>> I am searching for a small independently folding (or in presence of a
> metal ion), DNA binding domain. Would like it to be sequence specific, but
> would greatly appreciate all suggestions. Be as detailed as possible or
> please cite a reference, or name that I can locate it in the literature.
> Thanks very much.
Check out the T4 endonuclease V; it's a DNA-repair enzyme, preparing
thymine-dimers for the complete excision by the DNA polymerase.
I worked on this enzyme about 7 - 8 years ago, when I was a post-doc in
Unfortunately, it is nothing really known about the binding site, but
assuming the longest axis of this small protein (~16kDa) is equivalent
to the maximal number of basepairs that can bind, the number should be
<= 8 pairs.
We were never sure about the binding-site, because several of the really
important site-directed mutants were not expressed by E. coli. However,
there is a very good crystal structure available.
The institute's name was 'Protein Engineering Research Institute
(PERI)', but has now be changed to BERI. They have a web-page:
Look for papers with the names of Morikawa, Tomoko Doi and myself. There
was also a competitors group in the US, but I forgot the name of the