Adenosine 5′-O-(3-thio)triphosphate (ATPγS) Promotes Positive Supercoiling of DNA by T. maritima Reverse Gyrase

Journal of Molecular Biology

Volumn 371, Issue 1, 2007, Pages 197-209

  Jungblut, Stefan P ^a   Klostermeier, Dagmar ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

non hydrolyzable ATP analog; nucleotide driven conformational changes; reverse gyrase; topoisomerase

Indexed keywords

ADENOSINE 5' O (3 THIO)TRIPHOSPHATE; ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ADENOSINE TRIPHOSPHATE DERIVATIVE; DNA TOPOISOMERASE; HELICASE; REVERSE GYRASE; UNCLASSIFIED DRUG; ADENOSINE 5' O (3 THIOTRIPHOSPHATE); ADENOSINE 5'-O-(3-THIOTRIPHOSPHATE); BACTERIAL PROTEIN; DNA REVERSE GYRASE; DRUG DERIVATIVE; NUCLEOTIDE; RECOMBINANT PROTEIN;

ARTICLE; CONFORMATIONAL TRANSITION; DNA SUPERCOILING; ENZYME BINDING; HYDROLYSIS; HYPERTHERMOPHILIC BACTERIUM; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN DOMAIN; STIMULATION; TEMPERATURE; THERMOTOGA MARITIMA; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYMOLOGY; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MUTATION; PLASMID; PROTEIN TERTIARY STRUCTURE;

ARCHAEA; THERMOTOGA MARITIMA;

ADENOSINE TRIPHOSPHATE; BACTERIAL PROTEINS; DNA TOPOISOMERASES, TYPE I; DNA, SUPERHELICAL; MODELS, MOLECULAR; MUTATION; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; PLASMIDS; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; THERMOTOGA MARITIMA;

EID: 34447103886     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.05.031     Document Type: Article

References (37)

