3  structures 0  species 0  sequences

Motif: UMAC (RM00028)

Description: UMAC tetraloop

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 Tetraloop. More...

Structure of a GNRA tetraloop from a group I self-splicing intron.[1]

Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices.[2] There are many variants of the tetraloop. The published ones include ANYA,[3][4] CUYG,[5] GNRA,[6] UNAC[7] and UNCG.[8]

Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG, in which the N could be either uracil, adenine, cytosine, or guanine, and the R is either guanine or adenine. These three sequences form stable and conserved tetraloops that play an important role in structural stability and biological function of 16S rRNA.[9]

  • GNRA
    • The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3' to the helix. Tetraloops with the sequence UMAC have essentially the same backbone fold as the GNRA tetraloop,[10] but may be less likely to form tetraloop-receptor interactions. They may therefore be a better choice for closing stems when designing artificial RNAs.
    • The presence of the GNRA tetraloop provides an exceptional stability to RNA structure. GNRA occurs 50% more than other tetranucleotides due to their ability to withstand temperatures 4° C higher than other RNA hairpins. This allows them to act as nucleation sites for proper folding of RNA. The rare hydrogen bonds between the first guanine and fourth adenine nucleotide, extensive stacking of nucleotide bases and hydrogen bonds between 2' OH of a ribose sugar and nitrogenous bases makes the tetraloop thermodynamically stable.[11]
  • UNCG
    • In the UNCG is favorable thermodynamically and structurally due to hydrogen bonding. van der Waals interactions, coulombic interactions and the interactions between the RNA and the solvent. The UNCG tetraloops are more stable than DNA loops with the same sequence. The UUCG tetraloop is the most stable tetraloop.[12] UUCG and GNRA tetraloops make up 70% of all tetraloops in 16S-RNA .[13]
  • CUUG
    • The CUUG tetraloop has the highest likelihood of conformational changes due to its structural flexibility. Out of the three tetraloops mentioned, this tetraloop is the most flexible since the second uracil is comparatively unrestricted.[14] It is also very thermodynamically stable.[15]

