SMC) proteins function in chromosome condensation and several other aspects of DNA processing. They are large proteins characterized by an NH2-terminal nucleotide triphosphate (NTP)-binding domain, two long segments of coiled coil separated by a hinge, and a COOH-terminal domain. Here, we have visualized by EM the SMC protein from Bacillus subtilis (BsSMC) and MukB from Escherichia coli, which we argue is a divergent SMC protein. Both BsSMC and MukB show two thin rods with globular domains at the ends emerging from the hinge. The hinge appears to be quite flexible: the arms can open up to 180°, separating the terminal domains by 100 nm, or close to near 0°, bringing the terminal globular domains together. A surprising observation is that the ∼300–amino acid–long coiled coils are in an antiparallel arrangement. Known coiled coils are almost all parallel, and the longest antiparallel coiled coils known previously are 35–45 amino acids long. This antiparallel arrangement produces a symmetrical molecule with both an NH2- and a COOH-terminal domain at each end. The SMC molecule therefore has two complete and identical functional domains at the ends of the long arms. The bifunctional symmetry and a possible scissoring action at the hinge should provide unique biomechanical properties to the SMC proteins.

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