Structural studies of ribonuclease P

Protein Reviews

Volumn 10, Issue , 2010, Pages 63-78

  Mondragón, Alfonso ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBONUCLEASE P;

ARCHAEBACTERIUM; ENZYME STRUCTURE; EUKARYOTE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; REVIEW; RNA STRUCTURE; STRUCTURE ANALYSIS;

ARCHAEA;

EID: 77953394913     PISSN: 18713025     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4419-1142-1_4     Document Type: Review

References (79)

1. Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA (2004) Crystal structure of a self-splicing group I intron with both exons. Nature 430:45-50 (Pubitemid 38915218)
2. Alifano P, Rivellini F, Piscitelli C, Arraiano CM, Bruni CB, Carlomagno MS (1994) Ribonuclease E provides substrates for ribonuclease P-dependent processing of a polycistronic mRNA. Genes Dev 8:3021-3231
3. Altman S, Kirsebom LA (1999) In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 351-380
4. Altman S, Wesolowski D, Guerrier-Takada C, Li Y (2005) RNase P cleaves transient structures in some riboswitches. Proc Natl Acad Sci U S A 102:11284-11289
5. Amero CD, Boomershine WP, Xu Y, Foster M (2008) Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner. Biochemistry 47:11704-11710
6. Beebe JA, Kurz JC, Fierke CA (1996) Magnesium ions are required by Bacillus subtilis ribonuclease P RNA for both binding and cleaving precursor tRNAAsp. Biochemistry 35:10493-10505
7. Boomershine WP, McElroy CA, Tsai HY, Wilson RC, Gopalan V, Foster MP (2003) Structure of Mth11/Mth Rpp 29, an essential protein subunit of archaeal and eukaryotic RNase P. Proc Natl Acad Sci U S A 100:15398-15403
8. Buck AH, Kazantsev AV, Dalby AB, Pace NR (2005) Structural perspective on the activation of RNase P RNA by protein. Nat Struct Mol Biol 12(11):958-964
9. Chamberlain JR, Lee Y, Lane WS, Engelke DR (1998) Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev 12:1678-1690
10. Chen J-L, Pace NR (1997) Identification of the universally conserved core of ribonuclease P RNA. RNA 3:557-560
11. Christian EL, Zahler NH, Kaye NM, Harris ME (2002) Analysis of substrate recognition by the ribonucleoprotein endonuclease RNase P. Methods 28:307-322
12. Costa M, Michel F (1995) Frequent use of the same tertiary motif by self-folding RNAs. EMBO J 14:1276-1285
13. Doudna JA, Cech TR (1995) Self-assembly of a group I intron active site from its component tertiary structural domains. RNA 1:36-45
14. Evans D, Marquez SM, Pace NR (2006) RNase P: interface of the RNA and protein worlds. Trends Biochem Sci 31:333-341
15. Fang XW, Pan T, Sosnick TR (1999) Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Biol 6:1091-1095
16. Frank DN, Pace NR (1998) Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67:153-180
17. Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M (2006) A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3. Biochem Biophys Res Commun 343:956-964
18. Getz MM, Andrews AJ, Fierke CA, Al-Hashimi HM (2007) Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation. RNA 13:251-266
19. Golden BL, Kim H, Chase E (2005) Crystal structure of a phage Twort group I ribozyme-product complex. Nat Struct Mol Biol 12:82-89
20. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-857
21. Guo F, Gooding AR, Cech TR (2004) Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell 16:351-362
22. Hall TA, Brown JW (2004) Interactions between RNase P protein subunits in archaea. Archaea 1:247-254
23. Harris ME, Nolan JM, Malhotra A, Brown JW, Harvey SC, Pace NR (1994) Use of photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA. EMBO J 13:3953-3963
24. Hartmann E, Hartmann RK (2003) The enigma of ribonuclease P evolution. Trends Genet 19:561-569
25. Hartmann RK, Heinrich J, Schlegl J, Schuster H (1995) Precursor of C4 antisense RNA of bacteriophages P1 and P7 is a substrate for RNase P of Escherichia coli. Proc Natl Acad Sci U S A 92:5822-5826
