An end-healing enzyme from Clostridium thermocellum with 5′ kinase, 2′,3′ phosphatase, and adenylyltransferase activities

RNA

Volumn 11, Issue 8, 2005, Pages 1271-1280

  Martins, Alexandra ^a   Shuman, Stewart ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

DNA repair; End healing; Phosphoesterase; Polynucleotide kinase; RNA repair

Indexed keywords

AMINO ACID DERIVATIVE; BACTERIAL ENZYME; CALCINEURIN; CTHPNKP ENZYME; CYCLIC AMP; LIGASE; MANGANESE; NICKEL; PHOSPHATASE; PHOSPHOTRANSFERASE; POLYNUCLEOTIDE; TRANSFERASE; UNCLASSIFIED DRUG;

ADENYLATION; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIOPHAGE; BINDING SITE; CATALYSIS; CHEMICAL REACTION; CLOSTRIDIUM THERMOCELLUM; DEPHOSPHORYLATION; DNA REPAIR; ENZYME ACTIVITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN MODIFICATION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CLOSTRIDIUM THERMOCELLUM; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEOTIDASES; NUCLEOTIDYLTRANSFERASES; PHOSPHOTRANSFERASES (PHOSPHATE GROUP ACCEPTOR); SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

BACTERIOPHAGE LAMBDA; CLOSTRIDIUM THERMOCELLUM;

EID: 23644456852     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2690505     Document Type: Article

References (31)

