scholarly journals Structural basis for the coiled-coil architecture of human CtIP

2021 ◽  
Author(s):  
C. R. Morton ◽  
N. J. Rzechorzek ◽  
J. D. Maman ◽  
M. Kuramochi ◽  
H. Sekiguchi ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Strand Break ◽  
Structural Basis ◽  
Binding Motif ◽  
Chromosomal Dna ◽  
Dsb Repair ◽  
Critical Function ◽  
X Ray

AbstractThe DNA repair factor CtIP has a critical function in Double-Strand Break (DSB) repair by Homologous Recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, Small-angle X-ray Scattering (SAXS) and Diffracted X-ray Tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during recombinational repair. The zinc-binding motif in CtIP’s N-terminus alters dynamically the coiled coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.

scholarly journals Structural basis for the coiled-coil architecture of human CtIP

Open Biology ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 210060
Author(s):  
C. R. Morton ◽  
N. J. Rzechorzek ◽  
J. D. Maman ◽  
M. Kuramochi ◽  
H. Sekiguchi ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Strand Break ◽  
Structural Basis ◽  
Binding Motif ◽  
Chromosomal Dna ◽  
Dsb Repair ◽  
Critical Function ◽  
X Ray

The DNA repair factor CtIP has a critical function in double-strand break (DSB) repair by homologous recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here, we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, small-angle X-ray scattering (SAXS) and diffracted X-ray tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during the recombinational repair. The zinc-binding motif in the CtIP N-terminus alters dynamically the coiled-coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.

scholarly journals The Roles of Bacterial DNA Double-Strand Break Repair Proteins in Chromosomal DNA Replication

2020 ◽  
Vol 44 (3) ◽  
pp. 351-368 ◽  
Author(s):  
Anurag Kumar Sinha ◽  
Christophe Possoz ◽  
David R F Leach
Keyword(s):  
Dna Replication ◽  
Cell Viability ◽  
Strand Break ◽  
Double Strand Break ◽  
Replication Initiation ◽  
Genome Replication ◽  
Chromosomal Dna ◽  
Dsb Repair ◽  
Bacterial Dna ◽  
Dna Double Strand Break

ABSTRACT It is well established that DNA double-strand break (DSB) repair is required to underpin chromosomal DNA replication. Because DNA replication forks are prone to breakage, faithful DSB repair and correct replication fork restart are critically important. Cells, where the proteins required for DSB repair are absent or altered, display characteristic disturbances to genome replication. In this review, we analyze how bacterial DNA replication is perturbed in DSB repair mutant strains and explore the consequences of these perturbations for bacterial chromosome segregation and cell viability. Importantly, we look at how DNA replication and DSB repair processes are implicated in the striking recent observations of DNA amplification and DNA loss in the chromosome terminus of various mutant Escherichia coli strains. We also address the mutant conditions required for the remarkable ability to copy the entire E. coli genome, and to maintain cell viability, even in the absence of replication initiation from oriC, the unique origin of DNA replication in wild type cells. Furthermore, we discuss the models that have been proposed to explain these phenomena and assess how these models fit with the observed data, provide new insights and enhance our understanding of chromosomal replication and termination in bacteria.

scholarly journals Image Reconstructions of Microtubules Decorated with Monomeric and Dimeric Kinesins: Comparison with X-Ray Structure and Implications for Motility

1998 ◽  
Vol 141 (2) ◽  
pp. 419-430 ◽  
Author(s):  
A. Hoenger ◽  
S. Sack ◽  
M. Thormählen ◽  
A. Marx ◽  
J. Müller ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Image Reconstruction ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Cryoelectron Microscopy ◽  
Short Neck ◽  
X Ray ◽  
Dimensional Image ◽  
Tubulin Subunit ◽  
Image Reconstructions

We have decorated microtubules with monomeric and dimeric kinesin constructs, studied their structure by cryoelectron microscopy and three-dimensional image reconstruction, and compared the results with the x-ray crystal structure of monomeric and dimeric kinesin. A monomeric kinesin construct (rK354, containing only a short neck helix insufficient for coiled-coil formation) decorates microtubules with a stoichiometry of one kinesin head per tubulin subunit (α–β-heterodimer). The orientation of the kinesin head (an anterograde motor) on the microtubule surface is similar to that of ncd (a retrograde motor). A longer kinesin construct (rK379) forms a dimer because of the longer neck helix forming a coiled-coil. Unexpectedly, this construct also decorates the microtubule with a stoichiometry of one head per tubulin subunit, and the orientation is similar to that of the monomeric construct. This means that the interaction with microtubules causes the two heads of a kinesin dimer to separate sufficiently so that they can bind to two different tubulin subunits. This result is in contrast to recent models and can be explained by assuming that the tubulin–kinesin interaction is antagonistic to the coiled-coil interaction within a kinesin dimer.

scholarly journals A Newly Assigned Role of CTCF in Cellular Response to Broken DNAs

