Note_RNAProcessing – RNAProcessing

Name
WID Note_RNAProcessing
Name RNAProcessing
 
Comments
Comments Ribonuclease P Ribonuclease P removes 5' leader sequence from pre-tRNA by hydrolyzing phosphodiester bond immediately 5' of first nucleotide of mature tRNA. Ribonuclease P is a ribonucleoprotein contain 1 protein subunit (MG_465, rpnA) and 1 RNA subunit (MG_0003, P RNA, MCS5). Ribonuclease P kinetics were investigated by Hsieh et al [PUB_0013]: ParameterValue (Mg2+)Value (Ca2+) kcat0.27 ±0.02 s-1 KM0.08 ± 0.02 μM k20.3 ± 0.01 s-11.8 ± 0.3 × 10-5 s-1 KDpretRNA4 ± 2 × 10-4 μM KDtRNA1.2 ± 0.1 μM0.2 ± 0.06 μM Network reconstruction rRNA, sRNA, and tRNA cleavage was reconstructed from the primary literature [PUB_0038, PUB_0039, PUB_0042, PUB_0061, PUB_0068, PUB_0069, PUB_0070, PUB_0101, PUB_0102, PUB_0104, PUB_0110, PUB_0163, PUB_0166]. Specific parameters were obtained from the following sources: Kinetics: [PUB_0013, PUB_0069, PUB_0103] Complex composition: [PUB_0011] Cofactors: [PUB_0006, PUB_0012, PUB_0013, PUB_0039, PUB_0043, PUB_0071, PUB_0096, PUB_0165]
References
  1. Britton RA. Role of GTPases in bacterial ribosome assembly. Annu Rev Microbiol 63, 155-76 (2009). WholeCell: PUB_0104, PubMed: 19575570

  2. Callebaut I, Moshous D, Mornon JP, de Villartay JP. Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. Nucleic Acids Res 30, 3592-601 (2002). WholeCell: PUB_0163, PubMed: 12177301

  3. Cech TR, Bass BL. Biological catalysis by RNA. Annu Rev Biochem 55, 599-629 (1986). WholeCell: PUB_0012, PubMed: 2427016

  4. Charollais J, Dreyfus M, Iost I. CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Res 32, 2751-9 (2004). WholeCell: PUB_0070, PubMed: 15148362

  5. Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res 31, 474-7 (2003). WholeCell: PUB_0110, PubMed: 12520055, URL: http://www.ncbi.nlm.nih.gov/Structure/

  6. ... 17 more

  7. Cordin O, Banroques J, Tanner NK, Linder P. The DEAD-box protein family of RNA helicases. Gene 367, 17-37 (2006). WholeCell: PUB_0069, PubMed: 16337753

  8. Deutscher MP. Maturation and degradation of ribosomal RNA in bacteria. Prog Mol Biol Transl Sci 85, 369-91 (2009). WholeCell: PUB_0038, PubMed: 19215777

  9. Hase Y, Yokoyama S, Muto A, Himeno H. Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells. RNA 15, 1766-74 (2009). WholeCell: PUB_0101, PubMed: 19620234

  10. Himeno H, Hanawa-Suetsugu K, Kimura T, Takagi K, Sugiyama W, Shirata S, Mikami T, Odagiri F, Osanai Y, Watanabe D, Goto S, Kalachnyuk L, Ushida C, Muto A. A novel GTPase activated by the small subunit of ribosome. Nucleic Acids Res 32, 5303-9 (2004). WholeCell: PUB_0103, PubMed: 15466596

  11. Hsieh J, Andrews AJ, Fierke CA. Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P. Biopolymers 73, 79-89 (2004). WholeCell: PUB_0013, PubMed: 14691942

  12. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

  13. Kimura T, Takagi K, Hirata Y, Hase Y, Muto A, Himeno H. Ribosome-small-subunit-dependent GTPase interacts with tRNA-binding sites on the ribosome. J Mol Biol 381, 467-77 (2008). WholeCell: PUB_0102, PubMed: 18588897

  14. Madhugiri R, Evguenieva-Hackenberg E. RNase J is involved in the 5'-end maturation of 16S rRNA and 23S rRNA in Sinorhizobium meliloti. FEBS Lett 583, 2339-42 (2009). WholeCell: PUB_0166, PubMed: 19540834

  15. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 39, D52-7 (2011). WholeCell: PUB_0061, PubMed: 21115458, URL: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene

  16. Nicholson AW. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev 23, 371-90 (1999). WholeCell: PUB_0039, PubMed: 10371039

  17. Py B, Higgins CF, Krisch HM, Carpousis AJ. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381, 169-72 (1996). WholeCell: PUB_0068, PubMed: 8610017

  18. Rauhut R, Klug G. mRNA degradation in bacteria. FEMS Microbiol Rev 23, 353-70 (1999). WholeCell: PUB_0071, PubMed: 10371038

  19. Torres-Larios A, Swinger KK, Pan T, Mondragón A. Structure of ribonuclease P--a universal ribozyme. Curr Opin Struct Biol 16, 327-35 (2006). WholeCell: PUB_0011, PubMed: 16650980

  20. UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37, D169-74 (2009). WholeCell: PUB_0096, PubMed: 18836194, URL: http://www.uniprot.org/uniprot/

  21. Wu Q, Huang L, Zhang Y. The structure and function of catalytic RNAs. Sci China C Life Sci 52, 232-44 (2009). WholeCell: PUB_0043, PubMed: 19294348

  22. Yao S, Blaustein JB, Bechhofer DH. Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res 35, 4464-73 (2007). WholeCell: PUB_0042, PubMed: 17576666

  23. de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. Structural insights into the dual activity of RNase J. Nat Struct Mol Biol 15, 206-12 (2008). WholeCell: PUB_0165, PubMed: 18204464

 
Metadata
Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:58