Three-dimensional motifs from the SCOR, structural classification of RNA database: Extruded strands, base triples, tetraloops and U-turns

Nucleic Acids Research

Volumn 32, Issue 8, 2004, Pages 2342-2352

  Klosterman, Peter S ^a,c   Hendrix, Donna K ^a   Tamura, Makio ^b   Holbrook, Stephen R ^b   Brenner, Steven E ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA;

ARTICLE; ESCHERICHIA COLI; GENE SEQUENCE; HALOARCULA MARISMORTUI; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SULFOLOBUS ACIDOCALDARIUS; THERMUS THERMOPHILUS; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; CONFORMATION; CONSENSUS SEQUENCE; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE;

BASE PAIRING; BASE SEQUENCE; CONSENSUS SEQUENCE; DATABASES, NUCLEIC ACID; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA;

EID: 2342487400     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh537     Document Type: Article

References (98)

1. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
2. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
3. Holm,L. and Sander,C. (1996) Mapping the protein universe. Science, 273, 595-603.
4. Kruger,K., Grabowski,P.J., Zaug,A.J., Sands,J., Gottschling,D.E. and Cech,T.R. (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31, 147-157.
5. Guerrier-Takada,C., Gardiner,K., Marsh,T., Pace,N. and Altman,S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35, 849-857.
6. Nissen,P., Hansen,J., Ban,N., Moore,P.B. and Steitz,T.A. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.
7. Schmeing,T.M., Seila,A.C., Hansen,J.L., Freeborn,B., Soukup,J.K., Scaringe,S.A., Strobel,S.A., Moore,P.B. and Steitz,T.A. (2002) A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nature Struct. Biol., 9, 225-230.
8. Wimberly,B.T., Brodersen,D.E., Clemons,W.M.,Jr, Morgan-Warren,R.J., Carter,A.P., Vonrhein,C., Hartsch,T. and Ramakrishnan,V. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327-339.
9. Klein,D.J., Schmeing,T.M., Moore,P.B. and Steitz,T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J., 20, 4214-4221.
10. Nissen,P., Ippolito,J.A., Ban,N., Moore,P.B. and Steitz,T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA, 98, 4899-4903.
11. Nagaswamy,U., Larios-Sanz,M., Hury,J., Collins,S., Zhang,Z., Zhao,Q. and Fox,G.E. (2002) NCIR: a database of non-canonical interactions in known RNA structures. Nucleic Acids Res., 30, 395-397.
12. Leontis,N.B., Stombaugh,J. and Westhof,E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
13. Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
14. Leontis,N.B. and Westhof,E. (2003) Analysis of RNA motifs. Curr. Opin. Struct. Biol., 13, 300-308.
15. Klosterman,P.S., Tamura,M., Holbrook,S.R. and Brenner,S.E. (2002) SCOR: a structural classification of RNA database. Nucleic Acids Res., 30, 392-394.
16. Tamura,M., Hendrix,D.K., Klosterman,P.S., Schimmelman,N.R., Brenner,S.E. and Holbrook,S.R. (2004) SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res., 32, D182-D184.
17. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
18. Berman,H.M., Olson,W.K., Beveridge,D.L., Westbrook,J., Gelbin,A., Demeny,T., Hsieh,S.H., Srinivasan,A.R. and Schneider,B. (1992) The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759.
19. Fourmy,D., Recht,M.I., Blanchard,S.C. and Puglisi,J.D. (1996) Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science, 274, 1367-1371.
20. Ogle,J.M., Brodersen,D.E., Clemons,W.M.,Jr, Tarry,M.J., Carter,A.P. and Ramakrishnan,V. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science, 292, 897-902.
21. Ogle,J.M., Murphy,F.V., Tarry,M.J. and Ramakrishnan,V. (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell, 111, 721-732.
22. Schlunzen,F., Zarivach,R., Harms,J., Bashan,A., Tocilj,A., Albrecht,R., Yonath,A. and Franceschi,F. (2001) Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature, 413, 814-821.
