Mechanism of translocation and kinetics of DNA unwinding by the helicase RecG

Biochemistry

Volumn 44, Issue 51, 2005, Pages 16967-16976

  Martinez Senac, Maria M ^a   Webb, Martin R ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; ENZYME KINETICS; ENZYMES; HYDROLYSIS; REACTION KINETICS;

DNA UNWINDING; KINETIC MECHANISMS; TEMPLATE STRAND; TRANSLOCATION;

DNA;

ADENOSINE TRIPHOSPHATE; DNA HELICASE RECG; DOUBLE STRANDED DNA; HELICASE; PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CATALYST; DISSOCIATION; DNA DENATURATION; DNA REPAIR; ENZYME ACTIVITY; ENZYME BINDING; FLUORESCENCE ANALYSIS; HYDROLYSIS; KINETICS; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN TRANSPORT; QUANTITATIVE ASSAY; REACTION ANALYSIS; SENSOR;

ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; BASE SEQUENCE; CARBOCYANINES; COUMARINS; DNA; DNA HELICASES; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; P-DIMETHYLAMINOAZOBENZENE; PHOSPHATE-BINDING PROTEINS; PHOSPHATES; PROTEIN BINDING; SPECTROMETRY, FLUORESCENCE; THERMOTOGA MARITIMA;

EID: 29344449133     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0512851     Document Type: Article

References (39)

