1  structure 0  species 0  sequences

Clan: NiCo_riboswitch (CL00122)

Summary

NiCo_riboswitches

Nico riboswitches are selective metalloregulatory riboswitches [1], they bind four divalent metal ions, and use to be upstream of genes encoding transporters of Co2+, Zn2+ and Cd2+ [2]

This clan contains 2 families and the total number of sequence regions in the clan is 359.

Literature references

  1. Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR, Mol Cell. 2015;57:1088-1098.: Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. 25794617
  2. 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

Members

This clan contains the following 2 member families:

NiCo NiCo-AnGGAG

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 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.

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Secondary structures

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.

Alignments

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
NiCo-AnGGAG (RF03164) 7 (1.9%) View
NiCo (RF02683) 352 (98.1%) View