Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch

Chemistry and Biology

Volumn 22, Issue 7, 2015, Pages 829-837

  Trausch, Jeremiah J ^a,b   Marcano Velázquez, Joan G ^a   Matyjasik, Michal M ^a   Batey, Robert T ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATION; MAGNESIUM; MAGNESIUM ION; METAL ION; NUCLEIC ACID BASE; PHOSPHATE; RNA; TETRAHYDROFOLIC ACID; 5 AMINO 4 IMIDAZOLECARBOXAMIDE; 5,6,7,8-TETRAHYDROFOLIC ACID; 5-AMINOIMIDAZOLE-4-CARBOXAMIDE-1-RIBOFURANOSYL TRIPHOSPHATE; APTAMER; BACTERIAL RNA; RIBONUCLEOTIDE; RIBOSWITCH; TETRAHYDROFOLIC ACID DERIVATIVE;

ARTICLE; BASE PAIRING; BINDING AFFINITY; BIOSYNTHESIS; CARBON METABOLISM; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLIZATION; HUMAN; HYDROGEN BOND; LIGAND BINDING; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROXY; PURINE SYNTHESIS; RIBOSWITCH; RNA CONFORMATION; RNA SEQUENCE; STEREOSPECIFICITY; STOICHIOMETRY; ZTP RIBOSWITCH; CHEMISTRY; CONFORMATION; MOLECULAR GENETICS; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; X RAY CRYSTALLOGRAPHY;

AMINOIMIDAZOLE CARBOXAMIDE; APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBONUCLEOTIDES; RIBOSWITCH; RNA, BACTERIAL; TETRAHYDROFOLATES;

EID: 84937812058     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2015.06.007     Document Type: Article

References (61)

