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For: Crary SM, Kurz JC, Fierke CA. Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P. RNA 2002;8:933-47. [PMID: 12166648 PMCID: PMC1370310 DOI: 10.1017/s1355838202025025] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Number Cited by Other Article(s)
1
Huang T, Chamberlain A, Zhu J, Harris ME. A minimal RNA substrate with dual fluorescent probes enables rapid kinetics and provides insight into bacterial RNase P active site interactions. RSC Chem Biol 2024;5:652-668. [PMID: 38966670 PMCID: PMC11221534 DOI: 10.1039/d4cb00049h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/17/2024] [Indexed: 07/06/2024]  Open
2
Wu J, Niu S, Tan M, Huang C, Li M, Song Y, Wang Q, Chen J, Shi S, Lan P, Lei M. Cryo-EM Structure of the Human Ribonuclease P Holoenzyme. Cell 2018;175:1393-1404.e11. [PMID: 30454648 DOI: 10.1016/j.cell.2018.10.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/20/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022]
3
Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M. Structural insight into precursor tRNA processing by yeast ribonuclease P. Science 2018;362:science.aat6678. [PMID: 30262633 DOI: 10.1126/science.aat6678] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/18/2018] [Indexed: 11/02/2022]
4
Liu X, Chen Y, Fierke CA. Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA. J Am Chem Soc 2017;139:17457-17463. [PMID: 29116782 PMCID: PMC6020041 DOI: 10.1021/jacs.7b08755] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
5
Mechanistic Insights Into Catalytic RNA-Protein Complexes Involved in Translation of the Genetic Code. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017. [PMID: 28683922 DOI: 10.1016/bs.apcsb.2017.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
6
Liu Y, Wilson TJ, Lilley DM. The structure of a nucleolytic ribozyme that employs a catalytic metal ion. Nat Chem Biol 2017;13:508-513. [PMID: 28263963 PMCID: PMC5392355 DOI: 10.1038/nchembio.2333] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023]
7
Klemm BP, Wu N, Chen Y, Liu X, Kaitany KJ, Howard MJ, Fierke CA. The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions. Biomolecules 2016;6:biom6020027. [PMID: 27187488 PMCID: PMC4919922 DOI: 10.3390/biom6020027] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 12/30/2022]  Open
8
Chemical synthesis of RNA with site-specific methylphosphonate modifications. Methods 2016;107:79-88. [PMID: 27037236 PMCID: PMC5405801 DOI: 10.1016/j.ymeth.2016.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/25/2016] [Accepted: 03/26/2016] [Indexed: 11/21/2022]  Open
9
Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Site-directed spin-labeling strategies and electron paramagnetic resonance spectroscopy for large riboswitches. Methods Enzymol 2014;549:287-311. [PMID: 25432754 DOI: 10.1016/b978-0-12-801122-5.00013-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
10
Mondragón A. Structural studies of RNase P. Annu Rev Biophys 2013;42:537-57. [PMID: 23654306 DOI: 10.1146/annurev-biophys-083012-130406] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
11
Reiter NJ, Osterman AK, Mondragón A. The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning. Nucleic Acids Res 2012;40:10384-93. [PMID: 22904083 PMCID: PMC3488217 DOI: 10.1093/nar/gks744] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
12
Lin L, Sheng J, Huang Z. Nucleic acid X-ray crystallography via direct selenium derivatization. Chem Soc Rev 2011;40:4591-602. [PMID: 21666919 DOI: 10.1039/c1cs15020k] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
13
Chen WY, Xu Y, Cho IM, Oruganti SV, Foster MP, Gopalan V. Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P. J Mol Biol 2011;411:368-83. [PMID: 21683084 DOI: 10.1016/j.jmb.2011.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 05/09/2011] [Indexed: 12/31/2022]
14
Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragón A. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature 2010;468:784-9. [PMID: 21076397 PMCID: PMC3058908 DOI: 10.1038/nature09516] [Citation(s) in RCA: 237] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 09/17/2010] [Indexed: 01/22/2023]
15
Hsieh J, Koutmou KS, Rueda D, Koutmos M, Walter NG, Fierke CA. A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P. J Mol Biol 2010;400:38-51. [PMID: 20434461 PMCID: PMC2939038 DOI: 10.1016/j.jmb.2010.04.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 04/22/2010] [Accepted: 04/24/2010] [Indexed: 01/25/2023]
16
Sun FJ, Caetano-Anollés G. The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics 2010;11:153. [PMID: 20334683 PMCID: PMC2858038 DOI: 10.1186/1471-2105-11-153] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 03/24/2010] [Indexed: 12/20/2022]  Open
17
Koutmou KS, Zahler NH, Kurz JC, Campbell FE, Harris ME, Fierke CA. Protein-precursor tRNA contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease P. J Mol Biol 2010;396:195-208. [PMID: 19932118 PMCID: PMC2829246 DOI: 10.1016/j.jmb.2009.11.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 12/15/2022]
18
Koutmou KS, Casiano-Negroni A, Getz MM, Pazicni S, Andrews AJ, Penner-Hahn JE, Al-Hashimi HM, Fierke CA. NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P. Proc Natl Acad Sci U S A 2010;107:2479-84. [PMID: 20133747 PMCID: PMC2823894 DOI: 10.1073/pnas.0906319107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
19
Frederiksen JK, Piccirilli JA. Separation of RNA phosphorothioate oligonucleotides by HPLC. Methods Enzymol 2009;468:289-309. [PMID: 20946775 DOI: 10.1016/s0076-6879(09)68014-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