1. Singleton, M. R., and Wigley, D. B. (2002) Modularity and specialization in superfamily 1 and 2 helicases, J. Bacteriol. 184, 1819-1826.
2. Tuteja, N., and Tuteja, R. (2004) Prokaryotic and eukaryotic DNA helicases: Essential molecular motors for cellular machinery, Eur. J. Biochem. 271, 1835-1848.
3. McGlynn, P., and Lloyd, R. G. (2000) Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression, Cell 101, 35-45.
4. McGlynn, P., Lloyd, R. G., and Marians, K. J. (2001) Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: recG stimulates regression even when the DNA is negatively supercoiled, Proc. Natl. Acad. Sci. U.S.A. 98, 8235-8240.
5. Singleton, M. R., Scaife, S., and Wigley, D. B. (2001) Structural analysis of DNA replication fork reversal by RecG, Cell 107, 79-89.
6. McGlynn, P., and Lloyd, R. G. (2001) Rescue of stalled replication forks by recG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation, Proc. Natl. Acad. Sci. U.S.A. 98, 8227-8234.
7. Briggs, G. S., Mahdi, A. A., Wen, Q., and Lloyd, R. G. (2005) DNA Binding by the Substrate Specificity (Wedge) Domain of RecG Helicase Suggests a Role in Processivity, J. Biol. Chem. 280, 13921-13927.
8. Whitby, M. C., and Lloyd, R. G. (1998) Targeting Holliday junctions by the RecG branch migration protein of Escherichia coli, J. Biol. Chem. 273, 19729-19739.
9. Ali, J. A., and Lohman, T. M. (1997) Kinetic measurement of the step size of DNA unwinding by Escherichia coli UvrD helicase, Science 275, 377-380.
10. Ali, J. A., Maluf, N. K., and Lohman, T. M. (1999) An oligomeric form of E. coli UvrD is required for optimal helicase activity, J. Mol. Biol. 293, 815-833.
11. Jankowsky, E., Gross, C. H., Shuman, S., and Pyle, A. M. (2000) The DExH protein NPH-II is a processive and directional motor for unwinding RNA, Nature 403, 447-451.
12. Lucius, A. L., Vindigni, A., Gregorian, R., Ali, J. A., Taylor, A. F., Smith, G. R., and Lohman, T. M. (2002) DNA unwinding step-size of E. coli RecBCD helicase determined from single turnover chemical quenched-flow kinetic studies, J. Mol. Biol. 324, 409-428.
13. Galletto, R., Jezewska, M. J., and Bujalowski, W. (2004) Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: Quantitative analysis of the rate of the dsDNA unwinding, processivity and kinetic step-size of the Escherichia coli DnaB helicase using rapid quench-flow method, J. Mol. Biol. 343, 83-89.
14. Jeong, Y. J., Levin, M. K., and Patel, S. S. (2004) The DNA-unwinding mechanism of the ring helicase of bacteriophage T7, Proc. Natl. Acad. Sci. U.S.A. 101, 7264-7269.
15. Levin, M. K., Wang, Y. H., and Patel, S. S. (2004) The functional interaction of the hepatitis C virus helicase molecules is responsible for unwinding processivity, J. Biol. Chem. 279, 26005-26012.
16. Bjornson, K. P., Amaratunga, M., Moore, K. J., and Lohman, T. M. (1994) Single-turnover kinetics of helicase-catalyzed DNA unwinding monitored continuously by fluorescence energy transfer, Biochemistry 33, 14306-14316.
17. Houston, P., and Kodadek, T. (1994) Spectrophotometric assay for enzyme-mediated unwinding of double-stranded DNA, Proc. Natl. Acad. Sci. U.S.A. 91, 5471-5474.
18. Cheng, W., Hsieh, J., Brendza, K. M., and Lohman, T. M. (2001) E. coli Rep oligomers are required to initiate DNA unwinding in vitro, J. Mol. Biol. 310, 327-350.
19. Lucius, A. L., Wong, C. J., and Lohman, T. M. (2004) Fluorescence stopped-flow studies of single turnover kinetics of E. coli RecBCD helicase-catalyzed DNA unwinding, J. Mol. Biol. 339, 731-750.
20. Choudhary, S., Sommers, J. A., and Brosh, R. M., Jr. (2004) Biochemical and kinetic characterization of the DNA helicase and exonuclease activities of Werner syndrome protein, J. Biol. Chem. 279, 34603-34613.
21. Brune, M., Hunter, J. L., Howell, S. A., Martin, S. R., Hazlett, T. L., Corrie, J. E. T., and Webb, M. R. (1998) Mechanism of inorganic phosphate interaction with phosphate binding protein from Escherichia coli, Biochemistry 37, 10370-10380.
22. Fischer, C. J., Maluf, N. K., and Lohman, T. M. (2004) Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA, J. Mol Biol. 344, 1287-1309.
23. Bianco, P. R., and Kowalczykowski, S. C. (2000) Translocation step size and mechanism of the RecBC DNA helicase, Nature 405, 368-372.
24. Paolini, C., De Francesco, R., and Gallinari, P. (2000) Enzymatic properties of hepatitis C virus NS3-associated helicase, J. Gen. Virol. 81, 1335-1345.
25. Webb, M. R. (2003) A fluorescent sensor to assay inorganic phosphate, in Kinetic analysis: A practical approach (Johnson, K. A., Ed.) pp 131-152, Oxford University Press, Oxford, U.K.
26. Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., and Bairoch, A. (2003) ExPASy: The proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res. 31, 3784-3788.
27. Leatherbarrow, R. J. (2001) Grafit, version 5, Erithacus Software Ltd., Horley, U.K.
28. Tyagi, S., and Kramer, F. R. (1996) Molecular beacons: Probes that fluoresce upon hybridization, Nat. Biotechnol. 14, 303-308.
29. Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination, Nat. Biotechnol. 16, 49-53.
30. Marras, S. A., Kramer, F. R., and Tyagi, S. (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes, Nucleic Acids Res. 30, e122.
31. Yodh, J. G., and Bryant, F. R. (1993) Kinetics of ATP hydrolysis during the DNA helicase II-promoted unwinding of duplex DNA, Biochemistry 32, 7765-7771.
32. Dillingham, M. S., Wigley, D. B., and Webb, M. R. (2000) Demonstration of unidirectional single-stranded DNA translocation by pcrA helicase: Measurement of step size and translocation speed, Biochemistry 39, 205-212.
33. Mahdi, A., McGlynn, P., Levett, S., and Lloyd, R. (1997) DNA binding and helicase domains of the Escherichia coll recombination protein RecG, Nucleic Acids Res. 25, 3875-3880.
34. Soultanas, P., Dillingham, M., Wiley, P., Webb, M. R., and Wigley, D. B. (2000) Uncoupling DNA translocation and helicase activity in pcrA: Direct evidence for an active mechanism, EMBO J. 19, 3799-3810.
35. Velankar, S. S., Soultanas, P., Dillingham, M. S., Subramanya, H. S., and Wigley, D. B. (1999) Crystal structures of complexes of pcrA DNA helicase with a DNA substrate indicate an inchworm mechanism, Cell 97, 75-84.
36. Veigel, C., Coluccio, L. M., Jontes, J. D., Sparrow, J. C., Milligan, R. A., and Molloy, J. E. (1999) The motor protein myosin-I produces its working stroke in two steps, Nature 398, 530-533.
37. Whittaker, M., Wilson-Kubalek, E. M., Smith, J. E., Faust, L., Milligan, R. A., and Sweeney, H. L. (1995) A 35-Å movement of smooth muscle myosin on ADP release, Nature 378, 748-751.
38. Roman, L. J., and Kowalczykowski, S. C. (1989) Characterization of the helicase activity of the Escherichia coli RecBCD enzyme using a novel helicase assay, Biochemistry 28, 2863-2873.
39. von Hippel, P. H., and Delagoutte, E. (2001) A general model for nucleic acid helicases and their "coupling" within macromolecular machines, Cell 104, 177-190.