See also

References

  1. ^ Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., Doudna, J.A. (1996). "Crystal structure of a group I ribozyme domain: principles of RNA packing". Science. 273 (5282): 1676–1685. doi:10.1126/science.273.5282.1678. PMID 8781224. 
  2. ^ Woese, C.R., Winkers, S., Gutell, R.R. (1990). "Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops"". Proc. Natl. Acad. Sci. USA. 87 (21): 8467–71. doi:10.1073/pnas.87.21.8467. PMC 54977Freely accessible. PMID 2236056. 
  3. ^ Zirbel, CL; Sponer, JE; Sponer, J; Stombaugh, J; Leontis, NB (Aug 2009). "Classification and energetics of the base-phosphate interactions in RNA". Nucleic Acids Research. 37 (15): 4898–918. doi:10.1093/nar/gkp468. PMC 2731888Freely accessible. PMID 19528080. 
  4. ^ Klosterman, PS; Hendrix, DK; Tamura, M; Holbrook, SR; Brenner, SE (2004). "Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns". Nucleic Acids Research. 32 (8): 2342–52. doi:10.1093/nar/gkh537. PMC 419439Freely accessible. PMID 15121895. 
  5. ^ Jucker, FM; Pardi, A (Nov 7, 1995). "Solution structure of the CUUG hairpin loop: a novel RNA tetraloop motif". Biochemistry. 34 (44): 14416–27. doi:10.1021/bi00044a019. PMID 7578046. 
  6. ^ Jaeger, L; Michel, F; Westhof, E (Mar 11, 1994). "Involvement of a GNRA tetraloop in long-range RNA tertiary interactions". Journal of Molecular Biology. 236 (5): 1271–6. doi:10.1016/0022-2836(94)90055-8. PMID 7510342. 
  7. ^ Zhao, Q; Huang, HC; Nagaswamy, U; Xia, Y; Gao, X; Fox, GE (Aug 2012). "UNAC tetraloops: to what extent do they mimic GNRA tetraloops?". Biopolymers. 97 (8): 617–28. doi:10.1002/bip.22049. PMID 22605553. 
  8. ^ Molinaro, M; Tinoco I, Jr (Aug 11, 1995). "Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications". Nucleic Acids Research. 23 (15): 3056–63. doi:10.1093/nar/23.15.3056. PMC 307149Freely accessible. PMID 7544890. 
  9. ^ Baumruk, Vladimir; Gouyette, Catherine; Huynh-Dinh, Tam; Sun, Jian-Sheng; Ghomi, Mahmoud (2001-10-01). "Comparison between CUUG and UUCG tetraloops: thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy". Nucleic Acids Research. 29 (19): 4089–4096. doi:10.1093/nar/29.19.4089. ISSN 0305-1048. PMC 60239Freely accessible. PMID 11574692. 
  10. ^ Zhao, Q., Huang, H-C., Nagaswamy, U., Xia, Y., Gao, X., Fox, G.E. (2012). "UNAC tetraloops: To what extent do they mimic GNRA tetraloops?". Biopolymers. 97 (8): 617–628. doi:10.1002/bip.22049. PMID 22605553. 
  11. ^ Heus, Hans A.; Pardi, Arthur (1991-01-01). "Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops". Science. 253 (5016): 191–194. doi:10.1126/science.1712983. JSTOR 2878700. 
  12. ^ Antao, V. P.; Lai, S. Y.; Tinoco, I. (1991-11-11). "A thermodynamic study of unusually stable RNA and DNA hairpins". Nucleic Acids Research. 19 (21): 5901–5905. doi:10.1093/nar/19.21.5901. ISSN 0305-1048. PMC 329045Freely accessible. PMID 1719483. 
  13. ^ Woese, C. R.; Winker, S.; Gutell, R. R. (1990-11-01). "Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"". Proceedings of the National Academy of Sciences of the United States of America. 87 (21): 8467–8471. doi:10.1073/pnas.87.21.8467. ISSN 0027-8424. PMC 54977Freely accessible. PMID 2236056. 
  14. ^ Hall, Kathleen B. (October 15, 2013). "RNA does the folding dance of twist, turn, stack". Proceedings of the National Academy of Sciences of the United States of America. 110 (42): 16706–7. doi:10.1073/pnas.1316029110. JSTOR 23750643. PMC 3801021Freely accessible. 
  15. ^ Baumruk, V; Gouyette, C; Huynh-Dinh, T; Sun, JS; Ghomi, M (1 October 2001). "Comparison between CUUG and UUCG tetraloops: thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy". Nucleic Acids Research. 29 (19): 4089–96. doi:10.1093/nar/29.19.4089. PMC 60239Freely accessible. PMID 11574692. 


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

Alignments

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Formatting options

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Alignment format:
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Structures

There are 3 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 4A4S A 1 - 22
2 4A4R A 1 - 22
2 1JJ2 0 242 - 266

Family matches

There are 17 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 RF00102 VA RNA 21 0.389 296.5 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 31 0.313 428.7 Match Image
3 RF00195 RsmY RNA family 3 0.273 39.9 Match Image
3 RF00444 PrrF RNA 3 0.167 36.5 Match Image
3 RF00822 microRNA mir-274 2 0.286 25.7 Match Image
3 RF01066 6C RNA 2 0.111 27.0 Match Image
3 RF01405 STnc490 Hfq binding RNA 67 0.882 853.1 Match Image
3 RF01687 Acido-Lenti-1 RNA 34 0.391 571.2 Match Image
3 RF01772 Pseudomonas rnk leader 4 0.267 49.7 Match Image
3 RF01820 RNA Staph. aureus E 4 0.267 52.7 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 10 0.116 164.0 Match Image
3 RF02033 HNH endonuclease-associated RNA and ORF (HEARO) RNA 19 0.173 309.2 Match Image
3 RF02068 Enterobacterial sRNA STnc480 4 0.667 48.8 Match Image
3 RF02278 Betaproteobacteria toxic small RNA 6 0.118 85.9 Match Image
3 RF02399 Nitrogen stress-induced RNA 1 2 0.118 26.9 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 18 0.198 243.8 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 11 0.125 219.5 Match Image

References

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

Literature references

  1. Zhao Q, Huang HC, Nagaswamy U, Xia Y, Gao X, Fox GE Biopolymers. 2012;97:617-28. UNAC tetraloops: to what extent do they mimic GNRA tetraloops? PUBMED:22605553

  2. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR BMC Bioinformatics. 2002;3:2. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. PUBMED:11869452

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:22605553
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 14 15.86 67

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 12.0
Covariance model Download the Infernal CM for the motif here