26. Honda T, Kakuta Y, Kimura K, Saho J, Kimura M (2008) Structure of an archaeal homolog of the human protein complex Rpp 21-Rpp29 that is a key core component for the assembly of active ribonuclease P. J Mol Biol 384:652-662
27. Houser-Scott F, Xiao S, Millikin CE, Zengel JM, Lindahl L, Engelke DR (2002) Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase P. Proc Natl Acad Sci U S A 99:2684-2689
28. Jarrous N (2002) Human ribonuclease P: subunits, function, and intranuclear localization. RNA 8:1-7
29. Jiang T, Altman S (2001) Protein-protein interactions with subunits of human nuclear RNase P. Proc Natl Acad Sci U S A 98:920-925 (Pubitemid 32121163)
30. Kakuta Y, Ishimatsu I, Numata T, Kimura K, Yao M, Tanaka I, Kimura M (2005) Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp 21. Biochemistry 44:12086-12093
31. Kawano S, Nakashima T, Kakuta Y, Tanaka I, Kimura M (2006) Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme. J Mol Biol 357:583-591
32. Kazantsev AV, Pace NR (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat Rev Microbiol 4:729-740
33. Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR (2003) High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A 100:7497-7502
34. Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, Pace NR (2005) Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A 102:13392-13397
35. Kazantsev AV, Krivenko AA, Pace NR (2009) Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. RNA 15:266-276
36. Kent O, Chaulk SG, MacMillan AM (2000) Kinetic analysis of the M1 RNA folding pathway. J Mol Biol 304:699-705
37. Kifusa M, Fukuhara H, Hayashi T, Kimura M (2005) Protein-protein interactions in the subunits of ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Biosci Biotechnol Biochem 69:1209-1212
38. Kikovska E, Svard SG, Kirsebom LA (2007) Eukaryotic RNase P RNA mediates cleavage in the absence of protein. Proc Natl Acad Sci U S A 104:2062-2067
39. Kirsebom LA, Svard SG (1994) Base pairing between Escherichia coli RNase P RNA and its substrate. EMBO J 13:4870-4876
40. Komine Y, Kitabatake M, Yokogawa T, Nishikawa K, Inokuchi H (1994) A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc Natl Acad Sci U S A 91:9223-9227
41. Kouzuma Y, Mizoguchi M, Takagi H, Fukuhara H, Tsukamoto M, Numata T, Kimura M (2003) Reconstitution of archaeal ribonuclease P from RNA and four protein components. Biochem Biophys Res Commun 306:666-673
42. Krasilnikov AS, Mondragon A (2003) On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA 9:640-643
43. Krasilnikov AS, Yang X, Pan T, Mondragón A (2003) Crystal structure of the specificity domain of ribonuclease P. Nature 421:760-764
44. Krasilnikov AS, Xiao Y, Pan T, Mondragon A (2004) Basis for structural diversity in homologous RNAs. Science 306:104-107
45. Kurz JC, Fierke CA (2000) Ribonuclease P: a ribonucleoprotein enzyme. Curr Opin Chem Biol 4:553-558
46. LaGrandeur TE, Huttenhofer A, Noller HF, Pace NR (1994) Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA. EMBO J 13:3945-3952
47. Lee JC, Cannone JJ, Gutell RR (2003) The lonepair triloop: a new motif in RNA structure. J Mol Biol 325:65-83
48. Leeper TC, Martin MB, Kim H, Cox S, Semenchenko V, Schmidt FJ, Van Doren SR (2002) Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action. Nat Struct Biol 9:397-403
49. Li Y, Altman S (2003) A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs. Proc Natl Acad Sci U S A 100:13213-13218
50. Loria A, Pan T (1996) Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2:551-563
51. Loria A, Pan T (1997) Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 36:6317-6325
52. Mans RM, Guerrier-Takada C, Altman S, Pleij CW (1990) Interaction of RNase P from Escherichia coli with pseudoknotted structures in viral RNAs. Nucleic Acids Res 18:3479-3487
