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16  structures 0  species 0  sequences

Motif: U-turn (RM00030)

Description: U-turn motif

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Stem-loop. More...

An example of an RNA stem-loop

Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions.[1]

Formation and stability

The formation of a stem-loop structure is dependent on the stability of the resulting helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it contains (a small number are tolerable, especially in a long helix) and the base composition of the paired region. Pairings between guanine and cytosine have three hydrogen bonds and are more stable compared to adenine-uracil pairings, which have only two. In RNA, adenine-uracil pairings featuring two hydrogen bonds are equal to the adenine-thymine bond of the DNA. Base stacking interactions, which align the pi bonds of the bases' aromatic rings in a favorable orientation, also promote helix formation.

The stability of the loop also influences the formation of the stem-loop structure. "Loops" that are less than three bases long are sterically impossible and do not form. Large loops with no secondary structure of their own (such as pseudoknot pairing) are also unstable. Optimal loop length tends to be about 4-8 bases long. One common loop with the sequence UNCG is known as the "tetraloop" and is particularly stable due to the base-stacking interactions of its component nucleotides.

Structural contexts

Stem-loops occur in pre-microRNA structures and most famously in transfer RNA, which contain three true stem-loops and one stem that meet in a cloverleaf pattern. The anticodon that recognizes a codon during the translation process is located on one of the unpaired loops in the tRNA. Two nested stem-loop structures occur in RNA pseudoknots, where the loop of one structure forms part of the second stem.

Many ribozymes also feature stem-loop structures. The self-cleaving hammerhead ribozyme contains three stem-loops that meet in a central unpaired region where the cleavage site lies. The hammerhead ribozyme's basic secondary structure is required for self-cleavage activity.

Hairpin loops are often elements found within the 5'UTR of prokaryotes. These structures are often bound by proteins or cause the attenuation of a transcript in order to regulate translation.[2]

The mRNA stem-loop structure forming at the ribosome binding site may control an initiation of translation.[3][4]

Stem-loop structures are also important in prokaryotic rho-independent transcription termination. The hairpin loop forms in an mRNA strand during transcription and causes the RNA polymerase to become dissociated from the DNA template strand. This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences.

See also

References

  1. ^ Svoboda, P., & Cara, A. (2006). Hairpin RNA: A secondary structure of primary importance. Cellular and Molecular Life Sciences CMLS, 63(7), 901-908.
  2. ^ Meyer, Michelle; Deiorio-Haggar K; Anthony J (July 2013). "RNA structures regulating ribosomal protein biosynthesis in bacilli". RNA Biology. 7. 10: 1160–1164. doi:10.4161/rna.24151. PMC 3849166. PMID 23611891.
  3. ^ Malys N, Nivinskas R (2009). "Non-canonical RNA arrangement in T4-even phages: accommodated ribosome binding site at the gene 26-25 intercistronic junction". Mol Microbiol. 73 (6): 1115–1127. doi:10.1111/j.1365-2958.2009.06840.x. PMID 19708923.
  4. ^ Malys N, McCarthy JEG (2010). "Translation initiation: variations in the mechanism can be anticipated". Cellular and Molecular Life Sciences. 68 (6): 991–1003. doi:10.1007/s00018-010-0588-z. PMID 21076851.

This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Alignments

You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:
Download/view:

Structures

There are 16 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order PDB ID PDB chain ID PDB Residues
2 1c04 E 37 - 52
2 1j5e A 243 - 273
2 1mms C 37 - 52
2 1qa6 C 37 - 52
2 1s72 0 1189 - 1208
2 2avy A 247 - 277
2 1u9s A 102 - 120
2 1y69 0 2323 - 2350
2 2aw4 B 1086 - 1103
2 2j01 A 718 - 741
2 2a2e A 150 - 170
2 2i82 E 1 - 21
2 1ffk 0 1698 - 1718
2 1giy A 1133 - 1152
2 1mt4 A 2 - 23
2 3hhn C 102 - 121

