Summary

A multiple sequence alignment of 44 serine/threonine specific protein phosphatases has been performed. This reveals the position of a common conserved catalytic core, the location of invariant residues, insertions and deletions. The multiple alignment has been used to guide and improve a consensus secondary structure prediction for the common catalytic core. The location of insertions and deletions has aided in defining the positions of surface loops and turns. The prediction suggests that the core protein phosphatase structure comprises two domains, the first has a single - sheet flanked by - helices, while the second is predominantly - helical. Knowledge of the core secondary structures provides a guide for the design of site directed mutagenesis experiments that will not disrupt the native phosphatase fold. A sequence similarity between eukaryotic serine/threonine protein phosphatases and the Escherichia coli diadenosine tetra-phosphatase has been identified. This extends over the N-terminal 100 residues of bacteriophage phosphatases and Escherichia coli diadenosine tetra-phosphatase. Residues which are invariant amongst these classes are likely to be important in catalysis and protein folding. These include Arg 92, Asn 138, Asp 59, 88, Gly 58, 62, 87, 93, 137, His 61, 139 and Val 90 and fall into three clusters with the consensus sequences GD[IVTL]HG, GD[LYF]V[DA]RG and GNH, where brackets surround alternative amino acids. The first two consensus sequences are predicted to fall in the --and -loops of a ---secondary structure motif. This places the predicted phosphate-binding site at the N-terminus of the - helix where phosphate binding may be stabilised by the - helix dipole.