23. Vicens,Q. and Westhof,E. (2001) Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure, 9, 647-658.
24. Vicens,Q. and Westhof,E. (2002) Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chem. Biol., 9, 747-755.
25. Vicens,Q. and Westhof,E. (2003) Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide. J. Mol. Biol., 326, 1175-1188.
26. Russell,R.J., Muffay,J.B., Lentzen,G., Haddad,J. and Mobashery,S. (2003) The complex of a designer antibiotic with a model aminoacyl site of the 30S ribosomal subunit revealed by X-ray crystallography. J. Am. Chem. Soc., 125, 3410-3411.
27. Cate,J.H., Gooding,A.R., Podell,E., Zhou,K., Golden,B.L., Kundrot,C.E., Cech,T.R. and Doudna,J.A. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science, 273, 1678-1685.
28. Ippolito,J.A. and Steitz,T.A. (1998) A 1.3-Å resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation. Proc. Natl Acad. Sci. USA, 95, 9819-9824.
29. Batey,R.T., Rambo,R.P., Lucast,L., Rha,B. and Doudna,J.A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science, 287, 1232-1239.
30. Wedekind,J.E. and McKay,D.B. (1999) Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis. Nature Struct. Biol., 6, 261-268.
31. Nikulin,A., Eliseikina,I., Tishchenko,S., Nevskaya,N., Davydova,N., Platonova,O., Piendl,W., Selmer,M., Liljas,A., Drygin,D., Zimmermann,R., Garber,M. and Nikonov,S. (2003) Structure of the L1 protuberance in the ribosome. Nature Struct. Biol., 10, 104-108.
32. Saenger,W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York, 116.
33. Price,S.R., Evans,P.R. and Nagai,K. (1998) Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA. Nature, 394, 645-650.
34. Oubridge,C., Ito,N., Evans,P.R., Teo,C.H. and Nagai,K. (1994) Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature, 372, 432-438.
35. Allain,F.H., Howe,P.W., Neuhaus,D. and Varani,G. (1997) Structural basis of the RNA-binding specificity of human U1A protein. EMBO J., 16, 5764-5772.
36. Varani,L., Gunderson,S.I., Mattaj,I.W., Kay,L.E., Neuhaus,D. and Varani,G. (2000) The NMR structure of the 38 kDa U1A protein-PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein. Nature Struct. Biol., 7, 329-335.
37. Lewis,H.A., Musunuru,K., Jensen,K.B., Edo,C., Chen,H., Darnell,R.B. and Burley,S.K. (2000) Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell, 100, 323-332.
38. Eiler,S., Dock-Bregeon,A., Moulinier,L., Thierry,J.C. and Moras,D. (1999) Synthesis of aspartyl-tRNA(Asp) in Escherichia coli - a snapshot of the second step. EMBO J., 18, 6532-6541.
39. Briand,C., Poterszman,A., Eiler,S., Webster,G., Thierry,J. and Moras,D. (2000) An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase. J. Mol. Biol., 299, 1051-1060.
40. Silvian,L.F., Wang,J. and Steitz,T.A. (1999) Insights into editing from an ile-tRNA synthetase structure with tRNA(Ile) and mupirocin. Science, 285, 1074-1077.
41. Schmitt,E., Panvert,M., Blanquet,S. and Mechulam,Y. (1998) Crystal structure of methionyl-tRNA(fMet) transformylase complexed with the initiator formyl-methionyl-tRNA(fMet). EMBO J., 17, 6819-6826.
42. Ye,X, Kumar,R.A. and Patel,D,J. (1995) Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem. Biol., 2, 827-840.
43. Puglisi,J.D., Chen,L., Blanchard,S. and Frankel,A.D. (1995) Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science, 270, 1200-1203.
44. Borer,P.N., Lin,Y., Wang,S., Roggenbuck,M.W., Gott,J.M., Uhlenbeck,O.C. and Pelczer,I. (1995) Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry, 34, 6488-6503.
45. Dallas,A. and Moore,P.B. (1997) The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. Structure, 5, 1639-1653.
46. Durant,P.C. and Davis,D.R. (1999) Stabilization of the anticodon stem-loop of tRNA(Lys,3) by an A+-C base-pair and by pseudouridine. J. Mol. Biol., 285, 115-131.
