Metal-ion-dependent catalysis and specificity of CCA-adding enzymes: A comparison of two classes

Biochemistry

Volumn 44, Issue 38, 2005, Pages 12849-12859

  Hou, Ya Ming ^a   Gu, Shan Qing ^a   Zhou, Haiping ^a   Ingerman, Lindsey ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINETRIPHOSPHATE; BACTERIA; CARBOXYLATION; CATALYSIS; ESCHERICHIA COLI; POSITIVE IONS; RNA; SYNTHESIS (CHEMICAL);

CATALYTIC MECHANISM; METAL IONS; METAL-ION-DEPENDENT CATALYSIS; STRUCTURAL DIVERSITY;

ENZYMES;

DNA POLYMERASE; NUCLEOTIDYLTRANSFERASE; RNA POLYMERASE;

ADDITION REACTION; ARTICLE; CATALYSIS; ENZYME BINDING; ENZYME SPECIFICITY; ESCHERICHIA COLI; METAL BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; RNA SEQUENCE; SULFOLOBUS; SULFOLOBUS SHIBABAE;

BASE SEQUENCE; CATALYSIS; CATIONS, DIVALENT; ESCHERICHIA COLI; METALS; MOLECULAR SEQUENCE DATA; RNA NUCLEOTIDYLTRANSFERASES; RNA, TRANSFER, VAL; SUBSTRATE SPECIFICITY; SULFOLOBUS;

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SULFOLOBUS;

EID: 25444523192     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0509402     Document Type: Article

References (37)