53. Marquez SM, Chen JL, Evans D, Pace NR (2006) Structure and function of eukaryotic ribonuclease P RNA. Mol Cell 24:445-456
54. Massire C, Jaeger L, Westhof E (1998) Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J Mol Biol 279:773-793
55. Nagaswamy U, Fox GE (2002) Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. RNA 8:1112-1119
56. Niranjanakumari S, Stams T, Crary SM, Christianson DW, Fierke CA (1998) Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA. Proc Natl Acad Sci U S A 95:15212-15217
57. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc Natl Acad Sci U S A 98:4899-4903
58. Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M (2004) Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp 29. RNA 10:1423-1432
59. Odell L, Huang V, Jakacka M, Pan T (1998) Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. Nucleic Acids Res 26:3717-3723 (Pubitemid 28367977)
60. Pan T (1995) Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 34:902-909
61. Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW (1999) RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci USA 96:7803-7808
62. Peck-Miller KA, Altman S (1991) Kinetics of the processing of the precursor to 4.5 S RNA, a naturally occurring substrate for RNase P from Escherichia coli. J Mol Biol 221:1-5
63. Persson T, Cuzic S, Hartmann RK (2003) Catalysis by RNase P RNA: unique features and unprecedented active site plasticity. J Biol Chem 278:43394-43401
64. Schmitz M, Tinoco I Jr (2000) Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA. RNA 6:1212-1225
65. Sidote DJ, Hoffman DW (2003) NMR structure of an archaeal homologue of ribonuclease P protein Rpp 29. Biochemistry 42:13541-13550
66. Sidote DJ, Heideker J, Hoffman DW (2004) Crystal structure of archaeal ribonuclease P protein aRpp 29 from Archaeoglobus fulgidus. Biochemistry 43:14128-14138
67. Siegel RW, Banta AB, Haas ES, Brown JW, Pace NR (1996) Mycoplasma fermentans simplifies our view of the catalytic core of ribonuclease P RNA. RNA 2:452-462
68. Smith D, Pace NR (1993) Multiple magnesium ions in the ribonuclease P reaction mechanism. Biochemistry 32:5273-5281
69. Spitzfaden C, Nicholson N, Jones JJ, Guth S, Lehr R, Prescott CD, Hegg LA, Eggleston DS (2000) The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA. J Mol Biol 295:105-115
70. Stams T, Niranjanakumari S, Fierke CA, Christianson DW (1998) Ribonuclease P protein structure: evolutionary origins in the translational apparatus. Science 280:752-755
71. Takagi H, Watanabe M, Kakuta Y, Kamachi R, Numata T, Tanaka I, Kimura M (2004) Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3. Biochem Biophys Res Commun 319:787-794 (Pubitemid 38739390)
72. Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragon A (2005) Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437:584-587 (Pubitemid 41613559)
73. Torres-Larios A, Swinger KK, Pan T, Mondragon A (2006) Structure of ribonuclease P - a universal ribozyme. Curr Opin Struct Biol 16:327-335
74. Tsai HY, Masquida B, Biswas R, Westhof E, Gopalan V (2003) Molecular modeling of the threedimensional structure of the bacterial RNase P holoenzyme. J Mol Biol 325:661-675
75. Vicens Q, Cech TR (2006) Atomic level architecture of group I introns revealed. Trends Biochem Sci 31(1):41-51
76. Walker SC, Engelke DR (2006) Ribonuclease P: the evolution of an ancient RNA enzyme. Crit Rev Biochem Mol Biol 41:77-102
77. Waugh DS, Pace NR (1990) Complementation of an RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubacteria. J Bacteriol 172:6316-6322
78. Wilson RC, Bohlen CJ, Foster MP, Bell CE (2006) Structure of Pfu Pop5, an archaeal RNase P protein. Proc Natl Acad Sci U S A 103:873-878
79. Woodson SA (2005) Structure and assembly of group I introns. Curr Opin Struct Biol 15: 324-330