47. Jovine,L., Hainzl,T., Oubridge,C., Scott,W.G., Li,J., Sixma,T.K., Wonacott,A., Skarzynski,T. and Nagai,K. (2000) Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA. Structure Fold. Des., 8, 527-540.
48. Eddy,S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929.
49. Cannone,J.J., Subramanian,S., Schnare,M.N., Collett,J.R., D'Souza,L.M., Du,Y., Feng,B., Lin,N., Madabusi,L.V., Muller,K.M., Pande,N., Shang,Z., Yu,N. and Gutell,R.R. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics, 3, 2.
50. Moore,P.B. (1999) Structural motifs in RNA. Annu. Rev. Biochem., 68, 287-300.
51. Doherty,E.A., Batey,R.T., Masquida,B. and Doudna,J.A. (2001) A universal mode of helix packing in RNA. Nature Struct. Biol., 8, 339-343.
52. Robertus,J.D., Ladner,J.E., Finch,J.T., Rhodes,D., Brown,R.S., Clark,B.F. and Klug,A. (1974) Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature, 250, 546-551.
53. Kim,S.H., Suddath,F.L., Quigley,G.J., McPherson,A., Sussman,J.L., Wang,A.H., Seeman,N.C. and Rich,A. (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science, 185, 435-440.
54. Wimberly,B.T., Guymon,R., McCutcheon,J.P., White,S.W. and Ramakrishnan,V. (1999) A detailed view of a ribosomal active site: the structure of the L11-RNA complex. Cell, 97, 491-502.
55. Cai,Z., Gorin,A., Frederick,R., Ye,X., Hu,W., Majumdar,A., Kettani,A. and Patel,D.J. (1998) Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex. Nature Struct. Biol., 5, 203-212.
56. Scharpf,M., Sticht,H., Schweimer,K., Boehm,M., Hoffmann,S. and Rosch,P. (2000) Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex. Eur. J. Biochem., 267, 2397-2408.
57. Jiang,L. and Patel,D.J. (1998) Solution structure of the tobramycin-RNA aptamer complex. Nature Struct. Biol., 5, 769-774.
58. Cate,J.H., Gooding,A.R., Podell,E., Zhou,K., Golden,B.L., Szewczak,A.A., Kundrot,C.E., Cech,T.R. and Doudna,J.A. (1996) RNA tertiary structure mediation by adenosine platforms. Science, 273, 1696-1699.
59. Brunel,C., Romby,P., Westhof,E., Ehresmann,C. and Ehresmann,B. (1991) Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. J. Mol. Biol., 221, 293-308.
60. Leontis,N.B. and Westhof,E. (1998) A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. J. Mol. Biol., 283, 571-583.
61. Saenger,W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York.
62. Fan,P., Suri,A.K., Fiala,R., Live,D. and Patel,D.J. (1996) Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol., 258, 480-500.
63. Krasilnikov,A.S., Yang,X., Pan,T. and Mondragon,A. (2003) Crystal structure of the specificity domain of ribonuclease P. Nature, 421, 760-764.
64. Woese,C.R., Winker,S. and Gutell,R.R. (1990) Architecture of ribosomal RNA: constraints on the sequence of 'tetra-loops'. Proc. Natl Acad. Sci. USA, 87, 8467-8471.
65. Jucker,F.M. and Pardi,A. (1995) Solution structure of the CUUG hairpin loop: a novel RNA tetraloop motif. Biochemistry, 34, 14416-14427.
66. Pley,H.W., Flaherty,K.M. and McKay,D.B. (1994) Three-dimensional structure of a hammerhead ribozyme. Nature, 372, 68-74.
67. Mao,H., White,S.A. and Williamson,J.R. (1999) A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nature Struct. Biol., 6, 1139-1147.
68. Battiste,J.L., Mao,H., Rao,N.S., Tan,R., Muhandiram,D.R., Kay,L.E., Frankel,A.D. and Williamson,J.R. (1996) Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex. Science, 273, 1547-1551.
69. Baugh,C., Grate,D. and Wilson,C. (2000) 2.8 Å crystal structure of the malachite green aptamer. J. Mol. Biol., 301, 117-128.
70. Jiang,F., Kumar,R.A., Jones,R.A. and Patel,D.J. (1996) Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature, 382, 183-186.
71. Peterson,R.D. and Feigon,J. (1996) Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptide. J. Mol. Biol., 264, 863-877.
72. Kalurachchi,K. and Nikonowicz,E.P. (1998) NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA. J. Mol. Biol., 280, 639-654.