1. I. Amelio, F. Cutruzzola, A. Antonov, M. Agostini, and G. Melino Serine and glycine metabolism in cancer Trends Biochem. Sci. 39 2014 191 198
2. T.D. Ames, D.A. Rodionov, Z. Weinberg, and R.R. Breaker A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate Chem. Biol. 17 2010 681 685
3. P. Auffinger, N. Grover, and E. Westhof Metal ion binding to RNA Met. Ions Life Sci. 9 2011 1 35
4. R.T. Batey Recognition of S-adenosylmethionine by riboswitches Wiley Interdiscip. Rev. RNA 2 2011 299 311
5. R.T. Batey Structure and mechanism of purine-binding riboswitches Q. Rev. Biophys. 45 2012 345 381
6. T.G.G. Battye, L. Kontogiannis, O. Johnson, H.R. Powell, and A.G. Leslie iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM Acta Crystallogr. D Biol. Crystallogr. 67 2011 271 281
7. B.R. Bochner, and B.N. Ames ZTP (5-amino 4-imidazole carboxamide riboside 5′-triphosphate): a proposed alarmone for 10-formyl-tetrahydrofolate deficiency Cell 29 1982 929 937
8. J.H. Cate, A.R. Gooding, E. Podell, K. Zhou, B.L. Golden, C.E. Kundrot, T.R. Cech, and J.A. Doudna Crystal structure of a group I ribozyme domain: principles of RNA packing Science 273 1996 1678 1685
9. R.I. Christopherson, S.D. Lyons, and P.K. Wilson Inhibitors of de novo nucleotide biosynthesis as drugs Acc. Chem. Res. 35 2002 961 971
10. J.C. Cochrane, S.V. Lipchock, and S.A. Strobel Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Chem. Biol. 14 2007 97 105
11. L.A. Cone, M.M. Leung, and J. Hirschberg Actinomyces odontolyticus bacteremia Emerg. Infect. Dis. 9 2003 1629 1632
12. J.A. Cruz, and E. Westhof Sequence-based identification of 3D structural modules in RNA with RMDetect Nat. Methods 8 2011 513 521
13. J.H. Davis, M. Tonelli, L.G. Scott, L. Jaeger, J.R. Williamson, and S.E. Butcher RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex J. Mol. Biol. 351 2005 371 382
14. T. Dieckmann, E. Suzuki, G. Nakamura, and J. Feigon Solution structure of an ATP-binding RNA aptamer reveals a novel fold RNA 2 1996 628
15. G.S. Ducker, and J.D. Rabinowitz ZMP: a master regulator of one-carbon metabolism Mol. Cell 57 2015 203 204
16. T.E. Edwards, and A.R. Ferre-D'Amare Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition Structure 14 2006 1459 1468
17. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
18. A.D. Garst, A.L. Edwards, and R.T. Batey Riboswitches: structures and mechanisms Cold Spring Harbor Perspect. Biol. 3 2011 a003533
19. D. Gautheret, D. Konings, and R.R. Gutell A major family of motifs involving G.A mismatches in ribosomal RNA J. Mol. Biol. 242 1994 1 8
20. S.D. Gilbert, and R.T. Batey Monitoring RNA-ligand interactions using isothermal titration calorimetry Methods Mol. Biol. 540 2009 97 114
21. N. Gonen, and Y.G. Assaraf Antifolates in cancer therapy: structure, activity and mechanisms of drug resistance Drug Resist. Updat. 15 2012 183 210
22. S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S.R. Eddy, and A. Bateman Rfam: annotating non-coding RNAs in complete genomes Nucleic Acids Res. 33 2005 D121 D124
23. K. Han PSEUDOVIEWER2: visualization of RNA pseudoknots of any type Nucleic Acids Res. 31 2003 3432 3440
24. J.M. Harp, B.L. Hanson, D.E. Timm, and G.J. Bunick Macromolecular crystal annealing: evaluation of techniques and variables Acta Crystallogr. D Biol. Crystallogr. 55 1999 1329 1334
25. H.A. Heus, and A. Pardi Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops Science 253 1991 191 194
26. S.B. Jang, K. Baeyens, M.S. Jeong, J. SantaLucia, D. Turner, and S.R. Holbrook Structures of two RNA octamers containing tandem GA base pairs Acta Crystallogr. D Biol. Crystallogr. 60 2004 829 835
27. F. Jiang, R.A. Kumar, R.A. Jones, and D.J. Patel Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex Nature 382 1996 183 186
28. J.E. Johnson Jr., F.E. Reyes, J.T. Polaski, and R.T. Batey B12 cofactors directly stabilize an mRNA regulatory switch Nature 492 2012 133 137
29. C. Kao, M. Zheng, and S. Rüdisser A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase RNA 5 1999 1268 1272
30. A.Y. Keel, R.P. Rambo, R.T. Batey, and J.S. Kieft A general strategy to solve the phase problem in RNA crystallography Structure 15 2007 761 772
31. C.A. Kellenberger, S.C. Wilson, S.F. Hickey, T.L. Gonzalez, Y. Su, Z.F. Hallberg, T.F. Brewer, A.T. Iavarone, H.K. Carlson, Y.F. Hsieh, and et al. GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP Proc. Natl. Acad. Sci. USA 112 2015 5383 5388
