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Research Article

Dynamics of Loading the Escherichia coli DNA Polymerase Processivity Clamp

Pages 179-208 | Published online: 11 Oct 2008

REFERENCES

  • Alley S. C., Abel-Santos E., Benkovic S. J. Tracking sliding clamp opening and closing during bacteriophage T4 DNA polymerase holoenzyme assembly. Biochemistry 2000; 39: 3076–3090, [INFOTRIEVE], [CSA]
  • Alley S. C., Jones A. D., Soumillion P., Benkovic S. J. The carboxyl terminus of the bacteriophage T4 DNA polymerase contacts its sliding clamp at the subunit interface. J Biol Chem 1999a; 274: 24485–24489, [INFOTRIEVE], [CROSSREF], [CSA]
  • Alley S. C., Shier V. K., Abel-Santos E., Sexton D. J., Soumillion P., Benkovic S. J. Sliding clamp of the bacteriophage T4 polymerase has open and closed subunit interfaces in solution. Biochemistry 1999b; 38: 7696–7709, [INFOTRIEVE], [CROSSREF], [CSA]
  • Alley S. C., Trakselis M. A., Mayer M. U., Ishmael F. T., Jones A. D., Benkovic S. J. Building a replisome solution structure by elucidation of protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme. J Biol Chem 2001; 276: 39340–39349, [INFOTRIEVE], [CROSSREF], [CSA]
  • Ason B., Bertram J. G., Hingorani M. M., Beechem J. M., O'Donnell M., Goodman M. F., Bloom L. B. A model for Escherichia coli DNA polymerase III holoenzyme assembly at primer/template ends: DNA triggers a change in binding specificity of the γ complex clamp loader. J Biol Chem 2000; 275: 3006–3015, [INFOTRIEVE], [CROSSREF], [CSA]
  • Ason B., Handayani R., Williams C. R., Bertram J. G., Hingorani M. M., O'Donnell M., Goodman M. F., Bloom L. B. Mechanism of loading the Escherichia coli DNA polymerase III beta sliding clamp on DNA. Bona fide primer/templates preferentially trigger the gamma complex to hydrolyze ATP and load the clamp. J Biol Chem 2003; 278: 10033–10040, [INFOTRIEVE], [CROSSREF], [CSA]
  • Bell S. P., Dutta A. DNA replication in eukaryotic cells. Annu Rev Biochem 2002; 71: 333–374, [INFOTRIEVE], [CROSSREF], [CSA]
  • Benkovic S. J., Valentine A. M., Salinas F. Replisome-mediated DNA replication. Annu Rev Biochem 2001; 70: 181–208, [INFOTRIEVE], [CROSSREF], [CSA]
  • Bertram J. G., Bloom L. B., Hingorani M. M., Beechem J. M., O'Donnell M., Goodman M. F. Molecular mechanism and energetics of clamp assembly in Escherichia coli. The role of ATP hydrolysis when γ complex loads β on DNA. J Biol Chem 2000; 275: 28413–28420, [INFOTRIEVE], [CROSSREF], [CSA]
  • Bertram J. G., Bloom L. B., Turner J., O'Donnell M., Beechem J. M., Goodman M. F. Pre-steady state analysis of the assembly of wild type and mutant circular clamps of Escherichia coli DNA polymerase III onto DNA. J Biol Chem 1998; 273: 24564–24574, [INFOTRIEVE], [CROSSREF], [CSA]
  • Blinkowa A. L., Walker J. R. Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame. Nucleic Acids Res 1990; 18: 1725–1729, [INFOTRIEVE], [CSA]
  • Bloom L. B., Turner J., Kelman Z., Beechem J. M., O'Donnell M., Goodman M. F. Dynamics of loading the β sliding clamp of DNA polymerase III onto DNA. J Biol Chem 1996; 271: 30699–30708, [INFOTRIEVE], [CROSSREF], [CSA]
  • Bonner C. A., Stukenberg P. T., Rajagopalan M., Eritja R., O'Donnell M., McEntee K., Echols H., Goodman M. F. Processive DNA synthesis by DNA polymerase II ediated by DNA polymerase III sccessory proteins. J Biol Chem 1992; 267: 11431–11438, [INFOTRIEVE], [CSA]
  • Bowman G. D., Goedken E. R., Kazmirski S. L., O'Donnell M., Kuriyan J. DNA polymerase clamp loaders and DNA recognition. FEBS Lett 2005; 579: 863–867, [INFOTRIEVE], [CROSSREF], [CSA]
  • Bowman G. D., O'Donnell M., Kuriyan J. Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature 2004; 429: 724–730, [PUBMED], [INFOTRIEVE], [CROSSREF], [CSA]