20
Frederiksen JK, Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes. Methods 2009;49:148-66. [PMID: 19651216 DOI: 10.1016/j.ymeth.2009.07.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/20/2009] [Accepted: 07/29/2009] [Indexed: 01/05/2023]  Open
21
Hsieh J, Fierke CA. Conformational change in the Bacillus subtilis RNase P holoenzyme--pre-tRNA complex enhances substrate affinity and limits cleavage rate. RNA (NEW YORK, N.Y.) 2009;15:1565-77. [PMID: 19549719 PMCID: PMC2714742 DOI: 10.1261/rna.1639409] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
22
Kirsebom LA, Trobro S. RNase P RNA-mediated cleavage. IUBMB Life 2009;61:189-200. [DOI: 10.1002/iub.160] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
23
Kazantsev AV, Krivenko AA, Pace NR. Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. RNA (NEW YORK, N.Y.) 2009;15:266-76. [PMID: 19095619 PMCID: PMC2648716 DOI: 10.1261/rna.1331809] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
24
Smith JK, Hsieh J, Fierke CA. Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis. Biopolymers 2007;87:329-38. [PMID: 17868095 DOI: 10.1002/bip.20846] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
25
Cuzic S, Hartmann RK. A 2'-methyl or 2'-methylene group at G+1 in precursor tRNA interferes with Mg2+ binding at the enzyme-substrate interface in E-S complexes of E. coli RNase P. Biol Chem 2007;388:717-26. [PMID: 17570824 DOI: 10.1515/bc.2007.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
26
Niranjanakumari S, Day-Storms JJ, Ahmed M, Hsieh J, Zahler NH, Venters RA, Fierke CA. Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage. RNA (NEW YORK, N.Y.) 2007;13:521-35. [PMID: 17299131 PMCID: PMC1831860 DOI: 10.1261/rna.308707] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 12/21/2006] [Indexed: 05/03/2023]
27
Getz MM, Andrews AJ, Fierke CA, Al-Hashimi HM. Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation. RNA (NEW YORK, N.Y.) 2007;13:251-66. [PMID: 17194721 PMCID: PMC1781369 DOI: 10.1261/rna.264207] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
28
Kazantsev AV, Pace NR. Bacterial RNase P: a new view of an ancient enzyme. Nat Rev Microbiol 2006;4:729-40. [PMID: 16980936 DOI: 10.1038/nrmicro1491] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
29
Christian EL, Smith KMJ, Perera N, Harris ME. The P4 metal binding site in RNase P RNA affects active site metal affinity through substrate positioning. RNA (NEW YORK, N.Y.) 2006;12:1463-7. [PMID: 16822954 PMCID: PMC1524898 DOI: 10.1261/rna.158606] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
30
Terada A, Honda T, Fukuhara H, Hada K, Kimura M. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. J Biochem 2006;140:293-8. [PMID: 16829535 DOI: 10.1093/jb/mvj144] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
31
Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M. A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3. Biochem Biophys Res Commun 2006;343:956-64. [PMID: 16574071 DOI: 10.1016/j.bbrc.2006.02.192] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 02/27/2006] [Indexed: 11/30/2022]
32
Buck AH, Kazantsev AV, Dalby AB, Pace NR. Structural perspective on the activation of RNase P RNA by protein. Nat Struct Mol Biol 2005;12:958-64. [PMID: 16228004 DOI: 10.1038/nsmb1004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Accepted: 09/13/2005] [Indexed: 11/09/2022]
33
Hougland JL, Kravchuk AV, Herschlag D, Piccirilli JA. Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol 2005;3:e277. [PMID: 16092891 PMCID: PMC1184590 DOI: 10.1371/journal.pbio.0030277] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 06/09/2005] [Indexed: 12/03/2022]  Open
34
Xiao S, Day-Storms JJ, Srisawat C, Fierke CA, Engelke DR. Characterization of conserved sequence elements in eukaryotic RNase P RNA reveals roles in holoenzyme assembly and tRNA processing. RNA (NEW YORK, N.Y.) 2005;11:885-96. [PMID: 15872187 PMCID: PMC1370773 DOI: 10.1261/rna.7282205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 03/02/2005] [Indexed: 05/02/2023]
35
Day-Storms JJ, Niranjanakumari S, Fierke CA. Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay. RNA (NEW YORK, N.Y.) 2004;10:1595-608. [PMID: 15337847 PMCID: PMC1370646 DOI: 10.1261/rna.7550104] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
36
Hsieh J, Andrews AJ, Fierke CA. Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P. Biopolymers 2004;73:79-89. [PMID: 14691942 DOI: 10.1002/bip.10521] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
37
Mann H, Ben-Asouli Y, Schein A, Moussa S, Jarrous N. Eukaryotic RNase P. Mol Cell 2003;12:925-35. [PMID: 14580343 DOI: 10.1016/s1097-2765(03)00357-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
38
Banatao DR, Altman RB, Klein TE. Microenvironment analysis and identification of magnesium binding sites in RNA. Nucleic Acids Res 2003;31:4450-60. [PMID: 12888505 PMCID: PMC169872 DOI: 10.1093/nar/gkg471] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
39
Kouzuma Y, Mizoguchi M, Takagi H, Fukuhara H, Tsukamoto M, Numata T, Kimura M. Reconstitution of archaeal ribonuclease P from RNA and four protein components. Biochem Biophys Res Commun 2003;306:666-73. [PMID: 12810070 DOI: 10.1016/s0006-291x(03)01034-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
40
Harris ME, Christian EL. Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P. Curr Opin Struct Biol 2003;13:325-33. [PMID: 12831883 DOI: 10.1016/s0959-440x(03)00069-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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