Discrimination of RNA from DNA by polynucleotide phosphorylase

Biochemistry

Volumn 52, Issue 38, 2013, Pages 6702-6711

  Unciuleac, Mihaela Carmen ^a   Shuman, Stewart ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MYCOBACTERIUM SMEGMATIS; PHOSPHATE COMPLEXES; PHOSPHATE GROUP; PHOSPHODIESTERS; PHOSPHOROLYSIS; POLYNUCLEOTIDE PHOSPHORYLASE; POLYNUCLEOTIDES; RNA METABOLISMS;

BACTERIA; MAGNESIUM; MANGANESE; NUCLEOTIDES; PHOSPHORYLATION; RNA;

DNA;

DEOXYRIBONUCLEOTIDE; DNA; MAGNESIUM; MANGANESE; PHOSPHATE; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; RIBOSE; RNA;

ARTICLE; CATALYSIS; CHEMICAL INTERACTION; ENZYME STRUCTURE; MYCOBACTERIUM SMEGMATIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; RNA ANALYSIS;

BASE SEQUENCE; CATALYSIS; DEOXYRIBONUCLEOTIDES; DNA; MAGNESIUM; MANGANESE; MODELS, CHEMICAL; MYCOBACTERIUM SMEGMATIS; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; RNA; SUBSTRATE SPECIFICITY;

EID: 84884881185     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi401041v     Document Type: Article

References (23)

1. Littauer, U. Z. and Soreq, H. (1982) Polynucleotide phosphorylase Enzymes 15, 517-553
2. Mohanty, B. K. and Kushner, S. R. (2000) Polynucleotide phosphorylase functions both as a 3′-to-5′ exonuclease and a poly(A) polymerase in Escherichia coli Proc. Natl. Acad. Sci. U.S.A. 97, 11966-11971
3. Cardenas, P. P., Carrasco, B., Sanchez, H., Deikus, G., Bechhofer, D. H., and Alonso, J. C. (2009) Bacillus subtilis polynucleotide phosphorylase 3′-to-5′ DNase activity is involved in DNA repair Nucleic Acids Res. 37, 4157-4169
4. Cardenas, P. P., Carzaniga, T., Zangrossi, S., Briani, F., Garcia-Tirado, E., Deho, G., and Alonso, J. C. (2011) Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins Nucleic Acids Res. 39, 9250-9261
5. Gong, C., Bongiorno, P., Martins, A., Stephanou, N. C., Zhu, H., Shuman, S., and Glickman, M. S. (2005) Mechanism of non-homologous end joining in mycobacteria: A low-fidelity repair system driven by Ku, ligase D and ligase C Nat. Struct. Mol. Biol. 12, 304-312
6. Aniukwu, J., Glickman, M. S., and Shuman, S. (2008) The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends Genes Dev. 22, 512-527
7. Sinha, K. M., Unciuleac, M. C., Glickman, M. S., and Shuman, S. (2009) AdnAB: A new DSB-resecting motor-nuclease from Mycobacteria Genes Dev. 23, 1423-1437
8. Gupta, R., Barkan, D., Redelman-Sidi, G., Shuman, S., and Glickman, M. S. (2011) Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways Mol. Microbiol. 79, 316-330
9. Gupta, R., Ryzhikov, M., Koroleva, O., Unciuleac, M., Shuman, S., Korolev, S., and Glickman, M. (2013) A dual role for mycobacterial RecO in RecA-dependent homologous recombination and RecA-independent single-strand annealing Nucleic Acids Res. 41, 2284-2295
10. Unciuleac, M. and Shuman, S. (2013) Distinctive effects of domain deletions on the manganese-dependent DNA polymerase and DNA phosphorylase activities of Mycobacterium smegmatis polynucleotide phosphorylase Biochemistry 52, 2967-2981
11. Symmons, M. F., Jones, G. H., and Luisi, B. F. (2000) A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation Structure 8, 1215-1226
12. Shi, Z., Yang, W. Z., Lin-Chao, S., Chak, K. F., and Yuan, H. S. (2008) Crystal structure of Escherichia coli PNPase: Central channel residues are involved in processive RNA degradation RNA 14, 2361-2371
13. Nurmohamed, S., Vaidialingam, B., Callaghan, A. J., and Luisi, B. F. (2009) Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: Implications for catalytic mechanism and RNA degradosome assembly J. Mol. Biol. 389, 17-33
14. Lin, C. H., Wang, Y. T., Yang, W. Z., Hsiao, Y. Y., and Yuan, H. S. (2012) Crystal structure of human polynucleotide phosphorylase: Insights into its domain function in RNA binding and degradation Nucleic Acids Res. 40, 4146-4157
15. Hardwick, S. W., Gubbey, T., Hug, I., Jenal, U., and Luisi, B. F. (2012) Crystal structure of Caulobacter crescentus polynucleotide phosphorylase reveals a mechanism of RNA substrate channeling and RNA degradosome assembly Open Biol. 2, 120028
16. Das, U. and Shuman, S. (2013) Mechanism of RNA 2′,3′-cyclic phosphate end-healing by T4 polynucleotide kinase-phosphatase Nucleic Acids Res. 41, 355-365
17. Jarrige, A. C., Brechemier-Baey, D., Mathy, N., Duche, O., and Portier, C. (2002) Mutational analysis of polynucleotide phosphorylase from Escherichia coli J. Mol. Biol. 321, 397-409
18. Lorentzen, E., Dziembowski, A., Lindner, D., Seraphin, B., and Conti, E. (2007) RNA channeling by the archaeal exosome EMBO Rep. 8, 470-476
19. Lorentzen, E. and Conti, E. (2012) Crystal structure of a 9-subunit archaeal exosome in pre-catalytic states of the phosphorolytic reaction Archaea 2012, 721869
20. Chou, J. Y. and Singer, M. F. (1970) A kinetic analysis of the phosphorolysis of oligonucleotides by polynucleotide phosphorylase J. Biol. Chem. 245, 995-1004
21. Chou, J. Y. and Singer, M. F. (1970) The effect of chain length on the phosphorolysis of oligonucleotides by polynucleotide phosphorylase J. Biol. Chem. 245, 1005-1011
22. Zhu, H. and Shuman, S. (2005) Novel 3′-ribonuclease and 3′-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D J. Biol. Chem. 280, 25973-25981
23. Nair, P. A., Smith, P., and Shuman, S. (2010) Structure of bacterial LigD 3′-phosphoesterase unveils a DNA repair superfamily Proc. Natl. Acad. Sci. U.S.A. 107, 12822-12827