  • Brune M., Hunter J. L., Corrie J. E.T., Webb M. R. Direct, real-time measurement of rapid inorganic phosphate release using a novel fluorescent probe and its application to actomyosin subfragment 1 ATPase. Biochemistry 1994; 33: 8262–8271, [INFOTRIEVE], [CROSSREF], [CSA]
  • Brune M., Hunter J. L., Howell S. A., Martin S. R., Hazlett T. L., Corrie J. E., Webb M. R. Mechanism of inorganic phosphate interaction with phosphate binding protein from Escherichia coli. Biochemistry 1998; 37: 10370–10380, [INFOTRIEVE], [CROSSREF], [CSA]
  • Burgers P. M. Saccharomyces cerevisiae replication factor C. II. Formation and activity of complexes with the proliferating cell nuclear antigen and with DNA polymerases delta and epsilon. J Biol Chem 1991; 266: 22698–22706, [INFOTRIEVE], [CSA]
  • Burgers P. M.J., Kornberg A. ATP activation of DNA polymerase III holoenzyme of Escherichia coli. I. ATP-dependent formation of an initiation complex with a primed template. J Biol Chem 1982; 257: 11468–11473, [INFOTRIEVE], [CSA]
  • Cai J., Gibbs E., Uhlmann F., Phillips B., Yao N., O'Donnell M., Hurwitz J. A complex consisting of human replication factor C p40, p37, and p36 subunits is a DNA-dependent ATPase and an intermediate in the assembly of the holoenzyme. J Biol Chem 1997; 272: 18974–18981, [INFOTRIEVE], [CROSSREF], [CSA]
  • Capson T. L., Benkovic S. J., Nossal N. G. Protein-DNA crosslinking demonstrates stepwise ATP-dependent assembly of T4 DNA polymerase and its accessory proteins on the primer-template. Cell 1991; 65: 249–258, [INFOTRIEVE], [CROSSREF], [CSA]
  • Clegg R. M. Fluorescence resonance energy transfer. Curr Opin Biotechnol 1995; 6: 103–110, [INFOTRIEVE], [CROSSREF], [CSA]
  • Cullmann G., Fien K., Kobayashi R., Stillman B. Characterization of the five replication factor C genes of Saccharomyces cerevisiae. Mol Cell Biol 1995; 15: 4661–4671, [INFOTRIEVE], [CSA]
  • Dallmann H. G., Thimmig R. L., McHenry C. S. DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Central role of tau in initiation complex assembly and in determining the functional asymmetry of holoenzyme. J Biol Chem 1995; 270: 29555–29562, [INFOTRIEVE], [CROSSREF], [CSA]
  • Dalrymple B. P., Kongsuwan K., Wijffels G., Dixon N. E., Jennings P. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc Natl Acad Sci USA 2001; 98: 11627–11632, [INFOTRIEVE], [CROSSREF], [CSA]
  • Davey M. J., Jeruzalmi D., Kuriyan J., O'Donnell M. Motors and switches: AAA+ machines within the replisome. Nat Rev Mol Cell Biol 2002; 3: 826–835, [INFOTRIEVE], [CROSSREF], [CSA]
  • Dohrmann P. R., McHenry C. S. A sipartite polymerase-processivity factor interaction: only the internal beta binding site of the alpha subunit is required for processive replication by the DNA polymerase III holoenzyme. J Mol Biol 2005; 350: 228–239, [INFOTRIEVE], [CROSSREF], [CSA]
  • Ellison V., Stillman B. Opening of the clamp: an intimate view of an ATP-driven biological machine. Cell 2001; 106: 655–660, [INFOTRIEVE], [CROSSREF], [CSA]
  • Fay P. J., Johanson K. O., McHenry C. S., Bambara R. A. Size classes of products synthesized processively by DNA polymerase III and DNA polymerse III holoenzyme of Escherichia coli. J Biol Chem 1981; 256: 976–983, [INFOTRIEVE], [CSA]
  • Fay P. J., Johanson K. O., McHenry C. S., Bambara R. A. Size classes of products synthesized processively by two subassemblies of Escherichia coli DNA polymerase III holoenzyme. J Biol Chem 1982; 257: 5692–5699, [INFOTRIEVE], [CSA]
  • Fersht A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W.H. Freeman and Company, New York 1999; 132–158
  • Fien K., Stillman B. Identification of replication factor C from Saccharomyces cerevisiae: a component of the leading-strand DNA replication complex. Mol Cell Biol 1992; 12: 155–163, [INFOTRIEVE], [CSA]
  • Fierke C. A., Hammes G. G. Transient kinetic approaches to enzyme mechanisms. Methods Enzymol 1995; 249: 3–37, [INFOTRIEVE], [CSA]
