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For: Hoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferré-D'Amaré AR. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol Cell 2007;24:535-45. [PMID: 17188032 DOI: 10.1016/j.molcel.2006.09.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2006] [Revised: 09/04/2006] [Accepted: 09/22/2006] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Schaening-Burgos C, LeBlanc H, Fagre C, Li GW, Gilbert WV. RluA is the major mRNA pseudouridine synthase in Escherichia coli. PLoS Genet 2024;20:e1011100. [PMID: 39241085 PMCID: PMC11421799 DOI: 10.1371/journal.pgen.1011100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 09/24/2024] [Accepted: 07/14/2024] [Indexed: 09/08/2024]  Open
2
Lin TY, Kleemann L, Jeżowski J, Dobosz D, Rawski M, Indyka P, Ważny G, Mehta R, Chramiec-Głąbik A, Koziej Ł, Ranff T, Fufezan C, Wawro M, Kochan J, Bereta J, Leidel SA, Glatt S. The molecular basis of tRNA selectivity by human pseudouridine synthase 3. Mol Cell 2024;84:2472-2489.e8. [PMID: 38996458 PMCID: PMC11258540 DOI: 10.1016/j.molcel.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 03/14/2024] [Accepted: 06/13/2024] [Indexed: 07/14/2024]
3
Jalan A, Jayasree PJ, Karemore P, Narayan KP, Khandelia P. Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease. Mol Biotechnol 2024;66:1581-1598. [PMID: 37341888 DOI: 10.1007/s12033-023-00792-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
4
Grünberg S, Doyle LA, Wolf EJ, Dai N, Corrêa IR, Yigit E, Stoddard BL. The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1. PLoS One 2023;18:e0291267. [PMID: 37939088 PMCID: PMC10631681 DOI: 10.1371/journal.pone.0291267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/25/2023] [Indexed: 11/10/2023]  Open
5
McDermott SM, Pham V, Lewis I, Tracy M, Stuart K. mt-LAF3 is a pseudouridine synthase ortholog required for mitochondrial rRNA and mRNA gene expression in Trypanosoma brucei. Int J Parasitol 2023;53:573-583. [PMID: 37268169 PMCID: PMC10527287 DOI: 10.1016/j.ijpara.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 06/04/2023]
6
Song W, Podicheti R, Rusch DB, Tracey WD. Transcriptome-wide analysis of pseudouridylation in Drosophila melanogaster. G3 (BETHESDA, MD.) 2023;13:jkac333. [PMID: 36534986 PMCID: PMC9997552 DOI: 10.1093/g3journal/jkac333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
7
McDermott SM, Pham V, Lewis I, Tracy M, Stuart K. mt-LAF3 is a pseudouridine synthase ortholog required for mitochondrial rRNA and mRNA gene expression in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529727. [PMID: 36865177 PMCID: PMC9980140 DOI: 10.1101/2023.02.23.529727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
8
Kimura S, Srisuknimit V, McCarty KL, Dedon PC, Kranzusch PJ, Waldor MK. Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine. Nat Commun 2022;13:5994. [PMID: 36220828 PMCID: PMC9553926 DOI: 10.1038/s41467-022-33714-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022]  Open
9
Jeong H, Lee Y, Kim J. Structural and functional characterization of TrmM in m6 A modification of bacterial tRNA. Protein Sci 2022;31:e4319. [PMID: 35481631 PMCID: PMC9045083 DOI: 10.1002/pro.4319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
10
Laughlin ZT, Nandi S, Dey D, Zelinskaya N, Witek MA, Srinivas P, Nguyen HA, Kuiper EG, Comstock LR, Dunham CM, Conn GL. 50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA. Proc Natl Acad Sci U S A 2022;119:e2120352119. [PMID: 35357969 PMCID: PMC9168844 DOI: 10.1073/pnas.2120352119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022]  Open
11
Kiss DJ, Oláh J, Tóth G, Varga M, Stirling A, Menyhárd DK, Ferenczy GG. The Structure-Derived Mechanism of Box H/ACA Pseudouridine Synthase Offers a Plausible Paradigm for Programmable RNA Editing. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
