Conformational dynamics of bacteriophage T7 DNA polymerase and its processivity factor, Escherichia coli thioredoxin

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 34, 2010, Pages 15033-15038

  Akabayov, Barak ^a   Akabayov, Sabine R ^a   Lee, Seung Joo ^a   Tabor, Stanley ^a   Kulczyk, Arkadiusz W ^a   Richardson, Charles C ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Conformational transition; DNA replication; DNA protein interactions; Gene 5 protein

Indexed keywords

DNA POLYMERASE; THIOREDOXIN; BACTERIOPHAGE T7 INDUCED DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE; ESCHERICHIA COLI PROTEIN; PRIMER DNA; VIRUS DNA;

ARTICLE; BACTERIOPHAGE T7; DNA BINDING; DNA REPLICATION; ENZYME ACTIVITY; ESCHERICHIA COLI; IONIC STRENGTH; NONHUMAN; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY; ALLOSTERISM; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; NUCLEOTIDE SEQUENCE; OSMOLARITY; PROTEIN BINDING; PROTEIN CONFORMATION; SMALL ANGLE SCATTERING; X RAY DIFFRACTION;

ESCHERICHIA COLI;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; BACTERIOPHAGE T7; BASE SEQUENCE; BINDING SITES; DNA PRIMERS; DNA, VIRAL; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; KINETICS; MODELS, MOLECULAR; OSMOLAR CONCENTRATION; PROTEIN BINDING; PROTEIN CONFORMATION; SCATTERING, SMALL ANGLE; THIOREDOXINS; X-RAY DIFFRACTION;

EID: 77957014812     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1010141107     Document Type: Article

References (27)

1. Hamdan SM, Richardson CC (2009) Motors, switches, and contacts in the replisome. Annu Rev Biochem 78:205-243.
2. Huber HE, Russel M, Model P, Richardson CC (1986) Interaction of mutant thioredoxins of Escherichia coli with the gene 5 protein of phage T7: The redox capacity of thioredoxin is not required for stimulation of DNA polymerase activity. J Biol Chem 261:15006-15012. (Pubitemid 17218065)
3. Bedford E, Tabor S, Richardson CC (1997) The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I. Proc Natl Acad Sci USA 94:479-484.
4. Hamdan SM, et al. (2007) Dynamic DNA helicase-DNA polymerase interactions assure processive replication fork movement. Mol Cell 27:539-549.
5. Tabor S, Huber HE, Richardson CC (1987) Escherichia colithioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J Biol Chem 262:16212-16223.
6. Von Hippel PH, Fairfield FR, Dolejsi MK (1994) On the processivity of polymerases. Ann NY Acad Sci 726:118-131.
7. Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391:251-258. (Pubitemid 28099004)
8. Etson CM, Hamdan SM, Richardson CC, van Oijen AM (2010) Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA. Proc Natl Acad Sci USA 107:1900-1905.
9. Bu Z, Biehl R, Monkenbusch M, Richter D, Callaway DJ (2005) Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy. Proc Natl Acad Sci USA 102:17646-17651.
10. Tang KH, et al. (2008) Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways. Nucleic Acids Res 36:2948-2957.
11. Kornberg A, Baker TA (1992) DNA Replication (Freeman, San Francisco).
12. Ollis DL, Kline C, Steitz TA (1985) Domain of E. coli DNA polymerase I showing sequence homology to T7 DNA polymerase. Nature 313:818-819. (Pubitemid 15130837)
13. Huber HE, Tabor S, Richardson CC (1987) Escherichia coli thioredoxin stabilizes complexes of bacteriophage T7 DNA polymerase and primed templates. J Biol Chem 262:16224-16232.
14. Wuite GJ, Smith SB, Young M, Keller D, Bustamante C (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404:103-106.
15. Lechner RL, Richardson CC (1983) A preformed, topologically stable replication fork. Characterization of leading strand DNA synthesis catalyzed by T7 DNA polymerase and T7 gene 4 protein. J Biol Chem 258:11185-11196.
16. Notarnicola SM, Mulcahy HL, Lee J, Richardson CC (1997) The acidic carboxyl terminus of the bacteriophage T7 gene 4 helicase/primase interacts with T7 DNA polymerase. J Biol Chem 272:18425-18433.
17. Lee JB, et al. (2006) DNA primase acts as a molecular brake in DNA replication. Nature 439:621-624.
18. Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495-503.
19. Wakabayashi K, et al. (1992) Small-angle synchrotron x-ray scattering reveals distinct shape changes of the myosin head during hydrolysis of ATP. Science 258:443-447.
20. Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946-2953.
21. Richardson CC, Lehman IR, Kornberg A (1964) A deoxyribonucleic acid phosphatase-exonuclease from Escherichia coli. II. Characterization of the exonuclease activity. J Biol Chem 239:251-258.
22. Tama F, Brooks CL (2006) Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct 35:115-133. (Pubitemid 43877372)
23. Brieba LG, et al. (2004) Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. EMBO J 23:3452-3461.
24. Breyer WA, Matthews BW (2001) A structural basis for processivity. Protein Sci 10:1699-1711.
25. Lipfert J, et al. (2007) Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholera. J Mol Biol 365:1393-1406.
26. Svergun DI, Barberato C, Koch MHJ (1995) CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768-773.
27. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037-10041. (Pubitemid 32802969)