  • Flower A. M., McHenry C. S. The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting. Proc Natl Acad Sci USA 1990; 87: 3713–3717, [INFOTRIEVE], [CROSSREF], [CSA]
  • Fotedar R., Mossi R., Fitzgerald P., Rousselle T., Maga G., Brickner H., Messier H., Kasibhatla S., Hubscher U., Fotedar A. A conserved domain of the large subunit of replication factor C binds PCNA and acts like a dominant negative inhibitor of DNA replication in mammalian cells. EMBO J 1996; 15: 4423–4433, [INFOTRIEVE], [CSA]
  • Garg P., Burgers P. M. DNA polymerases that propagate the eukaryotic DNA replication fork. Crit Rev Biochem Mol Biol 2005; 40: 115–128, [INFOTRIEVE], [CROSSREF], [CSA]
  • Glover B. P., McHenry C. S. The DnaX-binding subunits δ′ and ψ are bound to γ and not τ in the DNA polymerase III holoenzyme. J Biol Chem 2000; 275: 3017–3020, [INFOTRIEVE], [CROSSREF], [CSA]
  • Glover B. P., McHenry C. S. The DNA polymerase III holoenzyme: an asymmetric dimeric replicative complex with leading and lagging strand polymerases. Cell 2001; 105: 925–934, [INFOTRIEVE], [CROSSREF], [CSA]
  • Gomes X. V., Schmidt S. L., Burgers P. M. ATP utilization by yeast replication factor C. II. Multiple stepwise ATP binding events are required to load proliferating cell nuclear antigen onto primed DNA. J Biol Chem 2001; 276: 34776–34783, [INFOTRIEVE], [CROSSREF], [CSA]
  • Griep M. A., McHenry C. S. The dimer of the β subunit of Escherichia coli DNA polymerase III holoenzyme is dissociated into monomers upon binding magnesium (II). Biochemistry 1988; 27: 5210–5215, [INFOTRIEVE], [CROSSREF], [CSA]
  • Guenther B., Onrust R., Sali A., O'Donnell M., Kuriyan J. Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 1997; 91: 335–345, [INFOTRIEVE], [CROSSREF], [CSA]
  • Gulbis J. M., Kelman Z., Hurwitz J., O'Donnell M., Kuriyan J. Structure of the C-terminal region of p21WAF1/CIP1 complexed with human PCNA. Cell 1996; 87: 297–306, [INFOTRIEVE], [CROSSREF], [CSA]
  • Hill J. J., Royer C. A. Fluorescence approaches to the study of protein–nucleic acid complexation. Methods Enzymol 1997; 278: 390–416, [INFOTRIEVE], [CSA]
  • Hillisch A., Lorenz M., Diekmann S. Recent advances in FRET: distance determination in protein-DNA complexes. Curr Opin Struct Biol 2001; 11: 201–207, [INFOTRIEVE], [CROSSREF], [CSA]
  • Hingorani M. M., Bloom L. B., Goodman M. F., O'Donnell M. Division of labor-sequential ATP hydrolysis drives assembly of a DNA polymerase sliding clamp around DNA. EMBO J 1999; 18: 5131–5144, [INFOTRIEVE], [CROSSREF], [CSA]
  • Hingorani M. M., O'Donnell M. ATP binding to the Escherichia coli clamp loader powers opening of the ring-shaped clamp of DNA polymerase III holoenzyme. J Biol Chem 1998; 273: 24550–24563, [INFOTRIEVE], [CROSSREF], [CSA]
  • Hirshberg M., Henrick K., Haire L. L., Vasisht N., Brune M., Corrie J. E., Webb M. R. Crystal structure of phosphate binding protein labeled with a coumarin fluorophore, a probe for inorganic phosphate. Biochemistry 1998; 37: 10381–10385, [INFOTRIEVE], [CROSSREF], [CSA]
  • Hurwitz J., Wickner S. Involvement of two protein factors and ATP in in vitro DNA synthesis catalyzed by DNA polymerase 3 of Escherichia coli. Proc Natl Acad Sci USA 1974; 71: 6–10, [INFOTRIEVE], [CROSSREF], [CSA]
  • Jeruzalmi D., O'Donnell M., Kuriyan J. Crystal structure of the processivity clamp loader gamma (γ) complex of E. coli DNA polymerase III. Cell 2001a; 106: 429–441, [INFOTRIEVE], [CROSSREF], [CSA]
  • Jeruzalmi D., O'Donnell M., Kuriyan J. Clamp loaders and sliding clamps. Curr Opin Struct Biol 2002; 12: 217–224, [INFOTRIEVE], [CROSSREF], [CSA]
  • Jeruzalmi D., Yurieva O., Zhao Y., Young M., Stewart J., Hingorani M., O'Donnell M., Kuriyan J. Mechanism of processivity clamp opening by the delta-subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 2001b; 106: 417–428, [INFOTRIEVE], [CROSSREF], [CSA]