Family matches

There are 115 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF00004 U2 spliceosomal RNA 30 0.144 392.1 Match Image
3 RF00007 U12 minor spliceosomal RNA 31 0.500 372.3 Match Image
3 RF00009 Nuclear RNase P 30 0.259 386.0 Match Image
3 RF00010 Bacterial RNase P class A 376 0.821 5926.2 Match Image
3 RF00018 CsrB/RsmB RNA family 8 0.211 80.8 Match Image
3 RF00023 transfer-messenger RNA 73 0.153 949.3 Match Image
3 RF00024 Vertebrate telomerase RNA 4 0.108 47.5 Match Image
3 RF00029 Group II catalytic intron 13 0.141 139.3 Match Image
3 RF00043 R1162-like plasmid antisense RNA 4 0.500 47.1 Match Image
3 RF00050 FMN riboswitch (RFN element) 14 0.097 154.6 Match Image
3 RF00078 MicA sRNA 2 0.118 24.3 Match Image
3 RF00082 SraG RNA 5 0.714 73.3 Match Image
3 RF00096 U8 small nucleolar RNA 11 0.200 123.8 Match Image
3 RF00107 FinP 5 0.833 65.8 Match Image
3 RF00126 ryfA RNA 3 0.333 45.3 Match Image
3 RF00156 Small nucleolar RNA SNORA70 9 0.209 96.8 Match Image
3 RF00166 PrrB/RsmZ RNA family 35 0.946 493.9 Match Image
3 RF00168 Lysine riboswitch 8 0.170 113.2 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 99 1.000 2802.4 Match Image
3 RF00209 Pestivirus internal ribosome entry site (IRES) 2 0.080 20.4 Match Image
3 RF00224 FGF-2 internal ribosome entry site (IRES) 4 0.667 41.9 Match Image
3 RF00263 Small nucleolar RNA SNORA68 5 0.192 59.3 Match Image
3 RF00291 Small nucleolar RNA snoR639/H1 5 0.556 55.8 Match Image
3 RF00357 Small nucleolar RNA R44/J54/Z268 family 2 0.069 20.0 Match Image
3 RF00369 sroC RNA 6 1.000 68.1 Match Image
3 RF00373 Archaeal RNase P 9 0.129 147.4 Match Image
3 RF00386 Enterovirus 5' cloverleaf cis-acting replication element 68 0.425 724.3 Match Image
3 RF00391 RtT RNA 6 0.105 85.1 Match Image
3 RF00403 Small nucleolar RNA SNORA41 2 0.065 23.7 Match Image
3 RF00495 Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES) 7 0.500 74.9 Match Image
3 RF00513 Tryptophan operon leader 3 0.136 36.0 Match Image
3 RF00514 Histidine operon leader 9 0.273 96.5 Match Image
3 RF00515 PyrR binding site 5 0.122 83.6 Match Image
3 RF00534 SgrS RNA 2 0.250 22.4 Match Image
3 RF00547 TrkB IRES 2 0.125 23.1 Match Image
3 RF00548 U11 spliceosomal RNA 7 0.097 77.0 Match Image
3 RF00558 Ribosomal protein L20 leader 11 0.256 135.9 Match Image
3 RF00602 Small Cajal body specific RNA 21 6 0.250 99.9 Match Image
3 RF00603 Small nucleolar RNA SNORD23 2 0.133 21.5 Match Image
3 RF00604 Small nucleolar RNA SNORD88 2 0.057 23.1 Match Image
3 RF00617 flavivirus capsid hairpin cHP 11 0.186 123.1 Match Image
3 RF00629 Pseudomonas sRNA P24 7 0.500 101.1 Match Image
3 RF00630 Pseudomonas sRNA P26 10 0.370 108.3 Match Image
3 RF00634 S-adenosyl methionine (SAM) riboswitch, 3 0.075 34.9 Match Image
3 RF00683 microRNA mir-143 11 0.611 111.1 Match Image
3 RF00723 microRNA mir-448 5 0.263 65.4 Match Image
3 RF00788 microRNA mir-287 7 0.778 74.8 Match Image
3 RF01071 Ornate Large Extremophilic RNA 5 0.250 58.5 Match Image
3 RF01089 Pseudoknot of the regulatory region of the repBA gene 2 0.286 20.2 Match Image
3 RF01268 Small Cajal body-specific RNA 2 3 0.150 31.2 Match Image
3 RF01330 CRISPR RNA direct repeat element 6 1.000 78.3 Match Image
3 RF01390 isrG Hfq binding RNA 5 1.000 51.7 Match Image
3 RF01401 rseX Hfq binding RNA 7 0.583 79.8 Match Image
3 RF01529 Cauldobacter sRNA CC3552 2 1.000 24.7 Match Image
3 RF01673 PhrS 2 0.154 21.0 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 17 0.895 191.9 Match Image
3 RF01687 Acido-Lenti-1 RNA 7 0.080 107.8 Match Image
3 RF01702 Cyano-2 RNA 4 0.070 44.4 Match Image
3 RF01703 Dictyoglomi-1 RNA 2 0.500 27.3 Match Image
3 RF01706 Gut-1 RNA 3 0.079 35.7 Match Image
3 RF01708 L17 ribosomal protein downstream element 6 0.115 71.2 Match Image
3 RF01721 Pseudomon-groES RNA 3 0.167 32.6 Match Image
3 RF01730 Termite-leu RNA 15 0.750 476.4 Match Image
3 RF01752 psaA RNA 2 0.065 21.6 Match Image
3 RF01756 rne-II RNA 5 0.312 60.9 Match Image
3 RF01796 Fumarate/nitrate reductase regulator sRNA 3 0.188 34.0 Match Image
3 RF01808 MicX Vibrio cholerae sRNA 5 0.500 61.9 Match Image
3 RF01849 Alphaproteobacteria transfer-messenger RNA 11 0.099 140.2 Match Image
