Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog

Nucleic Acids Research

Volumn 34, Issue 2, 2006, Pages 517-527

  Wang, Li Kai ^a   Schwer, Beate ^b   Englert, Markus ^c   Beier, Hildburg ^c   Shuman, Stewart ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ARGININE; ASPARTIC ACID; FUNGAL PROTEIN; HISTIDINE; PHOSPHATE; POLYNUCLEOTIDE 5' HYDROXYL KINASE; PROTEIN TRL1; RNA LIGASE; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; AMINO ACID SUBSTITUTION; ARABIDOPSIS; ARTICLE; CHEMICAL ANALYSIS; CLONING; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME STRUCTURE; GENE MUTATION; GENETIC COMPLEMENTATION; GENETIC CONSERVATION; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA SPLICING; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; YEAST;

2',3'-CYCLIC-NUCLEOTIDE PHOSPHODIESTERASES; AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CATALYTIC DOMAIN; DNA MUTATIONAL ANALYSIS; GENETIC COMPLEMENTATION TEST; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; RNA LIGASE (ATP); RNA SPLICING; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURE-ACTIVITY RELATIONSHIP;

ARABIDOPSIS; FUNGI; SACCHAROMYCES CEREVISIAE;

EID: 32644444603     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkj441     Document Type: Article

References (36)

