关于大型RNA分子中T环RNA折叠基序的出现。
On the occurrence of the T-loop RNA folding motif in large RNA molecules.
作者信息
Krasilnikov Andrey S, Mondragón Alfonso
出版信息
RNA. 2003 Jun;9(6):640-3. doi: 10.1261/rna.2202703.
Abstract
The T-loop RNA folding motif may be considered as a five-nucleotide motif composed of a U-turn flanked by a noncanonical base pair. It was recently proposed that the flanking noncanonical base pair is always a UA trans Watson-Crick/Hoogsteen base pair stacked on a Watson-Crick base pair on one side. Here we show that structural analysis of several large RNA molecules, including the recently solved crystal structure of the specificity domain of Bacillus subtilis RNase P, combined with sequence analysis, indicates a broader sequence consensus for the motif. Additionally, we show that the flanking base pair does not necessarily stack on a Watson-Crick base pair and the 3' terminus of the five-nucleotide motif is often followed by a sharp turn in the phosphate backbone rather than just a bulged base or bases.
摘要
T环RNA折叠基序可被视为一种由一个U型转弯侧翼连接一个非经典碱基对组成的五核苷酸基序。最近有人提出，侧翼非经典碱基对总是一个反式沃森-克里克/霍格斯坦UA碱基对，堆积在一侧的沃森-克里克碱基对上。在此我们表明，对几个大型RNA分子的结构分析，包括最近解析的枯草芽孢杆菌核糖核酸酶P特异性结构域的晶体结构，结合序列分析，表明该基序存在更广泛的序列共有模式。此外，我们表明侧翼碱基对不一定堆积在沃森-克里克碱基对上，并且五核苷酸基序的3'末端之后的磷酸主链往往会有一个急转弯，而不仅仅是一个或多个凸起的碱基。
相似文献
1
On the occurrence of the T-loop RNA folding motif in large RNA molecules.
RNA. 2003 Jun;9(6):640-3. doi: 10.1261/rna.2202703.
2
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs.
RNA. 2002 Sep;8(9):1112-9. doi: 10.1017/s135583820202006x.
3
The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits.
Biochemistry. 2006 Oct 3;45(39):11776-89. doi: 10.1021/bi0605787.
4
Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P.
Biochemistry. 1997 May 27;36(21):6317-25. doi: 10.1021/bi970115o.
5
RNA libraries and RNA recognition.
Ann N Y Acad Sci. 1996 May 15;782:526-33. doi: 10.1111/j.1749-6632.1996.tb40590.x.
6
Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator.
Biochemistry. 2017 May 30;56(21):2690-2700. doi: 10.1021/acs.biochem.7b00123. Epub 2017 May 17.
7
The lonepair triloop: a new motif in RNA structure.
J Mol Biol. 2003 Jan 3;325(1):65-83. doi: 10.1016/s0022-2836(02)01106-3.
8
Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules.
Biochimie. 2002 Sep;84(9):961-73. doi: 10.1016/s0300-9084(02)01463-3.
9
The interaction networks of structured RNAs.
Nucleic Acids Res. 2006;34(22):6587-604. doi: 10.1093/nar/gkl963. Epub 2006 Nov 28.
10
Predicting U-turns in ribosomal RNA with comparative sequence analysis.
J Mol Biol. 2000 Jul 21;300(4):791-803. doi: 10.1006/jmbi.2000.3900.
引用本文的文献
1
A potential role for RNA aminoacylation prior to its role in peptide synthesis.
Proc Natl Acad Sci U S A. 2024 Aug 27;121(35):e2410206121. doi: 10.1073/pnas.2410206121. Epub 2024 Aug 23.
2
A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.
Nucleic Acids Res. 2023 Sep 8;51(16):8367-8382. doi: 10.1093/nar/gkad605.
3
Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues.
Gigascience. 2022 Dec 28;12. doi: 10.1093/gigascience/giad042. Epub 2023 Jun 24.
4
Context-dependence of T-loop Mediated Long-range RNA Tertiary Interactions.
J Mol Biol. 2023 May 15;435(10):168070. doi: 10.1016/j.jmb.2023.168070. Epub 2023 Mar 31.
5
Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions.
Noncoding RNA. 2021 Dec 15;7(4):81. doi: 10.3390/ncrna7040081.
6
Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.
Crystals (Basel). 2021 Mar;11(3). doi: 10.3390/cryst11030273. Epub 2021 Mar 10.
7
In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules.
Nucleic Acids Res. 2021 Feb 26;49(4):2289-2305. doi: 10.1093/nar/gkab021.
8
Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes.
Nucleic Acids Res. 2020 Sep 4;48(15):8675-8685. doi: 10.1093/nar/gkaa610.
9
Unboxing the T-box riboswitches-A glimpse into multivalent and multimodal RNA-RNA interactions.
Wiley Interdiscip Rev RNA. 2020 Nov;11(6):e1600. doi: 10.1002/wrna.1600. Epub 2020 Jul 6.
10
Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding.
Nucleic Acids Res. 2020 Jul 27;48(13):7569-7583. doi: 10.1093/nar/gkaa507.
本文引用的文献
1
The CCP4 suite: programs for protein crystallography.
Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3. doi: 10.1107/S0907444994003112.
2
Crystal structure of the specificity domain of ribonuclease P.
Nature. 2003 Feb 13;421(6924):760-4. doi: 10.1038/nature01386.
3
The lonepair triloop: a new motif in RNA structure.
J Mol Biol. 2003 Jan 3;325(1):65-83. doi: 10.1016/s0022-2836(02)01106-3.
4
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs.
RNA. 2002 Sep;8(9):1112-9. doi: 10.1017/s135583820202006x.
5
The kink-turn: a new RNA secondary structure motif.
EMBO J. 2001 Aug 1;20(15):4214-21. doi: 10.1093/emboj/20.15.4214.
6
RNA tertiary interactions in the large ribosomal subunit: the A-minor motif.
Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):4899-903. doi: 10.1073/pnas.081082398. Epub 2001 Apr 10.
7
A universal mode of helix packing in RNA.
Nat Struct Biol. 2001 Apr;8(4):339-43. doi: 10.1038/86221.
8
The European Large Subunit Ribosomal RNA Database.
Nucleic Acids Res. 2001 Jan 1;29(1):175-7. doi: 10.1093/nar/29.1.175.
9
Structure of the 30S ribosomal subunit.
Nature. 2000 Sep 21;407(6802):327-39. doi: 10.1038/35030006.
10
The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.
RNA. 2000 Aug;6(8):1091-105. doi: 10.1017/s1355838200000364.
Zotero 插件