Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420
ADMAN@gouda.bmsc.washington.edu
A structure based alignment of 23 cupredoxin domains from both single and multiple-domained copper-containing proteins has been performed, by searching for a minimum of four consecutive residues with an rms deviation from the average under a defined cutoff. Fifty-three common core atoms could be identified in this manner. From this structure based alignment the twenty-three domains can be grouped by distance apart to form a tree that is consistent with the idea that a precursor to the human protein ceruloplasmin formed from gene duplication of a single cupredoxin domain, followed by gene triplication of the two-domain protein. The two-domain gene-duplication product could be the same as that for the trimeric protein nitrite reductase; however in nitrite reductase the second domain Type I copper would have been lost, whereas in ceruloplasmin, the first domain Type I copper would have been lost. Results from attempts to thread sequences expected to be related to these domains will be presented.