Different protein tyrosine phosphatase superfamilies resulting from different gene reading frames

Molecular Biology and Evolution

Volumn 20, Issue 5, 2003, Pages 815-820

  Huang, Jing Fei ^a  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

Circular permutation; Different gene reading frames; Divergent and convergent evolution; Gene duplication and fusion; Molecular evolution; Protein tyrosine phosphatase

Indexed keywords

NUCLEOTIDE; PROTEIN TYROSINE PHOSPHATASE;

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; FRAMESHIFT MUTATION; GENE DUPLICATION; GENE FUSION; MOLECULAR EVOLUTION; MOLECULAR WEIGHT; NUCLEOTIDE SEQUENCE; PROTEIN FAMILY;

AMINO ACID SEQUENCE; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN-TYROSINE-PHOSPHATASE; READING FRAMES; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY;

EID: 0038708522     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg094     Document Type: Article

References (26)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Bajaj, M., and T. Blundell. 1984. Evolution and the tertiary structure of proteins. Annu. Rev. Biophys. Bioeng. 13:453-492.
3. Barford, D., Z. Jia, and N. K. Tonks. 1995. Protein tyrosine phosphatases take off. Nat. Struct. Biol. 12:1043-1053.
4. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The protein data bank. Nucleic Acids Res. 28:235-242.
5. Cho, H., R. Krishnaraj, E. Kitas, W. Bannwarth, C. T. Walsh, and K. S. Anderson. 1992. Isolation and structural elucidation of a novel phosphocysteine intermediate in the LAR protein tyrosine phosphatase enzymatic pathway. J. Am. Chem. Soc. 114:7296-7298.
6. Guan, K. L., and J. E. Dixon. 1991. Evidence of protein-tyrosine-phosphatase catalysis proceeding via a cysteine-phosphate intermediate. J. Biol. Chem. 266:17026-17030.
7. Heringa, J., and W. R. Taylor. 1997. Three-dimensional domain duplication, swapping and stealing. Curr. Opin. Struct. Biol. 7: 416-421.
8. Huang, J., and C. Liu. 2002. Identification of protein superfamily from structure-based sequence motif. Chinese Sci. Bull. 47: 1377-1381.
9. Jeltsch, A. 1999. Circular permutations in the molecular evolution of DNA methyltransferases. J. Mol. Evol. 49:161-164.
10. Kolmodin, K., and J. Åqvist. 2001. The catalytic mechanism of protein tyrosine phosphatases revisited. FEBS Lett. 498:208-213.
11. Lindqvist, Y., and G. Schneider. 1997. Circular permutations of natural protein sequences: structural evidence. Curr. Opin. Struct. Biol. 7:422-427.
12. Lupas, A. 1996. A circular permutation event in the evolution of the SLH domain? Mol. Microbiol. 20:897-898.
13. Malone, T., R. M. Blumenthal, and X. Cheng. 1995. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol. 253:618-632.
14. Murphy, J. E., T. T. Tibbitts, and E. R. Kantrowitz. 1995. Mutation at positions 153 and 328 in Escherichia coli alkaline phosphatase provide insight towards the structure and function of mammalian and yeast alkaline phosphatases. J. Mol. Biol. 253:604-617.
15. Murray, A. W. 1992. Creative blocks. Cell-cycle checkpoints and feedback controls. Nature 359:599-604.
16. Murzin, A. G. 1998. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8:380-387.
17. Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP - a structural classification of protein database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
18. Ponting, C. P., and R. B. Russell. 1995. Swaposins: circular permutations within genes encoding saposin homologues. Trends Biochem. Sci. 20:79-180.
19. Pot, D. A., T. A. Woodford, E. Remboutsika, R. S. Haun, and J. E. Dixon. 1991. Cloning, bacterial expression, purification, and characterization of the cytoplasmic domain of rat LAR, a receptor-like protein tyrosine phosphatase. J. Biol. Chem. 266:19688-19696.
20. Rossmann, M. G., and P. Argos. 1977. The taxonomy of protein structure. J. Mol. Biol. 109:99-129.
21. Šali, A., and T. L. Blundell. 1990. The definition of topological equivalence in homologous and analogous structures: a procedure involving a comparison of local properties and relationship. J. Mol. Biol. 212:403-442.
22. Stone, R. L., and J. E. Dixon. 1994. Protein-tyrosine phosphatases. J. Biol. Chem. 269:1323-31326.
23. Streuli, M., N. X. Krueger, T. Thai, M. Tang, and H. Saito. 1990. Distinct functional roles of the two intracellular phosphatase-like domains of the receptor-like protein tyrosine phosphatases LCA and LAR. EMBO J. 9:2399-2407.
24. Sutcliffe, M. J., I. Haneef, D. Carney, and T. L. Blundell. 1987. Knowledge-based modeling of homologous proteins. Part I: three-dimensional frameworks derived from simultaneous superposition of multiple structures. Protein Eng. 1:377-384.
25. Taylor, W. R. 2000. Protein structure comparison using SAP. Methods Mol. Biol. 143:19-32.
26. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.