34  structures 8693  species 16245  sequences

Family: TPP (RF00059)

Description: TPP riboswitch aptamer (THI element)

Summary

Note on Riboswitches

This Rfam family TPP (RF00059) represents an aptamer domain of a full riboswitch TPP riboswitch aptamer (THI element). Riboswitches are non-coding RNA structures that regulate gene expression in response to ligand. Each riboswitch has two main parts: the aptamer domain and the expression platform. The aptamer domain is highly conserved to precisely bind its ligand. However, the expression platform has multiple modes of gene regulation, which introduces sequence and structure variability that increases difficulty in its detection through covariance model searching. For more information see the original publications.

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry TPP riboswitch. More...

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

Sequences

Alignment

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Alignment format:
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Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Trees

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Structures

For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the structures on which the TPP family has been found.

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References

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

Literature references

  1. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS J Biol Chem 2002;277:48949-48959. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. PUBMED:12376536

  2. Miranda-Rios J, Navarro M, Soberon M Proc Natl Acad Sci U S A 2001;98:9736-9741. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. PUBMED:11470904

  3. Winkler W, Nahvi A, Breaker RR Nature 2002;419:952-956. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. PUBMED:12410317

  4. Sudarsan N, Barrick JE, Breaker RR RNA 2003;9:644-647. Metabolite-binding RNA domains are present in the genes of eukaryotes. PUBMED:12756322

  5. Kubodera T, Watanabe M, Yoshiuchi K, Yamashita N, Nishimura A, Nakai S, Gomi K, Hanamoto H FEBS Lett 2003;555:516-520. Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5'-UTR. PUBMED:14675766

  6. Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ Nature. 2006;441:1167-1171. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. PUBMED:16728979

  7. Welz R, Breaker RR RNA. 2007;13:573-582. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. PUBMED:17307816

  8. Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K PLoS One. 2013;8:e70720. A genome-wide survey of highly expressed non-coding RNAs and biological validation of selected candidates in Agrobacterium tumefaciens. PUBMED:23950988

  9. Thore S, Leibundgut M, Ban N Science. 2006;312:1208-1211. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. PUBMED:16675665

  10. Welz R, Breaker RR RNA. 2007;13:573-582. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. PUBMED:17307816

  11. Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ Nature. 2006;441:1167-1171. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. PUBMED:16728979

  12. Edwards TE, Ferre-D'Amare AR Structure. 2006;14:1459-1468. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. PUBMED:16962976

  13. Thore S, Frick C, Ban N J Am Chem Soc. 2008;130:8116-8117. Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch. PUBMED:18533652

  14. Kulshina N, Edwards TE, Ferre-D'Amare AR RNA. 2010;16:186-196. Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. PUBMED:19948769

  15. Warner KD, Homan P, Weeks KM, Smith AG, Abell C, Ferre-D'Amare AR Chem Biol. 2014;21:591-595. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. PUBMED:24768306

External database links

Curation and family details

This section shows the detailed information about the Rfam family. 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 Vitreshchak A
Structure source Published; PMID:12376536;
Type Cis-reg; riboswitch;
Author Rodionov DAORCID logo, Vitreshchak AG, Mironov AA, Gelfand MSORCID logo, Bateman AORCID logo, Moxon SJORCID logo, Ontiveros-Palacios NORCID logo
Alignment details
Alignment Number of
sequences
full 16,130
seed 115

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
Gathering cutoff 54.3
Trusted cutoff 54.3
Noise cutoff 54.2
Covariance model Download