ADP

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Rfam ID: nan (nan)


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Timeline Description Structure&recognition References


Timeline

Start

    2004[1] Identification of ykkC motif that exhibit characteristics of riboswitch function

    Separation of ykkC subtype 2 2017[2]

    2018[3] Further classification of ykkC subtype 2 as subtypes 2a through 2d

    Identification of ykkC 2c RNAs as the ADP riboswitchs 2019[4]
2023...



Description

 The ykkC RNAs were initially found in 2004 and in 2017,ykkC subtype 2 RNAs were separated from ykkC RNAs. Further analysis of the RNA sequences and consensus models of ykkC subtype 2 RNAs, and the assessment of the diverse types of genes found downstream of these RNAs, revealed that there are probably at least four additional distinct riboswitch classes present within the ykkC subtype 2 collection, termed ykkC subtypes 2a-2d. At last, ykkC subtype 2c RNAs were proved to recognize adenosine and cytidine 5′-diphosphate molecules in either their ribose or deoxyribose forms (ADP, dADP, CDP, and dCDP)[2-4].


Gene association

Nearly all ykkC subtype 2c RNAs of phylum Firmicutes are located upstream of genes encoding nucleoside diphosphate linked to X (NUDIX) hydrolases. NUDIX hydrolases make up a broad family of proteins that cleave the phosphoester bond between the α- and β-phosphate moieties of various nucleotide substrates. Some nucleoside di- and triphosphate substrates can carry a ribose or a deoxyribose moiety (gray shading)[4].
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Gene regulation

Putative mechanisms for regulation of gene expression by ADP riboswitches in phylum Firmicutes. We present the prototypical mechanism, but not all possible mechanisms[2,4].
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Structure and Ligand recognition

2D representation

Consensus sequence and secondary structure model for the PRA riboswitch[4].


Document
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Ligand recognition

Chemical structures of ADP (adenosine-5'-diphosphate), dADP (2'-deoxyadenosine-5'-diphosphate), CDP (cytidine-5'-diphosphate) and dCDP (2'-deoxycytidine-5'-diphosphate). The apparent KD of each compound is shown on bottom. Refer to the corresponding references for comprehensive details regarding reaction conditions and species information in measuring the dissociation constant displayed below[4].
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References

[1] New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.
Barrick, J. E. et al.
Proc. Natl. Acad. Sci. U. S. A. 101, 6421–6426 (2004).

[2] Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class.
Nelson, J. W., Atilho, R. M., Sherlock, M. E., Stockbridge, R. B. & Breaker, R. R.
Mol. Cell 65, 220–230 (2017).

[3] Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria.
Sherlock, M. E., Sudarsan, N., Stav, S. & Breaker, R. R.
Elife 7, (2018).

[4] Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates.
Sherlock, M. E., Sadeeshkumar, H. & Breaker, R. R.
Biochemistry 58, 401–410 (2019).