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 363
Author(s):  
Mi Ae Kang ◽  
Jong-Soo Lee
Keyword(s):  
Dna Sequences ◽  
Transcriptional Activation ◽  
Cellular Response ◽  
Developmental Disorders ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Dna Double Strand Breaks ◽  
Dsb Repair ◽  
A Chain

Best known as a transcriptional factor, CCCTC-binding factor (CTCF) is a highly conserved multifunctional DNA-binding protein with 11 zinc fingers. It functions in diverse genomic processes, including transcriptional activation/repression, insulation, genome imprinting and three-dimensional genome organization. A big surprise has recently emerged with the identification of CTCF engaging in the repair of DNA double-strand breaks (DSBs) and in the maintenance of genome fidelity. This discovery now adds a new dimension to the multifaceted attributes of this protein. CTCF facilitates the most accurate DSB repair via homologous recombination (HR) that occurs through an elaborate pathway, which entails a chain of timely assembly/disassembly of various HR-repair complexes and chromatin modifications and coordinates multistep HR processes to faithfully restore the original DNA sequences of broken DNA sites. Understanding the functional crosstalks between CTCF and other HR factors will illuminate the molecular basis of various human diseases that range from developmental disorders to cancer and arise from impaired repair. Such knowledge will also help understand the molecular mechanisms underlying the diverse functions of CTCF in genome biology. In this review, we discuss the recent advances regarding this newly assigned versatile role of CTCF and the mechanism whereby CTCF functions in DSB repair.

scholarly journals Structural basis of NLR activation and innate immune signalling in plants

2022 ◽  
Author(s):  
Natsumi Maruta ◽  
Hayden Burdett ◽  
Bryan Y. J. Lim ◽  
Xiahao Hu ◽  
Sneha Desa ◽  
...  
Keyword(s):  
Immune Responses ◽  
Interleukin 1 ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Innate Immune ◽  
Structural Basis ◽  
Innate Immune Responses ◽  
Oligomeric State ◽  
Coiled Coil Domain ◽  
The Family

AbstractAnimals and plants have NLRs (nucleotide-binding leucine-rich repeat receptors) that recognize the presence of pathogens and initiate innate immune responses. In plants, there are three types of NLRs distinguished by their N-terminal domain: the CC (coiled-coil) domain NLRs, the TIR (Toll/interleukin-1 receptor) domain NLRs and the RPW8 (resistance to powdery mildew 8)-like coiled-coil domain NLRs. CC-NLRs (CNLs) and TIR-NLRs (TNLs) generally act as sensors of effectors secreted by pathogens, while RPW8-NLRs (RNLs) signal downstream of many sensor NLRs and are called helper NLRs. Recent studies have revealed three dimensional structures of a CNL (ZAR1) including its inactive, intermediate and active oligomeric state, as well as TNLs (RPP1 and ROQ1) in their active oligomeric states. Furthermore, accumulating evidence suggests that members of the family of lipase-like EDS1 (enhanced disease susceptibility 1) proteins, which are uniquely found in seed plants, play a key role in providing a link between sensor NLRs and helper NLRs during innate immune responses. Here, we summarize the implications of the plant NLR structures that provide insights into distinct mechanisms of action by the different sensor NLRs and discuss plant NLR-mediated innate immune signalling pathways involving the EDS1 family proteins and RNLs.

scholarly journals Structure and function of outer dynein arm intermediate and light chain complex

2016 ◽  
Vol 27 (7) ◽  
pp. 1051-1059 ◽  
Author(s):  
Toshiyuki Oda ◽  
Tatsuki Abe ◽  
Haruaki Yanagisawa ◽  
Masahide Kikkawa
Keyword(s):  
Molecular Mechanisms ◽  
Electron Tomography ◽  
3D Structure ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Chain Complex ◽  
Flagellar Motility ◽  
Chemically Induced Dimerization ◽  
And Function

The outer dynein arm (ODA) is a molecular complex that drives the beating motion of cilia/flagella. Chlamydomonas ODA is composed of three heavy chains (HCs), two ICs, and 11 light chains (LCs). Although the three-dimensional (3D) structure of the whole ODA complex has been investigated, the 3D configurations of the ICs and LCs are largely unknown. Here we identified the 3D positions of the two ICs and three LCs using cryo–electron tomography and structural labeling. We found that these ICs and LCs were all localized at the root of the outer-inner dynein (OID) linker, designated the ODA-Beak complex. Of interest, the coiled-coil domain of IC2 extended from the ODA-Beak to the outer surface of ODA. Furthermore, we investigated the molecular mechanisms of how the OID linker transmits signals to the ODA-Beak, by manipulating the interaction within the OID linker using a chemically induced dimerization system. We showed that the cross-linking of the OID linker strongly suppresses flagellar motility in vivo. These results suggest that the ICs and LCs of the ODA form the ODA-Beak, which may be involved in mechanosignaling from the OID linker to the HCs.

Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens

2017 ◽  
Vol 474 (2) ◽  
pp. 231-246 ◽  
Author(s):  
Leonor Morgado ◽  
Marta Bruix ◽  
P. Raj Pokkuluri ◽  
Carlos A. Salgueiro ◽  
David L. Turner
Keyword(s):  
Conformational Changes ◽  
Solution Structure ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Axial Ligand ◽  
Geobacter Sulfurreducens ◽  
Cellular Growth ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Natural Habitats

The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e−/H+ coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pKa values of the redox-Bohr center, providing insights into the e−/H+ coupling molecular mechanisms driven by PpcA in G. sulfurreducens.

Multiple Approaches to Visualizing Fibrin Clot Structure and Assembly

1997 ◽  
Vol 3 (S2) ◽  
pp. 329-330
Author(s):  
John W. Weisel
Keyword(s):  
Binding Sites ◽  
Molecular Mechanisms ◽  
Ex Vivo ◽  
Three Dimensional ◽  
Fibrin Clot ◽  
Structural Basis ◽  
Physiological Processes ◽  
Dimensional Network ◽  
Clot Structure

Fibrin clot formation is necessary for maintaining the integrity of the vasculature via physiological processes of hemostasis and wound healing and is also involved in pathological processes, such as thrombosis and atherosclerosis. A variety of structural and biophysical approaches has been used to examine intermediates in the formation of clots and to visualize in vitro clots and ex vivo thrombi.Structures at all stages of polymerization have been examined to learn about molecular mechanisms of assembly. Fibrinogen is a polyfunctional, multi-domain protein that is essential for platelet aggregation and for the formation of the three-dimensional network of fibrin fibers which is the structural basis of the clot. Distinctive functions for several of fibrinogen's domains in the fibrin assembly process have been elucidated. Enzymatic removal of the fibrinopeptides exposes binding sites in the central region which then interact with complementary sites at the ends of a neighboring molecule to yield fibrin oligomers.

A structural basis of light energy and electron transfer in biology1

1989 ◽  
Vol 9 (6) ◽  
pp. 635-673 ◽  
Author(s):  
Robert Huber
Keyword(s):  
Electron Transfer ◽  
Functional Data ◽  
Three Dimensional ◽  
Light Energy ◽  
Structural Basis ◽  
Reaction Centre ◽  
X Ray ◽  
X Ray Crystallography ◽  
Energy And Electron Transfer ◽  
And Function

Aspects of intramolecular light energy and electron transfer will be discussed for three protein cofactor complexes, whose three-dimensional structures have been elucidated by x-ray crystallography: Components of light harvesting cyanobacterial phycobilisomes, the purple bacterial reaction centre, and the blue multi-copper oxidases. A wealth of functional data is available for these systems which allow specific correlations between structure and function and general conclusions about light energy and electron transfer in biological materials to be made.

scholarly journals The Drosophila melanogaster DmRAD54 Gene Plays a Crucial Role in Double-Strand Break Repair after P-Element Excision and Acts Synergistically with Ku70 in the Repair of X-Ray Damage

1999 ◽  
Vol 19 (9) ◽  
pp. 6269-6275 ◽  
Author(s):  
Rolf Kooistra ◽  
Albert Pastink ◽  
José B. M. Zonneveld ◽  
Paul H. M. Lohman ◽  
Jan C. J. Eeken
Keyword(s):  
Drosophila Melanogaster ◽  
Homologous Recombination ◽  
Crucial Role ◽  
Double Mutant ◽  
Strand Break ◽  
P Element ◽  
Slight Reduction ◽  
Wild Type ◽  
Dsb Repair ◽  
X Ray

ABSTRACT The RAD54 gene has an essential role in the repair of double-strand breaks (DSBs) via homologous recombination in yeast as well as in higher eukaryotes. A Drosophila melanogasterstrain deficient in the RAD54 homolog DmRAD54is characterized by increased X-ray and methyl methanesulfonate (MMS) sensitivity. In addition, DmRAD54 is involved in the repair of DNA interstrand cross-links, as is shown here. However, whereas X-ray-induced loss-of-heterozygosity (LOH) events were completely absent in DmRAD54 −/− flies, treatment with cross-linking agents or MMS resulted in only a slight reduction in LOH events in comparison with those in wild-type flies. To investigate the relative contributions of recombinational repair and nonhomologous end joining in DSB repair, aDmRad54 −/−/DmKu70 −/−double mutant was generated. Compared with both single mutants, a strong synergistic increase in X-ray sensitivity was observed in the double mutant. No similar increase in sensitivity was seen after treatment with MMS. Apparently, the two DSB repair pathways overlap much less in the repair of MMS-induced lesions than in that of X-ray-induced lesions. Excision of P transposable elements inDrosophila involves the formation of site-specific DSBs. In the absence of the DmRAD54 gene product, no male flies could be recovered after the excision of a single P element and the survival of females was reduced to 10% compared to that of wild-type flies. P-element excision involves the formation of two DSBs which have identical 3′ overhangs of 17 nucleotides. The crucial role of homologous recombination in the repair of these DSBs may be related to the very specific nature of the breaks.

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