3 RF01850 Betaproteobacteria transfer-messenger RNA 2 0.286 22.8 Match Image
3 RF01852 Selenocysteine transfer RNA 9 0.083 106.3 Match Image
3 RF01942 microRNA mir-1937 32 0.187 361.0 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 86 1.000 4568.1 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 36 0.396 526.2 Match Image
3 RF02029 sraA 18 0.900 271.4 Match Image
3 RF02031 tpke11 4 0.143 45.0 Match Image
3 RF02033 HNH endonuclease-associated RNA and ORF (HEARO) RNA 12 0.109 145.4 Match Image
3 RF02053 Enterobacterial sRNA STnc430 5 0.714 55.8 Match Image
3 RF02055 Enterobacterial sRNA STnc380 4 0.800 50.8 Match Image
3 RF02057 Salmonella enterica sRNA STnc40 2 0.118 23.8 Match Image
3 RF02065 Enterobacterial sRNA STnc340 3 0.750 34.8 Match Image
3 RF02074 Enterobacterial sRNA STnc240 8 0.533 89.3 Match Image
3 RF02103 Deleted in lymphocytic leukemia 1 conserved region 1 3 0.115 35.4 Match Image
3 RF02118 FMR1 antisense RNA 1 conserved region 2 9 0.360 112.2 Match Image
3 RF02189 ST7 overlapping transcript 4 conserved region 3 2 0.100 22.8 Match Image
3 RF02219 ZNRD1 antisense RNA 1 conserved region 2 2 0.059 22.0 Match Image
3 RF02230 Proteobacterial sRNA sX11 2 0.200 20.2 Match Image
3 RF02249 Six3os1 conserved region 4 2 0.286 20.4 Match Image
3 RF02276 Hammerhead ribozyme (type II) 3 0.125 34.3 Match Image
3 RF02278 Betaproteobacteria toxic small RNA 7 0.137 87.0 Match Image
3 RF02342 Alphaproteobacterial sRNA ar7 6 0.207 68.7 Match Image
3 RF02343 Alphaproteobacterial sRNA ar9 16 0.571 166.8 Match Image
3 RF02351 Proteobacteria sRNA psRNA14 2 0.667 23.7 Match Image
3 RF02354 Bradyrhizobiaceae sRNA BjrC80 7 0.467 83.6 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 3 0.120 35.7 Match Image
3 RF02357 RNaseP truncated form 7 0.778 92.6 Match Image
3 RF02375 Aar sRNA 2 0.154 21.9 Match Image
3 RF02376 SR1 sRNA 2 0.333 26.3 Match Image
3 RF02379 Cia-dependent small RNA csRNA1 8 0.167 97.7 Match Image
3 RF02423 Burkholderia sRNA Bp1_Cand871_SIPHT 14 0.933 170.8 Match Image
3 RF02471 Actinobacteria sRNA Ms_IGR-5 6 0.286 66.5 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 3 0.111 31.2 Match Image
3 RF02524 Streptococcus sRNA sagA 3 0.500 37.0 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 83 0.912 3404.2 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 102 1.000 3700.8 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 43 0.935 832.7 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 80 0.909 2165.6 Match Image
3 RF02630 Hfq-regulated sRNA 12 2 1.000 28.6 Match Image
3 RF02684 Type-P5 twister ribozyme 4 0.267 47.2 Match Image
3 RF02809 RsmW RNA family 3 1.000 42.2 Match Image
3 RF02814 Sulfolobus sRNA133 2 0.667 24.4 Match Image
3 RF02829 Streptomyces RNA 4115 5 0.833 57.1 Match Image
3 RF02832 Streptomyces RNA 5676 4 0.800 51.7 Match Image
3 RF02866 Burkholderia sRNA 16 (Bc_KC_sr1) 4 1.000 51.9 Match Image
3 RF02877 Neisseria metabolic switch regulator b (RcoF1/NgncR163) 2 0.333 24.8 Match Image
3 RF02880 Mesorhizobail RNA 15 2 1.000 22.4 Match Image

References

This section shows the database cross-references that we have for this Rfam motif.

Literature references

  1. Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB J Math Biol. 2008;56:215-52. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PUBMED:17694311

  2. Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB Nucleic Acids Res. 2009;37:4898-918. Classification and energetics of the base-phosphate interactions in RNA. PUBMED:19528080

  3. Gutell RR, Cannone JJ, Konings D, Gautheret D J Mol Biol. 2000;300:791-803. Predicting U-turns in ribosomal RNA with comparative sequence analysis. PUBMED:10891269

  4. Quigley GJ, Rich A Science. 1976;194:796-806. Structural domains of transfer RNA molecules. PUBMED:790568

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.

Curation

Seed source Published; PMID:19528080
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 19 21.95 45

Model information

Build commands
cmbuild -F U-CM U-SEED
cmcalibrate --mpi --seed 1 U-CM
Gathering cutoff 10.0
Covariance model Download the Infernal CM for the motif here