I'm trying to check if the proteins I'm working on possess an arginine finger or not. The problem is that I've been having problems finding the sequence online (including papers). Most of the time papers refer to the arginine finger and all they show is a diagram of the protein with the arginine finger drawn (but no sequence!). Does anyone know how I can identify this motif? I believe there is no online software to do so. I've also tried to align my protein with other organisms' orthologues, but the thing is that I can't find info on their arginine finger sequence either. Thanks in advance.
Hi Catarina,
check out the publication:
Iyer LM, Leipe DD, Koonin EV, & Aravind L (2004) Evolutionary history and higher order
classifcation of AAA+ ATPases. Journal of Structural Biology 146:11–31.
There you will find appr. 80 representatives of the AAA+ family with sequence alignment and conserved motifs. As far as I know the Arginine-Finger is somewhat defined by its location between helix 4 and strand 5 and is usually followed by a hydrophobic residue. Some of AAA ATPases lack an arginine-finger as well as Sensor I and II, but AAA+ ATPases should have it.
Best Kai
Hi Hamid and Kai, Thank you very much for your replies. I'm still struggling, but they have defanetly helped. Best, Catarina
The Arg finger is a structural motif commonly located in an alpha-beta loop and positioned to interact with the Nucleotide gamma phosphate, see for example J Mol Biol. 2001 311, 297-310.
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