1. Abelson,J., Trotta,C.R. and Li,H. (1998) tRNA splicing. J. Biol. Chem., 273, 12685-12688.
2. Greer,C.L., Peebles,C.L., Gegenheimer,P. and Abelson,J. (1983) Mechanism of action of a yeast RNA ligase in tRNA splicing. Cell, 32, 537-546.
3. 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.
4. Phizicky,E.M., Consaul,S.A., Nehrke,K.W. and Abelson,J. (1992) Yeast tRNA ligase mutants are nonviable and accumulate tRNA splicing intermediates. J. Biol. Chem., 267, 4577-4582.
5. Westaway,S.K., Belford,H.G., Apostol,B.L., Abelson,J. and Greer,C.L. (1993) Novel activity of a yeast ligase deletion polypeptide: Evidence for GTP-dependent tRNA splicing. J. Biol. Chem., 268, 2435-2443.
6. 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.
7. Cranston,J.W., Silber,R., Malathi,V.G. and Hurwitz,J. (1974) Studies on ribonucleic acid ligase: Characterization of an adenosine triphosphateinorganic pyrophosphate exchange reaction and demonstration of an enzyme-adenylate complex with T4 bacteriophage-induced enzyme. J. Biol. Chem., 249, 7447-7456.
8. Sugino,A., Snopek,T.J. and Cozzarelli,N.R. (1977) Bacteriophage T4 RNA ligase: Reaction intermediates and interaction of substrates. J. Biol. Chem., 252, 1732-1738.
9. 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.
10. Schwer,B., Sawaya,R., Ho,C.K. and Shuman,S. (2004) Portability and fidelity of RNA-repair systems. Proc. Natl Acad. Sci. USA, 101, 2788-2793.
11. Wang,L.K. and Shuman,S. (2005) Structure-function analysis of yeast tRNA ligase. RNA, 11, 966-975.
12. 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.
13. Gegenheimer,P., Gabius,H.J., Peebles,C.L. and Abelson,J. (1983) An RNA ligase from wheat germ which participates in transfer RNA splicing in vitro. J. Biol. Chem., 258, 8365-8373.
14. Schwartz,R.C., Greer,C.L., Gegenheimer,P. and Abelson,J. (1983) Enzymatic mechanism of an RNA ligase from wheat germ. J. Biol. Chem., 258, 8374-8383.
15. Pick,L. and Hurwitz,J. (1986) Purification of wheat germ RNA ligase: characterization of a ligase-associated 5′-hydroxyl polynucleotide kinase activity. J. Biol. Chem., 261, 6684-6693.
16. Pick,L., Furneaux,H. and Hurwitz,J. (1986) Purification of wheat germ RNA ligase: Mechanism of action of wheat germ RNA ligase. J. Biol. Chem., 261, 6694-6704.
17. Konarska,M., Filipowicz,W., Domdey,H. and Gross,H.J. (1981) Formation of a 2′-phosphomonoester, 3′,5′-phosphodiester linkage by a novel RNA ligase in wheat germ. Nature, 293, 112-116.
18. Konarska,M., Filipowicz,W. and Gross,H.J. (1982) RNA ligation via 2′-phosphomonoester, 3′,5′-phosphodiester linkage: Requirement of 2′, 3′-cyclic phosphate termini and involvement of a 5′-hydroxyl polynucleotide kinase. Proc. Natl Acad. Sci. USA, 79, 1474-1478.
19. Englert,M. and Beier,H. (2005) Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Res., 33, 388-399.
20. Wang,L.K. and Shuman,S. (2001) Domain structure and mutational analysis of T4 polynucleotide kinase. J. Biol. Chem., 276, 26868-26874.
21. Wang,L.K. and Shuman,S. (2002) Mutational analysis defines the 5′ kinase and 3′ phosphatase active sites of T4 polynucleotide kinase. Nucleic Acids Res., 30, 1073-1080.
22. 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.
23. 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.
24. 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.
25. Wang,S.P.,Deng,L., Ho,C.K.and Shuman,S. (1997) Phylogeny of mRNA capping enzymes. Proc. Natl Acad. Sci. USA, 94, 9573-9578.
26. Kozlov,G., Lee,J., Elias,D., Gravel,M., Gutierrez,P., Ekiel,I., Braun,P.E. and Gehring,K. (2003) Structural evidence that brain cyclic nucleotide phosphodiesterase is a member of the 2H phosphodiesterase superfamily. J. Biol. Chem., 278, 46021-46028.
27. Sakamoto,Y., Tanaka,N., Ichimiya,T., Kurihara,T. and Nakamura,K.T. (2005) Crystal structure of the catalytic fragment of human brain 2′,3′-cyclic nucleotide 3′-phosphodiesterase. J. Mol. Biol., 346, 789-800.
28. Kato,M., Shirouzu,M., Terada,T., Yamaguchi,H., Murayama,K., Sakai,H., Kuramitsu,S. and Yokoyama,S. (2003) Crystal structure of the 2′-5′ RNA ligase from Thermus thermophilus HB8. J. Mol. Biol., 329, 903-911.
29. Hofmann,A., Zdanov,A., Genschik,P., Ruvinov,S., Filipowicz,W. and Wlodawer,A. (2000) Structure and mechanism of the cyclic phosphodiesterase of Apppr>p, a product of the tRNA splicing reaction. EMBO J., 19, 6207-6217.
30. Hofmann,A., Grella,M., Botos,I., Filipowicz,W. and Wlodawer,A. (2002) Crystal structures of the semireduced and inhibitor bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana. J. Biol. Chem., 277, 1419-1425.
31. Ballestero,R.P., Dybowski,J.A., Levy,G., Agranoff,B.W. and Uhler,M.D. (1999) Cloning and characterization of zRICH, a 2′,3′-cyclic-nucleotide 3′-phosphodiesterase induced during zebrafish optic nerve regeneration. J. Neurochem., 72, 1362-1371.
32. Lee,J., Gravel,M., Gao,E., O'Neill,R.C. and Braun,P.E. (2001) Identification of essential residues in 2′,3′-cyclic nucleotide 3′-phosphodiesterase. J. Biol. Chem., 276, 14804-14813.
33. Nasr,F. and Filipowicz,W. (2000) Characterization of the Saccharomyces cerevisiae cyclic nucleotide phosphodiesterase involved in the metabolism of ADP-ribose 1′,2′-cyclic phosphate. Nucleic Acids Res., 28, 1676-1683.
34. El Omari,K., Ren,J., Bird,L.E., Bona,M.K., Klarmann,G., LeGrice,S.F.J. and Stammers,D.K. (2005) Molecular architecture and ligand recognition determinants for T4 RNA ligase. J. Biol. Chem. (in press).
35. 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.
36. Martins,A. and Shuman,S. (2004) Characterization of a baculovirus enzyme with RNA ligase, polynucleotide 5′ kinase and polynucleotide 3′ phosphatase activities. J. Biol. Chem., 279, 18220-18231.