1. Amitsur, M., Levitz, R., and Kaufman, G. 1987. Bacteriophage T4 anticodon nuclease, polynucleotide kinase, and RNA ligase reprocess the host lysine tRNA. EMBO J. 6: 2499-2503.
2. Apostol, B.L., Westaway, S.K., Abelson, J., and Greer, C.L. 1991. Deletion analysis of a multifunctional yeast tRNA ligase polypeptide: Identification of essential and dispensable functional domains. J. Biol. Chem. 266: 7445-7455.
3. Aravind, L. and Koonin, E.V. 1998. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 23: 469-472.
4. Bernstein, N.K., Williams, R.S., Rakovszky, M.L., Cui, D., Green, R., Karimi-Busheri, F., Mani, R.S., Galicia, S., Koch, C.A., Cass, C.E., et al. 2005. The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase. Mol. Cell 17: 657-670.
5. Blondal, T., Hjorleifsdottir, S., Aevarsson, A., Fridjonsson, O.H., Skirnisdottir, S., Wheat, J.O., Hermannsdottir, A.G., Hreggvidsson, G.O., Smith, A.V., and Kristjansson, J.K. 2005. Characterization of a 5′- polynucleotide kinase/3′-phosphatase from bacteriophage RM378. J. Biol. Chem. 280: 5188-5194.
6. Cameron, V. and Uhlenbeck, O.C. 1977. 3′-Phosphatase activity in T4 polynucleotide kinase. Biochemistry 16: 5120-5126.
7. Collet, J.F., Stroobant, V., Pirard, M., Delpierre, G., and Van Schaftingen, E. 1998. A new class of phosphotransferases phosphorylated on an aspartate residue in an amino-terminal DXDX(T/V) motif. J. Biol. Chem. 273: 14107-14112.
8. Demain, A.L., Newcomb, M., and Wu, J.H.D. 2005. Cellulase, clostridia and ethanol. Microbiol. Mol. Biol. Rev. 69: 124-154.
9. Galburt, E.A., Pelletier, J., Wilson, G., and Stoddard, B.L. 2002. Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Structure 10: 1249- 1260.
10. Goldberg, J., Huang, H., Kwon, Y., Greengard, P., Nairn, A.C., and Kuriyan, J. 1995. Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1. Nature 376: 745-753.
11. Ho, C.K. and Shuman, S. 2002. Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc. Natl. Acad. Sci. 99: 12709-12714.
12. Lanzetta, P.A., Alvarez, L.J., Reinach, P.S., and Candia, O.A. 1979. An improved assay for nanomole amounts of inorganic phosphate. Anal. Biochem. 100: 95-97.
13. Martins, A. and Shuman, S. 2004a. An RNA ligase from Deinococcus radiodurans. J. Biol. Chem. 279: 50654-50661.
14. _. 2004b. Characterization of a baculovirus enzyme with RNA ligase, polynucleotide 5′ kinase and polynucleotide 3′ phosphatase activities J. Biol. Chem. 279: 18220-18231.
15. Mazumder, R., Iyer, L., Vasudevan, S., and Aravind. L. 2002. Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase family. Nucleic Acids Res. 30: 5229-5243.
16. Novogrodsky, A. and Hurwitz, J. 1966. The enzymatic phosphorylation of ribonucleic acid and deoxyribonucleic acid: Phosphorylation at 5′-hydroxyl termini. J. Biol. Chem. 241: 2923-2932.
17. Novogrodsky, A., Tal., M., Traub, A., and Hurwitz, J. 1966. The enzymatic phosphorylation of ribonucleic acid and deoxyribonucleic acid: Further properties of the 5′-hydroxyl polynucleotide kinase. J. Biol. Chem. 241: 2933-2943.
18. Odell, M., Sriskanda, V., Shuman, S., and Nikolov, D. 2000. Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol. Cell 6: 1183-1193.
19. Richardson, C.C. 1965. Phosphorylation of nucleic acid by an enzyme from T4 bacteriophage-infected Escherichia coli. Proc. Natl. Acad. Sci. 54: 158-165.
20. Sawaya, R., Schwer, B., and Shuman, S. 2003. Genetic and biochemical analysis of the functional domains of yeast tRNA ligase. J. Biol. Chem. 278: 43298-43398.
21. Shuman, S. and Lima, C.D. 2004. The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr. Opin. Struct. Biol. 14: 757-764.
22. Silber, R., Malathi, V.G., and Hurwitz, J. 1972. Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl. Acad. Sci. 69: 3009-3013.
23. Subramanya, H.S., Doherty, A.J., Ashford, S.R., and Wigley, D.B. 1996. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85: 607-615.
24. Voegtli, W.C., White, D.J., Reiter, N.J., Rusnak, F., and Rosenzweig, A.C. 2000. Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes. Biochemistry 39: 15365-15374.
25. Wang, L.K. and Shuman, S. 2001. Domain structure and mutational analysis of T4 polynucleotide kinase. J. Biol. Chem. 276: 26868-26874.
26. _. 2002. Mutational analysis defines the 5′-kinase and 3′-phosphatase active sites of T4 polynucleotide kinase. Nucleic Acids Res. 30: 1073-1080.
27. Wang, L.K., Lima, C.D., and Shuman, S. 2002. Structure and mechanism of T4 polynucleotide kinase: An RNA repair enzyme. EMBO J. 21: 3873-3880.
28. Wang, L.K., Ho, C.K., Pei, Y., and Shuman, S. 2003. Mutational analysis of bacteriophage T4 RNA ligase 1: Different functional groups are required for the nucleotidyl transfer and phosphodiester bond formation steps of the ligation reaction. J. Biol. Chem. 278: 29454-29462.
29. Yakunin, A.F., Proudfoot, M., Kuznetsova, E., Savchenko, A., Brown, G., Arrowsmith, C.H., and Edwards, A.M. 2004. The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2′,3′-cyclic phosphodiesterase, 2′-nucleotidase, and phosphatase activities. J. Biol. Chem. 279: 36819-36827.
30. Zhu, H., Yin, S., and Shuman, S. 2004. Characterization of polynucleotide kinase/phosphatase enzymes from mycobacteriophages Omega and Cjw1 and vibriophage KVP40. J. Biol. Chem. 279: 26358-26369.
31. Zhuo, S., Clemens, J.C., Hakes, D.J., Barford, D., and Dixon, J.E. 1993. Expression, purification, crystallization, and biochemical characterization of a recombinant protein phosphatase. J. Biol. Chem. 268: 17754-17761.