73. Stoldt,M., Wohnert,J., Ohlenschlager,O., Gorlach,M. and Brown,L.R. (1999) The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition. EMBO J., 18, 6508-6521.
74. Butcher,S.E., Dieckmann,T. and Feigon,J. (1997) Solution structure of a GAAA tetraloop receptor RNA. EMBO J., 16, 7490-7499.
75. Witherell,G.W., Gott,J.M. and Uhlenbeck,O.C. (1991) Specific interaction between RNA phage coat proteins and RNA. Prog. Nucleic Acid Res. Mol. Biol., 40, 185-220.
76. Convery,M.A., Rowsell,S., Stonehouse,N.J., Ellington,A.D., Hirao,I., Murray,J.B., Peabody,D.S., Phillips,S.E. and Stockley,P.G. (1998) Crystal structure of an RNA aptamer-protein complex at 2.8 Å resolution. Nature Struct. Biol., 5, 133-139.
77. Kerwood,D.J. and Borer,P,N. (1996) Structure refinement for a 24-nucleotide RNA hairpin. Magn. Resonance Chem., 34, S136-S146.
78. Smith,J.S. and Nikonowicz,E.P. (2000) Phosphorothioate substitution can substantially alter RNA conformation. Biochemistry, 39, 5642-5652.
79. De Guzman,R.N., Wu,Z.R., Stalling,C.C., Pappalardo,L., Borer,P.N. and Summers,M.F. (1998) Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element. Science, 279, 384-388.
80. Amarasinghe,G.K., De Guzman,R.N., Turner,R.B. and Summers,M.F. (2000) NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform. J. Mol. Biol., 299, 145-156.
81. Hingerty,B., Brown,R.S. and Jack,A. (1978) Further refinement of the structure of yeast tRNA(Phe). J. Mol. Biol., 124, 523-534.
82. Holbrook,S.R., Sussman,J.L., Warrant,R.W. and Kim,S.H. (1978) Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J. Mol. Biol., 123, 631-600.
83. Westhof,E. and Sundaralingam,M. (1986) Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters and base-pair propeller twist angles. Biochemistry, 25, 4868-4878.
84. Westhof,E., Dumas,P. and Moras,D. (1988) Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallogr. A, 44 (Pt 2), 112-123.
85. Gutell,R.R., Cannone,J.J., Konings,D. and Gautheret,D. (2000) Predicting U-turns in ribosomal RNA with comparative sequence analysis. J. Mol. Biol., 300, 791-803.
86. Dieckmann,T., Suzuki,E., Nakamura,G.K. and Feigon,J. (1996) Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA, 2, 628-640.
87. Jones,T.A., Zou,J.Y., Cowan,S.W. and Kjeldgaard,M. (1991) Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A, 47 (Pt 2), 110-119.
88. Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
89. Carson,M. (1997) Ribbons. Methods Enzymol., 277, 493-505.
90. Nikulin,A., Serganov,A., Ennifar,E., Tishchenko,S., Nevskaya,N., Shepard,W., Portier,C., Garber,M., Ehresmann,B., Ehresmann,C., Nikonov,S. and Dumas,P. (2000) Crystal structure of the S15-rRNA complex. Nature Struct. Biol., 7, 273-277.
91. Rowsell,S., Stonehouse,N.J., Convery,M.A., Adams,C.J., Ellington,A.D., Hirao,I., Peabody,D.S., Stockley,P.G. and Phillips,S.E. (1998) Crystal structures of a series of RNA aptamers complexed to the same protein target. Nature Struct. Biol., 5, 970-975.
92. Zhang,L. and Doudna,J.A. (2002) Structural insights into group II intron catalysis and branch-site selection. Science, 295, 2084-2088.
93. Shi,H. and Moore,P.B. (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA, 6, 1091-1105.
94. Zhang,L. and Doudna,J.A. (2002) Structural insights into group II intron catalysis and branch-site selection. Science, 295, 2084-2088.
95. Aboul-ela,F., Karn,J. and Varani,G. (1996) Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res., 24, 3974-3981.
96. Schmitz,U., Behrens,S., Freymann,D.M., Keenan,R.J., Lukavsky,P., Walter,P. and James,T.L. (1999) Structure of the phylogenetically most conserved domain of SRP RNA. RNA, 5, 1419-1429.
97. Yoshizawa,S., Fourmy,D. and Puglisi,J.D. (1998) Structural origins of gentamicin antibiotic action. EMBO J., 17, 6437-6448.
98. Ferre-D'Amare,A.R., Zhou,K. and Doudna,J.A. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 567-574.