32. P.B. Kim, J.W. Nelson, and R.R. Breaker An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism Mol. Cell 57 2015 317 328
33. D.J. Klein, and A.R. Ferré-D'Amaré Structural basis of glmS ribozyme activation by glucosamine-6-phosphate Science 313 2006 1752 1756
34. M. Legraverend, and D.S. Grierson The purines: potent and versatile small molecule inhibitors and modulators of key biological targets Bioorg. Med. Chem. 14 2006 3987 4006
35. N.B. Leontis, J. Stombaugh, and E. Westhof The non-Watson-Crick base pairs and their associated isostericity matrices Nucleic Acids Res. 30 2002 3497 3531
36. J.W. Locasale Serine, glycine and one-carbon units: cancer metabolism in full circle Nat. Rev. Cancer 13 2013 572 583
37. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674
38. M.M. Meyer, M.C. Hammond, Y. Salinas, A. Roth, N. Sudarsan, and R.R. Breaker Challenges of ligand identification for riboswitch candidates RNA Biol. 8 2011 5 10
39. E.P. Nawrocki, S.W. Burge, A. Bateman, J. Daub, R.Y. Eberhardt, S.R. Eddy, E.W. Floden, P.P. Gardner, T.A. Jones, J. Tate, and et al. Rfam 12.0: updates to the RNA families database Nucleic Acids Res. 43 2015 D130 D137
40. P. Nissen, J.A. Ippolito, N. Ban, P.B. Moore, and T.A. Steitz RNA tertiary interactions in the large ribosomal subunit: the A-minor motif Proc. Natl. Acad. Sci. USA 98 2001 4899 4903
41. J.S. Paige, T. Nguyen-Duc, W. Song, and S.R. Jaffrey Fluorescence imaging of cellular metabolites with RNA Science 335 2012 1194
42. M. Parisien, and F. Major The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data Nature 452 2008 51 55
43. A. Peselis, and A. Serganov Themes and variations in riboswitch structure and function Biochim. Biophys. Acta 1839 2014 908 918
44. J.S. Pfingsten, D.A. Costantino, and J.S. Kieft Structural basis for ribosome recruitment and manipulation by a viral IRES RNA Science 314 2006 1450 1454
45. H.W. Pley, K.M. Flaherty, and D.B. McKay Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix Nature 372 1994 111 113
46. C. Prodromou, and L.H. Pearl Recursive PCR: a novel technique for total gene synthesis Protein Eng. 5 1992 827 829
47. F.E. Reyes, A.D. Garst, and R.T. Batey Strategies in RNA crystallography Methods Enzymol. 469 2009 119 139
48. M.P. Robertson, Y.I. Chi, and W.G. Scott Solving novel RNA structures using only secondary structural fragments Methods 52 2010 168 172
49. A. Roth, and R.R. Breaker The structural and functional diversity of metabolite-binding riboswitches Annu. Rev. Biochem. 78 2009 305 334
50. M. Sassanfar, and J.W. Szostak An RNA motif that binds ATP Nature 364 1993 550 553
51. A. Serganov, A. Polonskaia, A.T. Phan, R.R. Breaker, and D.J. Patel Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature 441 2006 1167 1171
52. A. Serganov, L. Huang, and D.J. Patel Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Nature 458 2009 233 237
53. S.S. Shah, G. Rivera, and M. Ashfaq Recent advances in medicinal chemistry of sulfonamides. Rational design as anti-tumoral, anti-bacterial and anti-inflammatory agents Mini Rev. Med. Chem. 13 2013 70 86
54. S. Thore, M. Leibundgut, and N. Ban Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand Science 312 2006 1208 1211
55. J.J. Trausch, and R.T. Batey A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch Chem. Biol. 21 2014 205 216
56. J.J. Trausch, P. Ceres, F.E. Reyes, and R.T. Batey The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer Structure 19 2011 1413 1423
57. W.B. Turnbull, and A.H. Daranas On the value of c: can low affinity systems be studied by isothermal titration calorimetry? J. Am. Chem. Soc. 125 2003 14859 14866
58. Z. Weinberg, J.X. Wang, J. Bogue, J. Yang, K. Corbino, R.H. Moy, and R.R. Breaker Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes Genome Biol. 11 2010 R31
59. X. Yang, T. Gérczei, L. Glover, and C.C. Correll Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping Nat. Struct. Mol. Biol. 8 2001 968 973
60. J. Yeh, and W. Hol A flash-annealing technique to improve diffraction limits and lower mosaicity in crystals of glycerol kinase Acta Crystallogr. D Biol. Crystallogr. 54 1998 479 480
61. Y. Zhang, M. Morar, and S.E. Ealick Structural biology of the purine biosynthetic pathway Cell. Mol. Life Sci. 65 2008 3699 3724