Secondary structure prediction from multiple sequence data: blood clotting factor XIII and Yersinia protein-tyrosine phosphatase

Predictions of protein structure are best tested without prior knowledge of the protein three-dimensional structure. Three-dimensional atomic models will soon be determined by X-ray crystallography for the alpha-subunit of human blood clotting factor XIII and members of the family of protein tyrosine specific phosphatases. Accordingly, we here present secondary structure predictions for each of these proteins. The secondary structure predictions were generated from aligned sets of protein sequences. This technique has previously provided reliable predictions for the Annexins and the SH2 domains. The factor XIII alpha prediction contains 39 regions predicted in strand conformation (34% of the protein) with only 3 helices (4%). The protein tyrosine phosphatases have 12 predicted strands and 5 helices (30 and 17%, respectively). We expect greater reliability from regions of alignments that show clear patterns of residue conservation (61% of factor XIII alpha and 57% of the protein tyrosine phosphatases). The aligned protein tyrosine phosphatases show two regions (L39-L80 and I138-E253) with clear patterns of residue conservation separated by a region of variable amino acid composition. We suggest this indicates that the tyrosine phosphatase fold comprises two domains separated by an exposed linker. Potential phosphate binding sites are identified in the protein tyrosine phosphatases.