12
Jeong H, Kim J. Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNAVal. RNA (NEW YORK, N.Y.) 2021;27:1330-1338. [PMID: 34315814 PMCID: PMC8522699 DOI: 10.1261/rna.078863.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
13
Porat J, Kothe U, Bayfield MA. Revisiting tRNA chaperones: New players in an ancient game. RNA (NEW YORK, N.Y.) 2021;27:rna.078428.120. [PMID: 33593999 PMCID: PMC8051267 DOI: 10.1261/rna.078428.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 05/03/2023]
14
Tagel M, Ilves H, Leppik M, Jürgenstein K, Remme J, Kivisaar M. Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp. Microorganisms 2020;9:microorganisms9010025. [PMID: 33374637 PMCID: PMC7822408 DOI: 10.3390/microorganisms9010025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023]  Open
15
Loss of Pseudouridine Synthases in the RluA Family Causes Hypersensitive Nociception in Drosophila. G3-GENES GENOMES GENETICS 2020;10:4425-4438. [PMID: 33028630 PMCID: PMC7718762 DOI: 10.1534/g3.120.401767] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
16
Carpentier P, Leprêtre C, Basset C, Douki T, Torelli S, Duarte V, Hamdane D, Fontecave M, Atta M. Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Nucleic Acids Res 2020;48:9918-9930. [PMID: 32785618 PMCID: PMC7515727 DOI: 10.1093/nar/gkaa667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022]  Open
17
Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annu Rev Genet 2020;54:309-336. [PMID: 32870730 DOI: 10.1146/annurev-genet-112618-043830] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
18
Jaskolowski M, Ramrath DJF, Bieri P, Niemann M, Mattei S, Calderaro S, Leibundgut M, Horn EK, Boehringer D, Schneider A, Ban N. Structural Insights into the Mechanism of Mitoribosomal Large Subunit Biogenesis. Mol Cell 2020;79:629-644.e4. [PMID: 32679035 DOI: 10.1016/j.molcel.2020.06.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/04/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022]
19
Adachi H, De Zoysa MD, Yu YT. Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018;1862:230-239. [PMID: 30414851 DOI: 10.1016/j.bbagrm.2018.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 01/13/2023]
20
Ryu H, Grove TL, Almo SC, Kim J. Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res 2018;46:9160-9169. [PMID: 29982645 PMCID: PMC6158493 DOI: 10.1093/nar/gky592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/14/2018] [Accepted: 06/20/2018] [Indexed: 11/13/2022]  Open
21
Zhao Y, Dunker W, Yu YT, Karijolich J. The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events. Front Bioeng Biotechnol 2018;6:8. [PMID: 29473035 PMCID: PMC5809436 DOI: 10.3389/fbioe.2018.00008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022]  Open
22
Evolution of Eukaryal and Archaeal Pseudouridine Synthase Pus10. J Mol Evol 2018;86:77-89. [PMID: 29349599 DOI: 10.1007/s00239-018-9827-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
23
The Evolution of Substrate Specificity by tRNA Modification Enzymes. Enzymes 2017;41:51-88. [PMID: 28601226 DOI: 10.1016/bs.enz.2017.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
24
Zaganelli S, Rebelo-Guiomar P, Maundrell K, Rozanska A, Pierredon S, Powell CA, Jourdain AA, Hulo N, Lightowlers RN, Chrzanowska-Lightowlers ZM, Minczuk M, Martinou JC. The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules. J Biol Chem 2017;292:4519-4532. [PMID: 28082677 PMCID: PMC5377769 DOI: 10.1074/jbc.m116.771105] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/11/2017] [Indexed: 11/21/2022]  Open
25
Fitzsimmons CM, Fujimori DG. Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN. PLoS One 2016;11:e0167298. [PMID: 27902775 PMCID: PMC5130265 DOI: 10.1371/journal.pone.0167298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/12/2016] [Indexed: 11/19/2022]  Open
26