  • Johnson A., O'Donnell M. Ordered ATP hydrolysis in the gamma complex clamp loader AAA+ machine. J Biol Chem 2003; 278: 14406–14413, [INFOTRIEVE], [CSA]
  • Johnson A., O'Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu Rev Biochem 2005; 74: 283–315, [INFOTRIEVE], [CSA]
  • Johnson K. A. Rapid kinetic analysis of mechanochemical adenosinetriphosphotases. Methods Enzymol 1986; 134: 677–705, [INFOTRIEVE], [CSA]
  • Johnson K. A. Transient-state kinetic analysis of enzyme reaction pathways. Enzymes 1992; 20: 1–61, [CSA]
  • Kao H. I., Bambara R. A. The protein components and mechanism of eukaryotic Okazaki fragment maturation. Crit Rev Biochem Mol Biol 2003; 38: 433–452, [INFOTRIEVE], [CROSSREF], [CSA]
  • Kazmirski S. L., Podobnik M., Weitze T. F., O'Donnell M., Kuriyan J. Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Proc Natl Acad Sci USA 2004; 101: 16750–16755, [INFOTRIEVE], [CROSSREF], [CSA]
  • Kazmirski S. L., Zhao Y., Bowman G. D., O'Donnell M., Kuriyan J. Out-of-plane motions in open sliding clamps:Molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen. Proc Natl Acad Sci USA 2005; 102: 13801–13806, [PUBMED], [INFOTRIEVE], [CROSSREF], [CSA]
  • Kim D. R., McHenry C. S. Identification of the beta-binding domain of the alpha subunit of Escherichia coli polymerase III holoenzyme. J Biol Chem 1996; 271: 20699–20704, [INFOTRIEVE], [CROSSREF], [CSA]
  • Kim S., Dallman H. G., McHenry C. S., Marians K. J. Coupling of a replicative polymerase and helicase: A tau-DnaB interaction mediates rapid replication fork movement. Cell 1996a; 84: 643–650, [INFOTRIEVE], [CROSSREF], [CSA]
  • Kim S., Dallmann H. G., McHenry C. S., Marians K. J. tau couples the leading- and lagging-strand polymerases at the Escherichia coli DNA replication fork. J Biol Chem 1996b; 271: 21406–21412, [INFOTRIEVE], [CROSSREF], [CSA]
  • Kim S., Dallmann H. G., McHenry C. S., Marians K. J. Tau protects beta in the leading-strand polymerase complex at the replication fork. J Biol Chem 1996c; 271: 4315–4318, [INFOTRIEVE], [CROSSREF], [CSA]
  • Kong X. -P., Onrust R., O'Donnell M., Kuriyan J. Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp. Cell 1992; 69: 425–437, [INFOTRIEVE], [CROSSREF], [CSA]
  • Krishna T. S., Kong X. -P., Gary S., Burgers P. M., Kuriyan J. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 1994; 79: 1233–1243, [INFOTRIEVE], [CROSSREF], [CSA]
  • Lakowicz J. R. Principles of Fluorescence Spectroscopy. Plenum Publishers, New York 1999; 291–319
  • Latham G. J., Bacheller D. J., Pietroni P., von Hippel P. H. Structural analyses of gp45 sliding clamp interactions during assembly of the bacteriophage T4 DNA polymerase holoenzyme. II. The Gp44/62 clamp loader interacts with a single defined face of the sliding clamp ring. J Biol Chem 1997; 272: 31677–31684, [INFOTRIEVE], [CROSSREF], [CSA]
  • Ledvina P. S., Yao N., Choudhary A., Quiocho F. A. Negative electrostatic surface potential of protein sites specific for anionic ligands. Proc Natl Acad Sci USA 1996; 93: 6786–6791, [INFOTRIEVE], [CROSSREF], [CSA]
  • Lee S. H., Hurwitz J. Mechanism of elongation of primed DNA by DNA polymerase delta, proliferating cell nuclear antigen, and activator 1. Proc Natl Acad Sci USA 1990; 87: 5672–5676, [INFOTRIEVE], [CROSSREF], [CSA]
  • Lee S. H., Walker J. R. Escherichia coli DnaX product, the tau subunit of DNA polymerase III, is a multifunctional protein with single-stranded DNA-dependent ATPase activity. Proc Natl Acad Sci USA 1987; 84: 2713–2717, [INFOTRIEVE], [CROSSREF], [CSA]
  • Leu F. P., Georgescu R., O'Donnell M. Mechanism of the E. coli tau processivity switch during lagging-strand synthesis. Mol Cell 2003; 11: 315–327, [INFOTRIEVE], [CROSSREF], [CSA]
  • Leu F. P., Hingorani M. M., Turner J., O'Donnell M. The δ subunit of DNA polymerase III holoenzyme serves as a sliding clamp unloader in Escherichia coli. J Biol Chem 2000; 275: 34609–34618, [INFOTRIEVE], [CROSSREF], [CSA]
