Novel base triples in RNA structures revealed by graph theoretical searching methods

BMC Bioinformatics

Volumn 12, Issue SUPPL. 13, 2011, Pages

  Firdaus Raih, Mohd ^a,b   Harrison, Anne Marie ^a,c   Willett, Peter ^a   Artymiuk, Peter J ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITI KEBANGSAAN MALAYSIA   (Malaysia)

^c SHEFFIELD HALLAM UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

50S R-RNA; COMPARATIVE ANALYSIS; RIBOSOMAL RNA; RIBOZYMES; RNA FUNCTIONS; RNA MOLECULES; RNA STRUCTURES; SEARCHING METHODS; STRUCTURAL STABILIZATION; TERTIARY STRUCTURES;

GRAPH THEORY; HYDROGEN BONDS; RNA;

RNA; BIOINFORMATICS;

RNA; RNA 23S;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; GENETIC DATABASE; GENETICS; HALOARCULA MARISMORTUI; HYDROGEN BOND; THERMUS THERMOPHILUS;

BASE PAIRING; DATABASES, GENETIC; HALOARCULA MARISMORTUI; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; RNA, RIBOSOMAL, 23S; SOFTWARE; THERMUS THERMOPHILUS;

EID: 84864039860     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S13-S2     Document Type: Article

References (45)

1. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 Angstrom resolution. Science 2000, 289:905-920. 10.1126/science.289.5481.905, 10937989.
2. Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature 2000, 407:327-339. 10.1038/35030006, 11014182.
3. Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstrom resolution. Cell 2000, 102:615-623. 10.1016/S0092-8674(00)00084-2, 11007480.
4. Pley HW, Flaherty KM, McKay DB. 3-dimensional structure of a hammerhead ribozyme. Nature 1994, 372:68-74. 10.1038/372068a0, 7969422.
5. Scott WG, Finch JT, Klug A. The crystal-structure of an all-RNA Hammerhead ribozyme - a proposed mechanism for RNA catalytic cleavage. Cell 1995, 81:991-1002. 10.1016/S0092-8674(05)80004-2, 7541315.
6. Cate JH, Doudna JA. Metal-binding sites in the major groove of a large ribozyme domain. Structure 1996, 4:1221-1229. 10.1016/S0969-2126(96)00129-3, 8939748.
7. Kim SH, Suddath FL, Quigley GJ, McPherso A, Sussman JL, Wang AHJ, Seeman NC, Rich A. 3-dimensional tertiary structure of yeast phenylalanine transfer-RNA. Science 1974, 185:435-440. 10.1126/science.185.4149.435, 4601792.
8. Ladner JE, Jack A, Robertus JD, Brown RS, Rhodes D, Clark BFC, Klug A. Structure of yeast phenylalanine transfer-RNA at 2.5 A resolution. Proc Natl Acad Sci U S A 1975, 72:4414-4418. 10.1073/pnas.72.11.4414, 388732, 1105583.
9. Gautheret D, Major F, Cedergren R. Modeling the 3-dimensional structure of RNA using discrete nucleotide conformational sets. J Mol Biol 1993, 229:1049-1064. 10.1006/jmbi.1993.1104, 7680379.
10. Moore PB. Structural motifs in RNA. Annu Rev Biochem 1999, 68:287-300. 10.1146/annurev.biochem.68.1.287, 10872451.
11. Su L, Chen LQ, Egli M, Berger JM, Rich A. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat Struct Biol 1999, 6:285-292. 10.1038/6722, 10074948.
12. Guo F, Gooding AR, Cech TR. Structure of the tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell 2004, 16:351-362.
13. Nagaswamy U, Larios-Sanz M, Hury J, Collins S, Zhang ZD, Zhao Q, Fox GE. NCIR: a database of non-canonical interactions in known RNA structures. Nucleic Acids Res 2002, 30:395-397. 10.1093/nar/30.1.395, 99067, 11752347.
14. Walberer BJ, Cheng AC, Frankel AD. Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. J Mol Biol 2003, 327:767-780. 10.1016/S0022-2836(03)00090-1, 12654262.
15. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
16. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JHD. Structures of the bacterial ribosome at 3.5 Angstrom resolution. Science 2005, 310:827-834. 10.1126/science.1117230, 16272117.
17. Harrison AM, South DR, Willett P, Artymiuk PJ. Representation, searching and discovery of patterns of bases in complex RNA structures. J Comput-Aided Mol Des 2003, 17:537-549.
18. Ullmann JR. Algorithm for subgraph isomorphism. J Acm 1976, 23:31-42.
19. McDonald IK, Thornton JM. Satisfying hydrogen-bonding potential in proteins. J Mol Biol 1994, 238:777-793. 10.1006/jmbi.1994.1334, 8182748.
20. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the CLUSTAL series of programs. Nucleic Acids Res 2003, 31:3497-3500. 10.1093/nar/gkg500, 168907, 12824352.
21. Kabsch W. Solution for best rotation to relate 2 sets of vectors. Acta Crystallogr Sect A 1976, 32:922-923.
22. Bailey S. The CCP4 Suite - programs for protein crystallography. Acta Crystallogr Sect D-Biol Crystallogr 1994, 50:760-763.
23. Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA-Publ RNA Soc 2001, 7:499-512.
24. Duarte CM, Pyle AM. Stepping through an RNA structure: a novel approach to conformational analysis. J Mol Biol 1998, 284:1465-1478. 10.1006/jmbi.1998.2233, 9878364.
25. Ferre-D'Amare AR, Zhou K, Doudna JA. Crystal structure of a hepatitis delta virus ribozyme. Nature 1998, 395:567-574. 10.1038/26912, 9783582.
26. Ke AL, Zhou KH, Ding F, Cate JHD, Doudna JA. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 2004, 429:201-205. 10.1038/nature02522, 15141216.
27. Ravelli RBG, Leiros HKS, Pan BC, Caffrey M, McSweeney S. Specific radiation damage can be used to solve macromolecular crystal structures. Structure 2003, 11:217-224. 10.1016/S0969-2126(03)00006-6, 12575941.
28. Sekine S, Nureki O, Shimada A, Vassylyev DG, Yokoyama S. Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nat Struct Biol 2001, 8:203-206. 10.1038/84927, 11224561.
29. Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol Cell 2002, 10:117-128. 10.1016/S1097-2765(02)00570-1, 12150912.
30. Hansen JL, Schmeing TM, Moore PB, Steitz TA. Structural insights into peptide bond formation. Proc Natl Acad Sci U S A 2002, 99:11670-11675. 10.1073/pnas.172404099, 129327, 12185246.
31. Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc Natl Acad Sci U S A 2001, 98:4899-4903. 10.1073/pnas.081082398, 33135, 11296253.
32. Woese CR, Fox GE, Zablen L, Uchida T, Bonen L, Pechman K, Lewis BJ, Stahl D. Conservation of primary structure in 16S ribosomal-RNA. Nature 1975, 254:83-86. 10.1038/254083a0, 1089909.
33. Lu XJ, Olson WK. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 2003, 31:5108-5121. 10.1093/nar/gkg680, 212791, 12930962.
34. Hauenstein S, Zhang CM, Hou YM, Perona JJ. Shape-selective RNA recognition by cysteinyl-tRNA synthetase. Nat Struct Mol Biol 2004, 11:1134-1141. 10.1038/nsmb849, 15489861.
35. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science 2000, 289:920-930. 10.1126/science.289.5481.920, 10937990.
36. Green R, Switzer C, Noller HF. Ribosome-catalyzed peptide-bond formation with an a-site substrate covalently linked to 23S ribosomal RNA. Science 1998, 280:286-289. 10.1126/science.280.5361.286, 9535658.
37. Beringer M, Bruell C, Xiong LQ, Pfister P, Bieling P, Katunin VI, Mankin AS, Bottger EC, Rodnina MV. Essential mechanisms in the catalysis of peptide bond formation on the ribosome. J Biol Chem 2005, 280:36065-36072. 10.1074/jbc.M507961200, 16129670.
38. Bieling P, Beringer M, Adio S, Rodnina MV. Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat Struct Mol Biol 2006, 13:423-428. 10.1038/nsmb1091, 16648860.
39. Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA. Structural insights into the roles of water and the 2 ' hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell 2005, 20:437-448. 10.1016/j.molcel.2005.09.006, 16285925.
40. Schmeing TM, Huang KS, Strobel SA, Steitz TA. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 2005, 438:520-524. 10.1038/nature04152, 16306996.
41. Polacek N, Mankin AS. The ribosomal peptidyl transferase center: Structure, function, evolution, inhibition. Crit Rev Biochem Mol Biol 2005, 40:285-311. 10.1080/10409230500326334, 16257828.
42. Moore PB, Steitz TA. The structural basis of large ribosomal subunit function. Annu Rev Biochem 2003, 72:813-850. 10.1146/annurev.biochem.72.110601.135450, 14527328.
43. Xin Y, Olson WK. BPS: a database of RNA base-pair structures. Nucl Acids Res 2009, 37:D83-88. 10.1093/nar/gkn676, 2686499, 18845572.
44. Banatao DR, Altman RB, Klein TE. Microenvironment analysis and identification of magnesium binding sites in RNA. Nucl Acids Res 2003, 31:4450-4460. 10.1093/nar/gkg471, 169872, 12888505.
45. Klosterman PS, Tamura M, Holbrook SR, Brenner SE. SCOR: a structural classification of RNA database. Nucleic Acids Res 2002, 30:392-394. 10.1093/nar/30.1.392, 99131, 11752346.