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| posted 20 Jul, 2017 17:32
A number of B1 phages contain a gene that has been called as AlpA or AlpA like (Pham 30124). AlpA is a protein present in the E. coli prophage cp4-57 and overexpression of this protein leads to excision of the prophage. Uniprot lists the E. coli AlpA as a DNA binding protein with a helix turn helix motif. The papers about E. coli AlpA do not address directly whether this protein binds DNA but expression of AlpA leads to higher transcription levels of another prophage protein that is an excisionase. When the B1 homolog is run through the HTH prediction software, there is no significant result. Other HHPRED results for B1 phages include excisionases including TorI and Xis. Both Xis and TorI have winged helix structures for binding DNA. Other proteins with the winged helix that are very similar are repressors (MuR).
Ideas on whether we should continue to use AlpA or start calling these as winged helix proteins?
| posted 31 Jul, 2017 15:03
Sounds like it is not AlpA, and it is not likely to be excise either. I have tried to steer clear of names with just protein structures without any idea about what they do (so we don't say "alpha-helix protein", but "helix-turn-helix DNA binding protein" is OK).

Do winged helix proteins all have similar functions? Or is this a structural motif found in a variety of proteins ?
| posted 31 Jul, 2017 15:40
A quick search revealed a paper with the following abstract:

Transcription. 2012 Jan-Feb;3(1):2-7. doi: 10.4161/trns.3.1.18917.
Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.
Teichmann M1, Dumay-Odelot H, Fribourg S.

The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.
It seems we could call this a helix-turn helix or a winged helix would be more specific.
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