PROSITE documentation PDOC00044

Bacterial histone-like DNA-binding proteins signature

Bacteria synthesize a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [1,2]. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilizing it from denaturation under extreme environmental conditions. The sequence of a number of different types of these proteins is known:

• The HU proteins, which, in Escherichia coli, are a dimer of closely related α and β chains and, in other bacteria, can be dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae [3].
• The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [4] in enterobacteria.
• The bacteriophage sp01 transcription factor 1 (TF1) which selectively binds to and inhibits the transcription of hydroxymethyluracil-containing DNA, such as sp01 DNA, by RNA polymerase in vitro.
• The African Swine fever virus protein A104R (or LMW5-AR) [5].

As a signature pattern for this family of proteins, we use a twenty residue sequence which includes three perfectly conserved positions. According to the tertiary structure of one of these proteins [6], this pattern spans exactly the first half of the flexible DNA-binding arm.