Purine riboswitches

Riboswitches are metabolite binding domains within certain messenger RNAs that serve as precision sensors for their corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression. A class of riboswitches that selectively recognises guanine has been reporter first in [1]. It has also been shown that Purine riboswitch variants of this family are specific for adenine [2], hypoxanthine [3] and 2'-deoxyguanosine [6].

This clan contains 3 families and the total number of sequence regions in the clan is 4,133.

Literature references

1. Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR, Cell 2003;113:577-586.: Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria. 12787499
2. Mandal M, Breaker RR, Nat Struct Mol Biol 2004;11:29-35.: Adenine riboswitches and gene activation by disruption of a transcription terminator. 14718920
3. Batey RT, Gilbert SD, Montange RK, Nature. 2004;432:411-415.: Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. 15549109
4. Reining A, Nozinovic S, Schlepckow K, Buhr F, Furtig B, Schwalbe H, Nature. 2013;499:355-359.: Three-state mechanism couples ligand and temperature sensing in riboswitches. 23842498
5. Weinberg Z, Nelson JW, Lunse CE, Sherlock ME, Breaker RR, Proc Natl Acad Sci U S A. 2017;114:E2077.: Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. 28265071
6. Kim JN, Roth A, Breaker RR, Proc Natl Acad Sci U S A. 2007;104:16092-16097.: Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. 17911257

Members

This clan contains the following 3 member families:

Purine 2dG-I 2dG-II

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 mapping between the Rfam families in this clan, the corresponding EMBL entries, and the region of the three-dimensional structures that are available for that sequence.

This tool allows you to view the secondary structure images of two clan members side-by-side. Choose the family structures using the two drop-down menus below.

The table below shows the number of occurrences of each family throughout the sequence database. In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this family. The rightmost column provides a link to the alignments tab for each family.

Rfam family	Num. regions	Alignment
2dG-II (RF03165)	12 (0.3%)	View
2dG-I (RF01510)	24 (0.6%)	View
Purine (RF00167)	4,097 (99.1%)	View