  • Leu F. P., O'Donnell M. Interplay of clamp loader subunits in opening the beta sliding clamp of Escherichia coli DNA polymerase III holoenzyme. J Biol Chem 2001; 276: 47185–47194, [INFOTRIEVE], [CROSSREF], [CSA]
  • Lilley D. M., Wilson T. J. Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr Opin Chem Biol 2000; 4: 507–517, [INFOTRIEVE], [CROSSREF], [CSA]
  • Lopez De Saro F. J., Georgescu R. E., Goodman M. F., O'Donnell M. Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair. EMBO J 2003a; 22: 6408–6418, [INFOTRIEVE], [CROSSREF], [CSA]
  • Lopez De Saro F. J., Georgescu R. E., O'Donnell M. A peptide switch regulates DNA polymerase processivity. Proc Natl Acad Sci USA 2003b; 100: 14689–14694, [INFOTRIEVE], [CROSSREF], [CSA]
  • Lopez de Saro F. J., O'Donnell M. Interaction of the beta sliding clamp with MutS, ligase, and DNA polymerase I. Proc Natl Acad Sci USA 2001; 98: 8376–8380, [INFOTRIEVE], [CROSSREF], [CSA]
  • Luecke H., Quiocho F. A. High specificity of a phosphate transport protein determined by hydrogen bonds. Nature 1990; 347: 402–406, [INFOTRIEVE], [CROSSREF], [CSA]
  • Maga G., Hubscher U. Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J Cell Sci 2003; 116: 3051–3060, [INFOTRIEVE], [CROSSREF], [CSA]
  • Majka J., Burgers P. M. The PCNA-RFC families of DNA clamps and clamp loaders. Prog Nucleic Acid Res Mol Biol 2004; 78: 227–260, [INFOTRIEVE], [CSA]
  • Maki S., Kornberg K. DNA polymerase III holoenzyme of Escherichia coli. II. A novel complex including the γ subunit essential for processive synthesis. J Biol Chem 1988; 263: 6555–6560, [INFOTRIEVE], [CSA]
  • Marians K. J. Mechanisms of replication fork restart in Escherichia coli. Philos Trans R Soc Lond B Biol Sci 2004; 359: 71–77, [INFOTRIEVE], [CROSSREF], [CSA]
  • Matsumiya S., Ishino Y., Morikawa K. Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus. Protein Sci 2001; 10: 17–23, [INFOTRIEVE], [CROSSREF], [CSA]
  • McHenry C. S. Purification and characterization of DNA polymerase III′. Identification of tau as a subunit of the DNA polymerase III holoenzyme. J Biol Chem 1982; 257: 2657–2663, [INFOTRIEVE], [CSA]
  • McHenry C. S. Chromosomal replicases as asymmetric dimers: studies of subunit arrangement and functional consequences. Mol Microbiol 2003; 49: 1157–1165, [INFOTRIEVE], [CROSSREF], [CSA]
  • Millar D., Trakselis M. A., Benkovic S. J. On the solution structure of the T4 sliding clamp (gp45). Biochemistry 2004; 43: 12723–12727, [INFOTRIEVE], [CROSSREF], [CSA]
  • Miyata T., Oyama T., Mayanagi K., Ishino S., Ishino Y., Morikawa K. The clamp-loading complex for processive DNA replication. Nat Struct Mol Biol 2004; 11: 632–636, [PUBMED], [INFOTRIEVE], [CROSSREF], [CSA]
  • Miyata T., Suzuki H., Oyama T., Mayanagi K., Ishino Y., Morikawa K. Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis. Proc Natl Acad Sci USA 2005; 102: 13795–13800, [PUBMED], [INFOTRIEVE], [CROSSREF], [CSA]
  • Moarefi I., Jeruzalmi D., Turner J., O'Donnell M., Kuriyan J. Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage. J Mol Biol 2000; 296: 1215–1223, [INFOTRIEVE], [CROSSREF], [CSA]
  • Mossi R., Jonsson Z. O., Allen B. L., Hardin S. H., Hubscher U. Replication factor C interacts with the C-terminal side of proliferating cell nuclear antigen. J Biol Chem 1997; 272: 1769–1776, [INFOTRIEVE], [CROSSREF], [CSA]
  • Naktinis V., Onrust R., Fang F., O'Donnell M. Assembly of a chromosomal replication machine: Two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. J Biol Chem 1995; 270: 13358–13365, [INFOTRIEVE], [CROSSREF], [CSA]
  • Naktinis V., Turner J., O'Donnell M. A molecular switch in a replication machine defined by an internal competition for protein rings. Cell 1996; 84: 137–145, [INFOTRIEVE], [CROSSREF], [CSA]
