Sequence motif

In biochemistry, a sequence motif is a specific section on a nucleic acid ( DNA or RNA ) or a protein that recurs at different points (DNA) or on different molecules (RNA and protein) and that is given biological significance. Often there is some variability in the sequence; in such cases it makes sense to determine a consensus sequence . This defines the sequence less stringently because it allows alternatives at certain points.

Examples

DNA motif

An example of a DNA motif is the κB motif, the consensus sequence of which has the following structure:

5'-GGGRNNYYCC-3 '

The DNA is shown here from the 5 'to the 3' end (see nucleic acid nomenclature ), where R stands for a purine nucleotide, Y for pyrimidine nucleotide and N for any nucleotide.

The κB motif is located in the regulatory sections of numerous genes and is recognized by the transcription factor NF-κB . In most cases, binding strengthens the transcription of dependent genes.

Protein motif

There are many different protein motifs. They play an important role especially in phosphorylation in the context of signal transduction . The single-letter or three-letter code commonly used for amino acids is used to represent the motif . This is what the IQ motif says

IQxxxRxxxxR

I for isoleucine , Q for glutamine and R for arginine .

This sequence motif unfolds in the native protein to form a helical secondary structure which, as a structural motif, represents a binding domain for light chains.

literature

• Jeremy M. Berg, John L. Tymoczko, Lubert Stryer : Biochemistry. 6 edition, Spektrum Akademischer Verlag, Heidelberg 2007. ISBN 978-3-8274-1800-5 .
• Donald Voet, Judith G. Voet: Biochemistry. 3rd edition, John Wiley & Sons, New York 2004. ISBN 0-471-19350-X .
• Bruce Alberts , Alexander Johnson, Peter Walter, Julian Lewis, Martin Raff, Keith Roberts: Molecular Biology of the Cell , 5th Edition, Taylor & Francis 2007, ISBN 978-0815341062 .