RNA modification enzyme TruB is a tRNA chaperone. Proc Natl Acad Sci U S A 2016;113:14306-14311. [PMID: 27849601 DOI: 10.1073/pnas.1607512113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
27
Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. J Mol Biol 2016;428:4100-4114. [PMID: 27593161 PMCID: PMC5178103 DOI: 10.1016/j.jmb.2016.08.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 01/07/2023]
28
Veerareddygari GR, Singh SK, Mueller EG. The Pseudouridine Synthases Proceed through a Glycal Intermediate. J Am Chem Soc 2016;138:7852-5. [PMID: 27292228 PMCID: PMC4929527 DOI: 10.1021/jacs.6b04491] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
29
Schwalm EL, Grove TL, Booker SJ, Boal AK. Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA. Science 2016;352:309-12. [PMID: 27081063 PMCID: PMC5629962 DOI: 10.1126/science.aad5367] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/23/2016] [Indexed: 01/02/2023]
30
Shahbaaz M, Ahmad F, Imtaiyaz Hassan M. Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae. 3 Biotech 2015;5:317-336. [PMID: 28324295 PMCID: PMC4434415 DOI: 10.1007/s13205-014-0231-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 05/28/2014] [Indexed: 12/20/2022]  Open
31
Saliou JM, Manival X, Tillault AS, Atmanene C, Bobo C, Branlant C, Van Dorsselaer A, Charpentier B, Cianférani S. Combining native MS approaches to decipher archaeal box H/ACA ribonucleoprotein particle structure and activity. Proteomics 2015;15:2851-61. [DOI: 10.1002/pmic.201400529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/06/2015] [Accepted: 02/24/2015] [Indexed: 12/23/2022]
32
Spenkuch F, Hinze G, Kellner S, Kreutz C, Micura R, Basché T, Helm M. Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor. Nucleic Acids Res 2014;42:12735-45. [PMID: 25300485 PMCID: PMC4227767 DOI: 10.1093/nar/gku908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
33
Friedt J, Leavens FMV, Mercier E, Wieden HJ, Kothe U. An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation. Nucleic Acids Res 2014;42:3857-70. [PMID: 24371284 PMCID: PMC3973310 DOI: 10.1093/nar/gkt1331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 11/27/2013] [Accepted: 11/30/2013] [Indexed: 11/12/2022]  Open
34
Spenkuch F, Motorin Y, Helm M. Pseudouridine: still mysterious, but never a fake (uridine)! RNA Biol 2014;11:1540-54. [PMID: 25616362 PMCID: PMC4615568 DOI: 10.4161/15476286.2014.992278] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 01/15/2023]  Open
35
Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM. The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs. Nucleic Acids Res 2013;42:2037-48. [PMID: 24214967 PMCID: PMC3919597 DOI: 10.1093/nar/gkt1050] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
36
Joardar A, Jana S, Fitzek E, Gurha P, Majumder M, Chatterjee K, Geisler M, Gupta R. Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10. RNA (NEW YORK, N.Y.) 2013;19:1279-94. [PMID: 23898217 PMCID: PMC3753934 DOI: 10.1261/rna.039230.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/25/2013] [Indexed: 05/25/2023]
37
Kamalampeta R, Keffer-Wilkes LC, Kothe U. tRNA binding, positioning, and modification by the pseudouridine synthase Pus10. J Mol Biol 2013;425:3863-74. [PMID: 23743107 DOI: 10.1016/j.jmb.2013.05.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 05/17/2013] [Accepted: 05/22/2013] [Indexed: 10/26/2022]
38
Czudnochowski N, Wang AL, Finer-Moore J, Stroud RM. In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities. J Mol Biol 2013;425:3875-87. [PMID: 23707380 DOI: 10.1016/j.jmb.2013.05.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/11/2013] [Accepted: 05/17/2013] [Indexed: 10/26/2022]
39
Leppik M, Ero R, Liiv A, Kipper K, Remme J. Different sensitivity of H69 modification enzymes RluD and RlmH to mutations in Escherichia coli 23S rRNA. Biochimie 2012;94:1080-9. [PMID: 22586702 DOI: 10.1016/j.biochi.2012.02.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
