Structural and Evolutionary Relationships
among Protein Tyrosine Phosphatase Domains
Jannik N. Andersen, Ole H. Mortensen, GŁnther H. Peters Paul G. Drake,
Lars F. Iversen, Ole Hvilsted Olsen, Peter Gildsig Jansen,
Henrik S. Andersen, Nicholas K. Tonks and Niels Peter H. Moller.
Novo Nordisk, Denmark; Dept. of Chemistry, Technical University of Denmark
Cold Spring Harbor Laboratory, New York, USA.

This section support our publications in Molecular & Cellular Biology (2001) and in Methods (2005).

Our PTP database provides a non-redundant set of PTP domains derived from 61 species and five phyla. It provides a foundation for structure-function studies and contains 601 PTP domains, including 123 membrane-distal domains (D2) from tandem domain receptor PTPs.

Multiple amino acid sequence alignments, generated from this catalog of PTP accession numbers, defines the conserved PTP domain as comprising ~280 amino acids and ten conserved motifs.

All PTPs retrieved from GenBank (the nr database) have been grouped according to PTP domain sequence homology, thereby providing an overview of common names and synonyms used for each enzyme. Notably, our phylogenetic analysis, which identified groups of orthologous relationships, revealed the existence of 17 principal PTP subtypes in vertebrates. Of these, 5 PTP subtypes are conserved between human, fly and worm.

To assist the annotation and classification of PTP sequences identified in newly sequenced genomes we have set up a PTP-domain BLAST server and developed a web-based classification tool. In the Bioinformatics section , the user can align a sequence against our reference set of pre-aligned PTP domains and see via a neighbor-joining tree how it compares to the 17 principal vertebrate subtypes.