1. Deutscher, M. P. (1982) tRNA nucleotidyltransferase, Enzymes 15, 183-215.
2. Maizels, N., and Weiner, A. M. (1994) Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation, Proc. Natl. Acad. Sci. U.S.A. 91, 6729-34.
3. Li, F., Xiong, Y., Wang, J., Cho, H. D., Tomita, K., Weiner, A. M., and Steitz, T. A. (2002) Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP, Cell 111, 815-24.
4. Okabe, M., Tomita, K., Ishitani, R., Ishii, R., Takeuchi, N., Arisaka, F., Nureki, O., and Yokoyama, S. (2003) Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure, EMBO J. 22, 5918-27.
5. Xiong, Y., Li, F., Wang, J., Weiner, A. M., and Steitz, T. A. (2003) Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes, Mol. Cell 12, 1165-72.
6. Augustin, M. A., Reichert, A. S., Betat, H., Huber, R., Morl, M., and Steegborn, C. (2003) Crystal Structure of the Human CCA-adding Enzyme: Insights into Template-independent Polymerization, J. Mol. Biol. 328, 985-94.
7. Xiong, Y., and Steitz, T. A. (2004) Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template, Nature 430, 640-5.
8. Tomita, K., Fukai, S., Ishitani, R., Ueda, T., Takeuchi, N., Vassylyev, D. G., and Nureki, O. (2004) Structural basis for template-independent RNA polymerization, Nature 430, 700-4.
9. Yue, D., Weiner, A. M., and Maizels, N. (1998) The CCA-adding enzyme has a single active site, J. Biol. Chem. 273, 29693-700.
10. Steitz, T. A., and Steitz, J. A. (1993) A general two-metal-ion mechanism for catalytic RNA, Proc. Natl. Acad. Sci. U.S.A. 90, 6498-502.
11. Steitz, T. A. (1998) A mechanism for all polymerases [news; comment], Nature 391, 231-2.
12. Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., and Kraut, J. (1994) Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP, Science 264, 1891-903.
13. Martin, G., Keller, W., and Doublie, S. (2000) Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP [In Process Citation], EMBO J. 19, 4193-203.
14. Fedor, M. J. (2002) The role of metal ions in RNA catalysis, Curr. Opin. Struct. Biol. 12, 289-95.
15. Vermote, C. L., Vipond, I. B., and Halford, S. E. (1992) EcoRV restriction endonuclease: communication between DNA recognition and catalysis, Biochemistry 31, 6089-97.
16. Hsu, M., and Berg, P. (1978) Altering the specificity of restriction endonuclease: effect of replacing Mg2+ with Mn2+, Biochemistry 17, 131-38.
17. Lagunavicius, A., Grazulis, S., Balciunaite, E., Vainius, D., and Siksnys, V. (1997) DNA binding specificity of Muni restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues, Biochemistry 36, 11093-9.
18. Jeltsch, A., Alves, J., Wolfes, H., Maass, G., and Pingoud, A. (1994) Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA, Biochemistry 33, 10215-9.
19. Tabor, S., and Richardson, C. C. (1989) Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I, Proc. Natl. Acad. Sci. U.S.A. 86, 4076-80.
20. Hou, Y. M. (2000) Unusual synthesis by the Escherichia coli CCA-adding enzyme [In Process Citation], RNA 6, 1031-43.
21. Seth, M., Thurlow, D. L., and Hou, Y. M. (2002) Poly(C) synthesis by class I and class II CCA-adding enzymes, Biochemistry 41, 4521-32.
22. Arthur, P. G., and Hochachka, P. W. (1995) Automated analysis of cellular metabolites at nanomolar to micromolar concentrations using bioluminescent methods, Anal. Biochem. 227, 281-4.
23. Turnbough, C. L., Jr. (1983) Regulation of Escherichia coli aspartate transcarbamylase synthesis by guanosine tetraphosphate and pyrimidine ribonucleoside triphosphates, J. Bacteriol. 153, 998-1007.
24. Shi, P. Y., Weiner, A. M., and Maizels, N. (1998) A top-half tDNA minihelix is a good substrate for the eubacterial CCA- adding enzyme, RNA 4, 276-84.
25. Hegg, L. A., Kou, M., and Thurlow, D. L. (1990) Recognition of the tRNA-like structure in tobacco mosaic viral RNA by ATP/CTP: tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae, J. Biol. Chem. 265, 17441-5.
26. Tomari, Y., Suzuki, T., Watanabe, K., and Ueda, T. (2000) The role of tightly bound ATP in Escherichia coli tRNA nucleotidyltransferase, Genes Cells 5, 689-98.
27. Shi, P. Y., Maizels, N., and Weiner, A. M. (1998) CCA addition by tRNA nucleotidyltransferase: polymerization without translocation?, EMBO J. 17, 3197-206.
28. Doan, L., Handa, B., Roberts, N. A., and Klumpp, K. (1999) Metal ion catalysis of RNA cleavage by the influenza virus endonuclease, Biochemistry 38, 5612-9.
29. Westover, K. D., Bushnell, D. A., and Kornberg, R. D. (2004) Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center, Cell 119, 481-9.
30. Vipond, I. B., Baldwin, G. S., and Halford, S. E. (1995) Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases, Biochemistry 34, 697-704.
31. Beernink, P. T., Segelke, B. W., Hadi, M. Z., Erzberger, J. P., Wilson, D. M., 3rd, and Rupp, B. (2001) Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism, J. Mol. Biol. 307, 1023-34.
32. Lott, W. B., Pontius, B. W., and von Hippel, P. H. (1998) A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate, Proc. Natl. Acad. Sci. U.S.A. 95, 542-7.
33. Ohmichi, T., and Sugimoto, N. (1997) Role of Nd3+ and Pb2+ on the RNA cleavage reaction by a small ribozyme, Biochemistry 36, 3514-21.
34. Shen, Y., Zhukovskaya, N. L., Guo, Q., Florian, J., and Tang, W. J. (2005) Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor, EMBO J. 24, 929-41.
35. Cao, W., Mayer, A. N., and Barany, F. (1995) Stringent and relaxed specificities of TaqI endonuclease: interactions with metal cofactors and DNA sequences, Biochemistry 34, 2276-83.
36. Sam, M. D., and Perona, J. J. (1999) Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease, Biochemistry 38, 6576-86.
37. Betat, H., Rammelt, C., Martin, G., and Morl, M. (2004) Exchange of regions between bacterial poly(A) polymerase and the CCA-adding enzyme generates altered specificities, Mol. Cell 15, 389-98.