1. Kikuchi A., and Asai K. Reverse gyrase-a topoisomerase which introduces positive superhelical turns into DNA. Nature 309 (1984) 677-681
2. Brochier-Armanet C., and Forterre P. Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2 (2006) 83-93
3. Omelchenko M.V., Wolf Y.I., Gaidamakova E.K., Matrosova V.Y., Vasilenko A., Zhai M., et al. Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol. Biol. 5 (2005) 57
4. Forterre P. A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet. 18 (2002) 236-237
5. Atomi H., Matsumi R., and Imanaka T. Reverse gyrase is not a prerequisite for hyperthermophilic life. J. Bacteriol. 186 (2004) 4829-4833
6. Kampmann M., and Stock D. Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucl. Acids Res. 32 (2004) 3537-3545
7. Hsieh T.S., and Plank J.L. Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate. J. Biol. Chem. 281 (2006) 5640-5647
8. Confalonieri F., Elie C., Nadal M., de La Tour C., Forterre P., and Duguet M. Reverse gyrase: a helicase-like domain and a type I topoisomerase in the same polypeptide. Proc. Natl Acad. Sci. USA 90 (1993) 4753-4757
9. Rodriguez A.C., and Stock D. Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO J. 21 (2002) 418-426
10. Matoba K., Mayanagi K., Nakasu S., Kikuchi A., and Morikawa K. Three-dimensional electron microscopy of the reverse gyrase from Sulfolobus tokodaii. Biochem. Biophys. Res. Commun. 297 (2002) 749-755
11. Declais A.C., Marsault J., Confalonieri F., de La Tour C.B., and Duguet M. Reverse gyrase, the two domains intimately cooperate to promote positive supercoiling. J. Biol. Chem. 275 (2000) 19498-19504
12. Shibata T., Nakasu S., Yasui K., and Kikuchi A. Intrinsic DNA-dependent ATPase activity of reverse gyrase. J. Biol. Chem. 262 (1987) 10419-10421
13. Rodriguez A.C. Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional "latch" in the mechanism of reverse gyrase. J. Biol. Chem. 277 (2002) 29865-29873
14. Hsieh T.S., and Capp C. Nucleotide- and stoichiometry-dependent DNA supercoiling by reverse gyrase. J. Biol. Chem. 280 (2005) 20467-20475
15. Jaxel C., Nadal M., Mirambeau G., Forterre P., Takahashi M., and Duguet M. Reverse gyrase binding to DNA alters the double helix structure and produces single-strand cleavage in the absence of ATP. EMBO J. 8 (1989) 3135-3139
16. Rodriguez A.C. Investigating the role of the latch in the positive supercoiling mechanism of reverse gyrase. Biochemistry 42 (2003) 5993-6004
17. Andera L., Mikulika K., and Savelyevab N.D. Characterization of a reverse gyrase from the extremely thermophilic hydrogen-oxidizing eubacterium Calderobacterium hydrogenophilum. FEMS Microbiol. Letters 110 (1993) 107
18. Bouthier de la Tour C., Portemer C., Kaltoum H., and Duguet M. Reverse gyrase from the hyperthermophilic bacterium Thermotoga maritima: properties and gene structure. J. Bacteriol. 180 (1998) 274-281
19. Krah R., O'Dea M.H., and Gellert M. Reverse gyrase from Methanopyrus kandleri. Reconstitution of an active extremozyme from its two recombinant subunits. J. Biol. Chem. 272 (1997) 13986-13990
20. Reinstein J., Schlichting I., and Wittinghofer A. Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli. Biochemistry 29 (1990) 7451-7459
21. Solem A., Zingler N., and Pyle A.M. A DEAD protein that activates intron self-splicing without unwinding RNA. Mol. Cell 24 (2006) 611-617
22. Saraste M., Sibbald P.R., and Wittinghofer A. The P-loop-a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15 (1990) 430-434
23. Eckstein F. Nucleoside phosphorothioates. Annu. Rev. Biochem. 54 (1985) 367-402
24. Forterre P., Mirambeau G., Jaxel C., Nadal M., and Duguet M. High positive supercoiling in vitro catalyzed by an ATP and polyethylene glycol-stimulated topoisomerase from Sulfolobus acidocaldarius. EMBO J. 4 (1985) 2123-2128
25. Eckstein F. Investigation of enzyme mechanisms with nucleoside phosphorothioates. Angew Chem. Int. Ed. Engl. 14 (1975) 160-166
26. Gorbalenya A.E., and Koonin E.V. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3 (1993) 419-429
27. Peck M.L., and Herschlag D. Adenosine 5′-O-(3-thio)triphosphate (ATPgammaS) is a substrate for the nucleotide hydrolysis and RNA unwinding activities of eukaryotic translation initiation factor eIF4A. Rna 9 (2003) 1180-1187
28. Caruthers J.M., Johnson E.R., and McKay D.B. Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase. Proc. Natl Acad. Sci. USA 97 (2000) 13080-13085
29. Story R.M., Li H., and Abelson J.N. Crystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii. Proc. Natl Acad. Sci. USA 98 (2001) 1465-1470
30. Cheng Z., Coller J., Parker R., and Song H. Crystal structure and functional analysis of DEAD-box protein Dhh1p. RNA 11 (2005) 1258-1270
31. Shi H., Cordin O., Minder C.M., Linder P., and Xu R.M. Crystal structure of the human ATP-dependent splicing and export factor UAP56. Proc. Natl Acad. Sci. USA 101 (2004) 17628-17633
32. Yao N., Hesson T., Cable M., Hong Z., Kwong A.D., Le H.V., and Weber P.C. Structure of the hepatitis C virus RNA helicase domain. Nature Struct. Biol. 4 (1997) 463-467
33. Andersen C.B., Ballut L., Johansen J.S., Chamieh H., Nielsen K.H., Oliveira C.L., et al. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313 (2006) 1968-1972
34. Sengoku T., Nureki O., Nakamura A., Kobayashi S., and Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125 (2006) 287-300
35. Hiratsuka T. New ribose-modified fluorescent analogs of adenine and guanine nucleotides available as substrates for various enzymes. Biochim. Biophys. Acta 742 (1983) 496-508
36. Adam H. Adenosin-5′diphosphat und adenosin-5′monophosphat. Methoden der Enzymatischen Analyse (1962), Bergmeyer, H.U. (Hrsg.), Verlag Chemie, Weinheim 573-577
37. Mondragon A., and DiGate R. The structure of Escherichia coli DNA topoisomerase III. Struct. Fold. Des. 7 (1999) 1373-1383