title: Superdomains in the protein structure hierarchy: The case of PTP-C2.
abstract: Superdomain is uniquely defined in this work as a conserved combination of different globular domains in different proteins. The amino acid sequences of 25 structurally and functionally diverse proteins from fungi, plants, and animals have been analyzed in a test of the superdomain hypothesis. Each of the proteins contains a protein tyrosine phosphatase (PTP) domain followed by a C2 domain. Four novel conserved sequence motifs have been identified, one in the PTP domain and three in the C2 domain. All contribute to the PTP-C2 domain interface in PTEN, a tumor suppressor, and all are more conserved than the PTP signature motif, HCX3 (K/R)XR, in the 25 sequences. We show that PTP-C2 was formed prior to the fungi, plant, and animal kingdom divergence. A superdomain as defined here does not fit the usual protein structure classification system. The demonstrated existence of one superdomain suggests the existence of others.
authors.affiliation: Department of Physics, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida, 33620.
authors.forename: Donald T
authors.initials: DT
authors.lastname: Haynie
authors.forename: Bin
authors.initials: B
authors.lastname: Xue
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics*; D000818:Animals; D047390:Casein Kinase II / Q000737:chemistry / Q000235:genetics; D020134:Catalytic Domain / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D005658:Fungi / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D051059:PTEN Phosphohydrolase / Q000737:chemistry* / Q000235:genetics; D010944:Plants / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D017027:Protein Tyrosine Phosphatases / Q000737:chemistry / Q000235:genetics; D017386:Sequence Homology, Amino Acid
chemical_list: D047390:Casein Kinase II; D017027:Protein Tyrosine Phosphatases; D051059:PTEN Phosphohydrolase; C494929:PTEN protein, human
keywords: domain; evolution; hierarchy; protein; structure; superdomain