Nucleotide analogs and molecular modeling studies reveal key interactions involved in substrate recognition by the yeast RNA triphosphatase

Nucleic Acids Research

Volumn 37, Issue 11, 2009, Pages 3714-3722

  Issur, Moheshwarnath ^a   Despins, Simon ^a   Bougie, Isabelle ^a   Bisaillon, Martin ^a  

^a UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE; GUANOSINE TRIPHOSPHATASE; NUCLEOTIDE DERIVATIVE; PHOSPHATASE; RIBOSE TRIPHOSPHATE; RNA TRIPHOSPHATASE; UNCLASSIFIED DRUG;

AMINO ACID COMPOSITION; ARTICLE; COMPETITIVE INHIBITION; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME INHIBITION; ENZYME SUBSTRATE COMPLEX; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN HYDROLYSIS; PROTEIN RNA BINDING; YEAST;

ACID ANHYDRIDE HYDROLASES; CATALYTIC DOMAIN; GUANOSINE TRIPHOSPHATE; MODELS, MOLECULAR; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

DNA VIRUSES; EUKARYOTA; FUNGI; PROTOZOA;

EID: 67649884096     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp227     Document Type: Article

References (31)

1. Shatkin,A.J. (1976) Capping of eucaryotic mRNAs. Cell, 9, 645-653.
2. Furuichi,Y. and Shatkin,A.J. (2000) Viral and cellular mRNA capping: past and prospects. Adv. Virus Res., 55, 135-184.
3. Shuman,S. and Schwer,B. (1995) RNA capping enzyme and DNA ligase: A superfamily of covalent nucleotidyl transferases. Mol. Microbiol., 17, 405-410.
4. Bisaillon,M. and Lemay,G. (1997) Viral and cellular enzymes involved in synthesis of mRNA cap structure. Virology, 236, 1-7.
5. Shuman,S. (2001) Structure, mechanism, and evolution of the mRNA capping apparatus. Prog. Nucleic. Acids Res. Mol. Biol., 66, 1-40.
6. Shuman,S. (2002) What messenger RNA capping tells us about eukaryotic evolution. Nat. Rev. Mol. Cell Biol., 3, 619-625.
7. Tagaki,T., Moore,C.R., Diehn,F. and Buratowski,S. (1997) An RNA 5′-triphosphatase related to the protein tyrosine phosphatases. Cell, 89, 867-873.
8. Changela,A., Ho,C.K., Martins,A., Shuman,S. and Mondragon,A. (2001) Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme. EMBO J., 20, 2575-2586.
9. Ho,C.K., Pei,Y. and Shuman,S. (1998) Yeast and viral RNA 5′ triphosphatases comprise a new nucleoside triphosphatase family. J. Biol. Chem., 273, 34151-34156.
10. Ho,C.K. and Shuman,S. (2001) A yeast-like mRNA capping apparatus in Plasmodium falciparum. Proc. Natl Acad. Sci. USA, 98, 3050-3055.
11. Hausmann,S., Altura,M.A., Witmer,M., Singer,S.M., Elmendorf,H.G. and Shuman,S. (2005) Yeast-like mRNA capping apparatus in Giardia lamblia. J. Biol. Chem., 280, 12077-12086.
12. Hausmann,S., Vivares,C.P. and Shuman,S. (2002) Characterization of the mRNA capping apparatus of the microsporidian parasite Encephalitozoon cuniculi. J. Biol. Chem., 277, 96-103.
13. Myette,J. and Niles,E.G. (1996) Characterization of the vaccinia virus RNA 5′-triphosphatase and nucleotide triphosphate phosphohydrolase activities. Demonstrate that both activities are carried out at the same active site. J. Biol. Chem., 271, 11945-11952.
14. Martins,A. and Shuman,S. (2001) Mutational analysis of baculovirus capping enzyme Lef4 delineates an autonomous triphosphatase domain and structural determinants of divalent cation specificity. J. Biol. Chem., 276, 45522-45529.
15. Lima,C.D., Wang,L.K. and Shuman,S. (1999) Structure and mechanism of yeast RNA triphosphatase: An essential component of the mRNA capping apparatus. Cell, 99, 533-543.
16. Gong,C., Smith,P. and Shuman,S. (2006) Structure-function analysis of Plasmodium RNA triphosphatase and description of a triphosphate tunnel metalloenzyme superfamily that includes Cet1-like RNA triphosphatases and CYTH proteins. RNA, 12, 1468-1474.
17. Bisaillon,M. and Shuman,S. (2001) Structure-function analysis of the active site tunnel of yeast RNA triphosphatase. J. Biol. Chem., 276, 17261-17266.
18. Bisaillon,M. and Shuman,S. (2001) Functional groups required for the stability of yeast RNA triphosphatase in vitro and in vivo. J. Biol. Chem., 276, 30514-30520.
19. Pei,Y., Ho,C.K., Schwer,B. and Shuman,S. (1999) Mutational analyses of yeast RNA triphosphatases highlight a common mechanism of metal-dependent NTP hydrolysis and a means of targeting enzymes to pre-mRNAs in vivo by fusion to the guanylyltransferase component of the capping apparatus. J. Biol. Chem., 274, 28865-28874.
20. Benarroch,D., Smith,P. and Shuman,S. (2008) Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain. Structure, 16, 501-512.
21. Bisaillon,M. and Bougie,I. (2003) Investigating the role of metal ions in the catalytic mechanism of the yeast RNA triphosphatase. J. Biol. Chem., 278, 33963-33971.
22. Bougie,I. and Bisaillon,M. (2006) Inhibition of a metal-dependent viral RNA triphosphatase by decavanadate. Biochem. J., 398, 557-567.
23. Mayo,S.L., Olafson,B.D. and Goddard,W.A. (1990) DREIDING: A generic force field for molecular simulations. J. Phys. Chem., 94, 8897-8909.
24. Stewart,J.P.P. (2007) Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements. J. Mol. Model., 13, 1173-1213.
25. Morris,G.M., Goodsell,D.S., Halliday,R.S., Huey,R., Hart,W.E., Belew,R.K. and Olson,A.J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem., 19, 1639-1662.
26. Solis,F.J. and Wets,R.J.B. (1981) Minimization by Random Search Techniques. Math. Operat. Res., 6, 19-30.
27. Frith,M.C., Valen,E., Krogh,A., Hayashizaki,Y., Carninci,P. and Sandelin,A. (2008) A code for transcription initiation in mammalian genomes. Genome Res., 18, 1-12.
28. Pei,Y., Schwer,B., Hausmann,S. and Shuman,S. (2001) Characterization of Schizosaccharomyces pombe RNA triphosphatase. Nucleic Acids Res., 29, 387-396.
29. Keppetipola,N., Jain,R. and Shuman,S. (2007) Novel triphosphate phosphohydrolase activity of Clostridium thermocellum TTM, a member of the triphosphate tunnel metalloenzyme superfamily. J. Biol. Chem., 282, 11941-11949.
30. Jain,R. and Shuman,S. (2008) Polyphosphatase activity of CthTTM, a bacterial triphosphate tunnel metalloenzyme. J. Biol. Chem., 283, 31047-31057.
31. Gong,C. and Shuman,S. (2002) Chlorella virus RNA triphosphatase. Mutational analysis and mechanism of inhibition by tripolyphosphate. J. Biol. Chem., 277, 15317-15324.