The reverse gyrase helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain

Nucleic Acids Research

Volumn 36, Issue 18, 2008, Pages 5882-5895

  del Toro Duany, Yoandris ^a   Jungblut, Stefan P ^a   Schmidt, A S Andreas S ^a   Klostermeier, Dagmar ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DNA TOPOISOMERASE (ATP HYDROLYSING); PLASMID DNA;

ARTICLE; BACTERIUM ISOLATION; BINDING AFFINITY; CELL CYCLE; CONTROLLED STUDY; DNA BINDING; DNA SUPERCOILING; GENE SEQUENCE; MOLECULAR CLONING; MUTAGENESIS; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN HYDROLYSIS; PROTEIN PROCESSING; SEQUENCE ANALYSIS; THERMOTOGA MARITIMA;

ADENINE NUCLEOTIDES; ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; DNA; DNA TOPOISOMERASES, TYPE I; DNA TOPOISOMERASES, TYPE I, BACTERIAL; DNA, SINGLE-STRANDED; MUTATION; POLY U; PROTEIN STRUCTURE, TERTIARY; THERMOTOGA MARITIMA;

BACTERIA (MICROORGANISMS); THERMOTOGA MARITIMA;

EID: 54549124757     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn587     Document Type: Article

References (33)

1. Kikuchi,A. and Asai,K. (1984) Reverse gyrase-a topoisomerase which introduces positive superhelical turns into DNA. Nature, 309 677-681.
2. Forterre,P. (2002) A hot story from comparative genomics: Reverse gyrase is the only hyperthermophile-specific protein. Trends Genet., 18, 236-237.
3. Atomi,H., Matsumi,R. and Imanaka,T. (2004) Reverse gyrase is not a prerequisite for hyperthermophilic life. J. Bacteriol., 186, 4829-4833.
4. Kampmann,M. and Stock,D. (2004) Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Res. 32, 3537-3545.
5. Hsieh,T.S. and Plank,J.L. (2006) Reverse gyrase functions as a DNA renaturase: Annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate. J. Biol. Chem., 281, 5640-5647.
6. Krah,R., Kozyavkin,S.A., Slesarev,A.I. and Gellert,M. (1996) A two-subunit type I DNA topoisomerase (reverse gyrase) from an extreme hyperthermophile. Proc. Natl Acad. Sci. USA, 93, 106-110.
7. Krah,R., O'Dea,M.H. and Gellert,M. (1997) Reverse gyrase from Methanopyrus kandleri. Reconstitution of an active extremozyme from its two recombinant subunits. J. Biol. Chem., 272, 13986-13990.
8. Declais,A.C., Marsault,J., Confalonieri,F., de La Tour,C.B. and Duguet,M. (2000) Reverse gyrase, the two domains intimately cooperate to promote positive supercoiling. J. Biol. Chem., 275, 19498-19504.
9. Confalonieri,F., Elie,C., Nadal,M., de La Tour,C., Forterre,P. and Duguet,M. (1993) Reverse gyrase: A helicase-like domain and a type I topoisomerase in the same polypeptide. Proc. Natl Acad Sci. USA, 90, 4753-4757.
10. Rodriguez,A.C. and Stock,D. (2002) Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO J., 21, 418-426.
11. Rodriguez,A.C. (2002) Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional "latch" in the mechanism of reverse gyrase. J. Biol. Chem., 277, 29865-29873.
12. Rodriguez,A.C. (2003) Investigating the role of the latch in the positive supercoiling mechanism of reverse gyrase. Biochemistry, 42, 5993-6004.
13. Theissen,B., Karow,A.R., Kohler,J., Gubaev,A. and Klostermeier,D. (2008) Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase. Proc. Natl Acad. Sci. USA, 105, 548-553.
14. Jungblut,S.P. and Klostermeier,D. (2007) Adenosine 5′-O-(3-thio)-triphosphate (ATPgammaS) promotes positive supercoiling of DNA by T. maritima reverse gyrase. J. Mol. Biol., 371 197-209.
15. Peck,M.L. and Herschlag,D. (2003) 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, 1180-1187.
16. Studier,F.W. (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif., 41, 207-234.
17. Kovalsky,O.I., Kozyavkin,S.A. and Slesarev,A.I. (1990) Archaebacterial reverse gyrase cleavage-site specificity is similar to that of eubacterial DNA topoisomerases I. Nucleic Acids Res., 18, 2801-2805.
18. Jaxel,C., Duguet,M. and Nadal,M. (1999) Analysis of DNA cleavage by reverse gyrase from Sulfolobus shibatae B12. Eur. J. Biochem. 260, 103-111.
19. Hiratsuka,T. (1983) New ribose-modified fluorescent analogs of adenine and guanine nucleotides available as substrates for various enzymes. Biochim. Biophys. Acta, 742, 496-508.
20. Rogers,G.W. Jr, Richter,N.J. and Merrick,W.C. (1999) Biochemical and kinetic characterization of the RNA helicase activity of eukaryotic initiation factor 4A. J. Biol. Chem., 274, 12236-12244.
21. Shibata,T., Nakasu,S., Yasui,K. and Kikuchi,A. (1987) Intrinsic DNA-dependent ATPase activity of reverse gyrase. J. Biol. Chem., 262, 10419-10421.
22. Lorsch,J.R. and Herschlag,D. (1998) The DEAD box protein eIF4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry, 37, 2180-2193.
23. Lorsch,J.R. and Herschlag,D. (1998) The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes. Biochemistry, 37, 2194-2206.
24. Polach,K.J. and Uhlenbeck,O.C. (2002) Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA. Biochemistry, 41, 3693-3702.
25. Yang,Q. and Jankowsky,E. (2006) The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases. Nat. Struct. Mol. Biol., 13, 981-986.
26. Yang,Q. and Jankowsky,E. (2005) ATP- and ADP-dependent modulation of RNA unwinding and strand annealing activities by the DEAD-box protein DED1. Biochemistry, 44, 13591-13601.
27. Kirkegaard,K. and Wang,J.C. (1985) Bacterial DNA topoisomerase I can relax positively supercoiled DNA containing a single-stranded loop. J. Mol. Biol., 185, 625-637.
28. Pyle,A.M. (2008) Translocation and unwinding mechanisms of RNA and DNA helicases. Annu. Rev. Biophys., 37, 317-336.
29. Morlang,S., Weglohner,W. and Franceschi,F. (1999) Hera from Thermus thermophilus: The first thermostable DEAD-box helicase with an RNase P protein motif. J. Mol. Biol., 294, 795-805.
30. Rogers,G.W. Jr, Richter,N.J., Lima,W.F. and Merrick,W.C. (2001) Modulation of the helicase activity of eIF4A by eIF4B, eIF4H, and eIF4F. J. Biol. Chem., 276, 30914-30922.
31. Kossen,K., Karginov,F.V. and Uhlenbeck,O.C. (2002) The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA. J. Mol. Biol., 324, 625-636.
32. Ma,E., MacRae,I.J., Kirsch,J.F. and Doudna,J.A. (2008) Autoinhibition of human dicer by its internal helicase domain. J. Mol. Biol., 380 237-243.
33. Gee,P., Chua,P.K., Gevorkyan,J., Klumpp,K., Najera,I., Swinney,D.C. and Deval,J. (2008) Essential role of the N-terminal domain in the regulation of RIG-I ATPase activity. J. Biol. Chem., 283, 9488-9496.