  • O'Donnell M. E. Accessory proteins bind a primed template and mediate rapid cycling of DNA polymerase III holoenzyme from Escherichia coli. J Biol Chem 1987; 262: 16558–16565, [INFOTRIEVE], [CSA]
  • Ogura T., Whiteheart S. W., Wilkinson A. J. Conserved arginine residues implicated in ATP hydrolysis, nucleotide-sensing, and inter-subunit interactions in AAA and AAA+ ATPases. J Struct Biol 2004; 146: 106–112, [INFOTRIEVE], [CROSSREF], [CSA]
  • Ogura T., Wilkinson A. J. AAA+ superfamily ATPases: common structure—diverse function. Genes Cells 2001; 6: 575–597, [INFOTRIEVE], [CROSSREF], [CSA]
  • Olson M. W., Dallmann H. G., McHenry C. S. DnaX of Escherichia coli DNA polymerase III holoenzyme. The χ ψ complex functions by increasing the affinity of τ and γ for δ–δ′ to a physiologically relevant range. J Biol Chem 1995; 270: 29570–29577, [INFOTRIEVE], [CROSSREF], [CSA]
  • Onrust R., Finkelstein J., Naktinis V., Turner J., Fang L., O'Donnell M. Assembly of a chromosomal replication machine: Two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. I. Organization of the clamp loader. J Biol Chem 1995a; 270: 13348–13357, [INFOTRIEVE], [CROSSREF], [CSA]
  • Onrust R., Finkelstein J., Turner J., Naktinis V., O'Donnell M. Assembly of a chromosomal replication machine: Two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. III. Interface between two polymerases and the clamp loader. J Biol Chem 1995b; 270: 13366–13377, [INFOTRIEVE], [CROSSREF], [CSA]
  • Onrust R., O'Donnell M. DNA polymerase III accessory proteins. II. Characterization of δ and δ′. J Biol Chem 1993; 268: 11766–11772, [INFOTRIEVE], [CSA]
  • Onrust R., Stukenberg P. T., O'Donnell M. Analysis of the ATPase subassembly which initiates processive DNA synthesis by DNA polymerase III holoenzyme. J Biol Chem 1991; 266: 21681–21686, [INFOTRIEVE], [CSA]
  • Pietroni P., Young M. C., Latham G. J., von Hippel P. H. Dissection of the ATP-driven reaction cycle of the bacteriophage T4 DNA replication processivity clamp loading system. J Mol Biol 2001; 309: 869–891, [INFOTRIEVE], [CROSSREF], [CSA]
  • Podobnik M., Weitze T. F., O'Donnell M., Kuriyan J. Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit. Structure (Camb) 2003; 11: 253–263, [CROSSREF], [CSA]
  • Podust V. N., Tiwari N., Ott R., Fanning E. Functional interactions among the subunits of replication factor C potentiate and modulate its ATPase activity. J Biol Chem 1998; 273: 12935–12942, [INFOTRIEVE], [CROSSREF], [CSA]
  • Pritchard A. E., Dallman H. G., Glover B. P., McHenry C. S. A novel assembly mechanism for the DNA polymerase III holoenzyme DnaX complex: association of δ δ′ with DnaX4 forms DnaX3δ δ′. EMBO J 2000; 19: 6536–6545, [INFOTRIEVE], [CROSSREF], [CSA]
  • Purich D. L. Enzyme catalysis: a new definition accounting for noncovalent substrate- and product-like states. Trends Biochem Sci 2001; 26: 417–421, [INFOTRIEVE], [CSA]
  • Richardson R. W., Ellis R. L., Nossal N. G. Protein-protein interactions within the bacteriophage T4 DNA replication complex. Molecular mechanisms in DNA replication and recombination. UCLA Symp Mol Cell Biol 1990; 127: 247–259, [CSA]
  • Rusinova E., Tretyachenko-Ladokhina V., Vele O. E., Senear D. F., Alexander Ross J. B. Alexa and Oregon Green dyes as fluorescence anisotropy probes for measuring protein-protein and protein-nucleic acid interactions. Anal Biochem 2002; 308: 18–25, [INFOTRIEVE], [CROSSREF], [CSA]
  • Schmidt S. L., Gomes X. V., Burgers P. M. ATP utilization by yeast replication factor C. III. The ATP-binding domains of Rfc2, Rfc3, and Rfc4 are essential for DNA recognition and clamp loading. J Biol Chem 2001; 276: 34784–34791, [INFOTRIEVE], [CROSSREF], [CSA]
  • Selvin P. R. Fluorescence resonance energy transfer. Methods Enzymol 1995; 246: 300–334, [INFOTRIEVE], [CSA]