40
Zhang H, Gao ZQ, Wei Y, Wang WJ, Liu GF, Shtykova EV, Xu JH, Dong YH. Structural insights into the function of 23S rRNA methyltransferase RlmG (m²G1835) from Escherichia coli. RNA (NEW YORK, N.Y.) 2012;18:1500-1509. [PMID: 22753782 PMCID: PMC3404371 DOI: 10.1261/rna.033407.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/22/2012] [Indexed: 06/01/2023]
41
Wei Y, Zhang H, Gao ZQ, Wang WJ, Shtykova EV, Xu JH, Liu QS, Dong YH. Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA. J Struct Biol 2012;179:29-40. [PMID: 22561317 DOI: 10.1016/j.jsb.2012.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/18/2012] [Accepted: 04/19/2012] [Indexed: 02/04/2023]
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Ferré-D'Amaré AR. Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. Philos Trans R Soc Lond B Biol Sci 2012;366:2942-8. [PMID: 21930586 DOI: 10.1098/rstb.2011.0131] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
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Deigan KE, FerrÉ-D’AmarÉ AR. Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res 2011;44:1329-38. [PMID: 21615107 DOI: 10.1021/ar200039b] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wright JR, Keffer-Wilkes LC, Dobing SR, Kothe U. Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis. RNA (NEW YORK, N.Y.) 2011;17:2074-84. [PMID: 21998096 PMCID: PMC3222121 DOI: 10.1261/rna.2905811] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 08/29/2011] [Indexed: 05/20/2023]
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Miracco EJ, Bogdanov B, Mueller EG. Unexpected linear ion trap collision-induced dissociation and Fourier transform ion cyclotron resonance infrared multi-photon dissociation fragmentation of a hydrated C-glycoside of 5-fluorouridine formed by the action of the pseudouridine synthases RluA and TruB. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011;25:2627-2632. [PMID: 23657957 PMCID: PMC5728650 DOI: 10.1002/rcm.5162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 06/10/2011] [Accepted: 06/24/2011] [Indexed: 06/02/2023]
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Yu AT, Ge J, Yu YT. Pseudouridines in spliceosomal snRNAs. Protein Cell 2011;2:712-25. [PMID: 21976061 PMCID: PMC4722041 DOI: 10.1007/s13238-011-1087-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 08/22/2011] [Indexed: 01/14/2023]  Open
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Miracco EJ, Mueller EG. The products of 5-fluorouridine by the action of the pseudouridine synthase TruB disfavor one mechanism and suggest another. J Am Chem Soc 2011;133:11826-9. [PMID: 21744792 DOI: 10.1021/ja201179f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Guelorget A, Golinelli-Pimpaneau B. Mechanism-Based Strategies for Trapping and Crystallizing Complexes of RNA-Modifying Enzymes. Structure 2011;19:282-91. [DOI: 10.1016/j.str.2011.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/22/2010] [Accepted: 01/11/2011] [Indexed: 11/26/2022]
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Zhou J, Liang B, Li H. Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide. RNA (NEW YORK, N.Y.) 2011;17:244-250. [PMID: 21149572 PMCID: PMC3022274 DOI: 10.1261/rna.2415811] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 11/07/2010] [Indexed: 05/28/2023]
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McDonald MK, Miracco EJ, Chen J, Xie Y, Mueller EG. The handling of the mechanistic probe 5-fluorouridine by the pseudouridine synthase TruA and its consistency with the handling of the same probe by the pseudouridine synthases TruB and RluA. Biochemistry 2010;50:426-36. [PMID: 21142053 DOI: 10.1021/bi101737z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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