  • Sexton D. J., Carver T. E., Berdis A. J., Benkovic S. J. Protein–protein and protein–DNA interactions at the bacteriophage T4 DNA replication fork: Characterization of a fluorescently labeled DNA polymerase sliding clamp. J Biol Chem 1996; 271: 28045–28051, [INFOTRIEVE], [CROSSREF], [CSA]
  • Sexton D. J., Kaboord B. F., Berdis A. J., Carver T. E., Benkovic S. J. Dissecting the order of bacteriophage T4 DNA polymerase holoenzyme assembly. Biochemistry 1998; 37, [CROSSREF], [CSA]
  • Shamoo Y., Steitz T. A. Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell 1999; 99: 155–166, [INFOTRIEVE], [CROSSREF], [CSA]
  • Snyder A. K., Williams C. R., Johnson A., O'Donnell M., Bloom L. B. Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: II. Uncoupling the β and DNA binding activites of the γ complex. J Biol Chem 2004; 279: 4386–4393, [INFOTRIEVE], [CROSSREF], [CSA]
  • Soumillion P., Sexton D. J., Benkovic S. J. Clamp subunit dissociation dictates bacteriophage T4 DNA polymerase holoenzyme disassembly. Biochemistry 1998; 37: 1819–1827, [INFOTRIEVE], [CROSSREF], [CSA]
  • Steiner R. F. Fluorescence anisotropy: Theory and applications. Topics in Fluorescence Spectroscopy, J. R. Lakowicz. Plenum Press, New York 1991; 1–52
  • Stewart J., Hingorani M. M., Kelman Z., O'Donnell M. Mechanism of β clamp opening by the δ subunit of Escherichia coli DNA polymerase III holoenzyme. J Biol Chem 2001; 276: 19182–19189, [INFOTRIEVE], [CROSSREF], [CSA]
  • Stryer L. Fluorescence energy transfer as a spectroscopic ruler. Annu Rev Biochem 1978; 47: 819–846, [INFOTRIEVE], [CROSSREF], [CSA]
  • Studwell-Vaughan P. S., O'Donnell M. Constitution of the twin polymerase of DNA polymerase III holoenzyme. J Biol Chem 1991; 266: 19833–19841, [INFOTRIEVE], [CSA]
  • Stukenberg P. T., Studwell-Vaughan P. S., O'Donnell M. Mechanism of the sliding β -clamp of DNA polymerase III holoenzyme. J Biol Chem 1991; 266: 11328–11334, [INFOTRIEVE], [CSA]
  • Trakselis M. A., Alley S. C., Abel-Santos E., Benkovic S. J. Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer. Proc Natl Acad Sci USA 2001a; 98: 8368–8375, [INFOTRIEVE], [CROSSREF], [CSA]
  • Trakselis M. A., Benkovic S. J. Intricacies in ATP-dependent clamp loading: variations across replication systems. Structure (Camb) 2001; 9: 999–1004, [CROSSREF], [CSA]
  • Trakselis M. A., Berdis A. J., Benkovic S. J. Examination of the role of the clamp-loader and ATP hydrolysis in the formation of the bacteriophage T4 polymerase holoenzyme. J Mol Biol 2003; 326: 435–451, [INFOTRIEVE], [CROSSREF], [CSA]
  • Trakselis M. A., Mayer M. U., Ishmael F. T., Roccasecca R. M., Benkovic S. J. Dynamic protein interactions in the bacteriophage T4 replisome. Trends Biochem Sci 2001b; 26: 566–572, [INFOTRIEVE], [CROSSREF], [CSA]
  • Tsuchihashi Z., Kornberg A. ATP interactions of the τ and γ subunits of DNA polymerase III holoenzyme of Escherichia coli. J Biol Chem 1989; 264: 17790–17795, [INFOTRIEVE], [CSA]
  • Tsuchihashi Z., Kornberg A. Translational frameshifting generates the γ subunit of DNA polymerase III holoenzyme. Proc Natl Acad Sci USA 1990; 87: 2516–2520, [INFOTRIEVE], [CROSSREF], [CSA]
  • Turner J., Hingorani M. M., Kelman Z., O'Donnell M. The internal workings of a DNA polymerase clamp-loading machine. EMBO J 1999; 18: 771–783, [INFOTRIEVE], [CROSSREF], [CSA]
  • Uhlmann F., Cai J., Gibbs E., O'Donnell M., Hurwitz J. Deletion analysis of the large subunit p140 in human replication factor C reveals regions required for complex formation and replication activities. J Biol Chem 1997; 272: 10058–10064, [INFOTRIEVE], [CROSSREF], [CSA]
  • Vivona J. B., Kelman Z. The diverse spectrum of sliding clamp interacting proteins. FEBS Lett 2003; 546: 167–172, [INFOTRIEVE], [CROSSREF], [CSA]
  • Waga S., Stillman B. The DNA replication fork in eukaryotic cells. Annu Rev Biochem 1998; 67: 721–751, [INFOTRIEVE], [CROSSREF], [CSA]
  • Walker J. R., Hervas C., Ross J. D., Blinkova A., Walbridge M. J., Pumarega E. J., Park M. O., Neely H. R. Escherichia coli DNA polymerase III tau- and gamma-subunit conserved residues required for activity in vivo and in vitro. J Bacteriol 2000; 182: 6106–6113, [INFOTRIEVE], [CROSSREF], [CSA]
  • Warbrick E. PCNA binding through a conserved motif. BioEssays 1998; 20: 195–199, [INFOTRIEVE], [CROSSREF], [CSA]
  • Warbrick E. The puzzle of PCNA's many partners. BioEssays 2000; 22: 997–1006, [INFOTRIEVE], [CROSSREF], [CSA]
  • Wickner S. Mechanism of DNA elongation catalyzed by Escherichia coli DNA polymerase III, dnaZ protein, and DNA elongation factors I and III. Proc Natl Acad Sci USA 1976; 73: 3511–3515, [INFOTRIEVE], [CROSSREF], [CSA]
  • Wickner S., Hurwitz J. Conversion of ϕ X174 viral DNA to double-stranded form by purified Escherichia coli proteins. Proc Natl Acad Sci USA 1974; 71: 4120–4124, [INFOTRIEVE], [CROSSREF], [CSA]
  • Wijffels G., Dalrymple B., Kongsuwan K., Dixon N. E. Conservation of eubacterial replicases. IUBMB Life 2005; 57: 413–419, [INFOTRIEVE], [CSA]
  • Williams C. R., Snyder A. K., Kuzmic P., O'Donnell M., Bloom L. B. Mechanism of loading the Escherichia coli DNA polymerase III sliding clamp: I. Two distinct activities for individual ATP sites in the γ complex. J Biol Chem 2004; 279: 4376–4385, [INFOTRIEVE], [CROSSREF], [CSA]
  • Wu P., Brand L. Resonance energy transfer: methods and applications. Anal Biochem 1994; 218: 1–13, [INFOTRIEVE], [CROSSREF], [CSA]
  • Xi J., Zhang Z., Zhuang Z., Yang J., Spiering M. M., Hammes G. G., Benkovic S. J. Interaction between the T4 helicase loading protein (gp59) and the DNA polymerase (gp43): unlocking of the gp59-gp43-DNA complex to initiate assembly of a fully functional replisome. Biochemistry 2005a; 44: 7747–7756, [INFOTRIEVE], [CROSSREF], [CSA]
  • Xi J., Zhuang Z., Zhang Z., Selzer T., Spiering M. M., Hammes G. G., Benkovic S. J. Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly. Biochemistry 2005b; 44: 2305–2318, [INFOTRIEVE], [CROSSREF], [CSA]
  • Xiao H., Dong Z., O'Donnell M. DNA polymerase III accessory proteins. IV. Characterization of chi and psi. J Biol Chem 1993; 268: 11779–11784, [INFOTRIEVE], [CSA]
  • Xiao H., Naktinis V., O'Donnell M. Assembly of a chromosomal replication machine: Two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. IV. ATP-binding site mutants identify the clamp loader. J Biol Chem 1995; 270: 13378–13383, [INFOTRIEVE], [CROSSREF], [CSA]
  • Yao N., Leu F. P., Anjelkovic J., Turner J., O'Donnell M. DNA structure requirements for the Escherichia coli gamma complex clamp loader and DNA polymerase III holoenzyme. J Biol Chem 2000; 275: 11440–11450, [INFOTRIEVE], [CROSSREF], [CSA]
  • Yao N., Turner J., Kelman Z., Stukenberg P. T., Dean F., Shechter D., Pan Z. -Q., Hurwitz J., O'Donnell M. Clamp loading, unloading, and intrinsic stability of the PCNA, β and gp45 sliding clamps of human, E. coli and T4 replicases. Genes Cells 1996; 1: 101–113, [INFOTRIEVE], [CROSSREF], [CSA]
  • Yoder B. L., Burgers P. M. Saccharomyces cerevisiae replication factor C. I. Purification and characterization of its ATPase activity. J Biol Chem 1991; 266: 22689–22697, [INFOTRIEVE], [CSA]
  • Young M. C., Weitzel S. E., von Hippel P. H. The kinetic mechanism of formation of the bacteriophage T4 DNA polymerase sliding clamp. J Mol Biol 1996; 264: 440–452, [INFOTRIEVE], [CROSSREF], [CSA]
  • Zhang Z., Spiering M. M., Trakselis M. A., Ishmael F. T., Xi J., Benkovic S. J., Hammes G. G. Assembly of the bacteriophage T4 primosome: single-molecule and ensemble studies. Proc Natl Acad Sci USA 2005; 102: 3254–3259, [INFOTRIEVE], [CROSSREF], [CSA]
  • Zhuang Z., Spiering M. M., Berdis A. J., Trakselis M. A., Benkovic S. J. ‘Screw-cap’ clamp loader proteins that thread. Nat Struct Mol Biol 2004; 11: 580–581, [PUBMED], [INFOTRIEVE], [CROSSREF], [CSA]

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