Discovery and analysis of cofactor-dependent phosphoglycerate mutase homologs as novel phosphoserine phosphatases in hydrogenobacter thermophilus

Journal of Biological Chemistry

Volumn 287, Issue 15, 2012, Pages 11934-11941

  Chiba, Yoko ^a   Oshima, Kenro ^a   Arai, Hiroyuki ^a   Ishii, Masaharu ^a   Igarashi, Yasuo ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVITY LEVELS; ARABIDOPSIS THALIANA; BACTERIAL GENUS; CELL-FREE EXTRACTS; CHEMOLITHOAUTOTROPHIC; DEPHOSPHORYLATIONS; FIRMICUTES; HYDROGENOBACTER THERMOPHILUS; IN-VIVO; INORGANIC PHOSPHATES; MUTASE ACTIVITY; ORTHOLOGS; SUBSTRATE SPECIFICITY; SYNTHETIC PATHWAYS; THERMOPHILIC BACTERIA; THERMOPHILUS; THERMUS THERMOPHILUS;

AMINO ACIDS; BACTERIA; CATALYSIS; GENES; METABOLISM; PHOSPHATASES;

PROTEINS;

ESTERASE; HISTIDINE PHOSPHATASE; PHOSPHATASE; PHOSPHOGLYCERATE MUTASE; PHOSPHOSERINE PHOSPHATASE; SERINE; UNCLASSIFIED DRUG;

AMINO ACID METABOLISM; ARABIDOPSIS; ARTICLE; BACTERIAL STRAIN; BIOSYNTHESIS; CONTROLLED STUDY; CYANOBACTERIUM; ENZYME ACTIVITY; ENZYME SPECIFICITY; FIRMICUTES; HETEROLOGOUS EXPRESSION; HYDROGENOBACTER THERMOPHILUS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN SYNTHESIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; THERMOPHILIC BACTERIUM;

AMINO ACID SEQUENCE; BACTERIA, AEROBIC; BACTERIAL PROTEINS; CHROMATOGRAPHY, LIQUID; COENZYMES; ENZYME ASSAYS; KINETICS; MOLECULAR WEIGHT; PHOSPHOGLYCERATE MUTASE; PHOSPHORIC MONOESTER HYDROLASES; PHYLOGENY; PROTEIN SUBUNITS; RECOMBINANT PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); CYANOBACTERIA; FIRMICUTES; HYDROGENOBACTER THERMOPHILUS; THERMUS THERMOPHILUS;

EID: 84859506937     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.330621     Document Type: Article

References (40)

1. Snell, K. (1984) Enzymes of serine metabolism in normal, developing, and neoplastic rat tissues. Adv. Enzyme. Regul. 22, 325-400
2. Ho, C. L., Noji, M., and Saito, K. (1999) Plastidic pathway of serine biosynthesis. Molecular cloning and expression of 3-phosphoserine phosphatase from Arabidopsis thaliana. J. Biol. Chem. 274, 11007-11012
3. Hart, C. E., Race, V., Achouri, Y., Wiame, E., Sharrard, M., Olpin, S. E., Watkinson, J., Bonham, J. R., Jaeken, J., Matthijs, G., and Van Schaftingen, E. (2007) Phosphoserine aminotransferase deficiency. A novel disorder of the serine biosynthesis pathway. Am. J. Hum. Genet. 80, 931-937 (Pubitemid 46668461)
4. Helgadóttir, S., Rosas-Sandoval, G., Söll, D., and Graham, D. E. (2007) Biosynthesis of phosphoserine in the Methanococcales. J. Bacteriol. 189, 575-582 (Pubitemid 46106389)
5. Veeranna and Shetty K. T. (1990) Phosphoserine phosphatase of human brain. Partial purification, characterization, regional distribution, and effect of certain modulators including psychoactive drugs. Neurochem. Res. 15, 1203-1210
6. Ho, C. L., and Saito, K. (2001) Molecular biology of the plastidic phosphorylated serine biosynthetic pathway in Arabidopsis thaliana. Amino. Acids. 20, 243-259
7. Wang, W., Cho, H. S., Kim, R., Jancarik, J., Yokota, H., Nguyen, H. H., Grigoriev, I. V., Wemmer, D. E., and Kim, S. H. (2002) Structural characterization of the reaction pathway in phosphoserine phosphatase. Crystallographic "snapshots" of intermediate states. J. Mol. Biol. 319, 421-431 (Pubitemid 34729469)
8. Colman, B., and Norman, E. G. (1997) Serine synthesis in cyanobacteria by a nonphotorespiratory pathway. Physiol. Plant. 100, 133-136 (Pubitemid 27235693)
9. Knoop, H., Zilliges, Y., Lockau, W., and Steuer, R. (2010) The metabolic network of Synechocystis sp. PCC 6803. Systemic properties of autotrophic growth. Plant Physiol. 154, 410-422
10. Kawasumi, T., Igarashi, Y., Kodama, T., and Minoda, Y. (1980) Isolation of strictly thermophilic and obligately autotrophic hydrogen bacteria. Agric. Biol. Chem. 44, 1985-1986
11. Kawasumi, T., Igarashi, Y., Kodama, T., and Minoda, Y. (1984) Hydrogenobacter thermophilus gen. nov., sp. nov., an extremely thermophilic, aerobic, hydrogen-oxidizing bacterium. Int. J. Syst. Bacteriol. 34, 5-10 (Pubitemid 14164228)
12. 2 assimilation via the reductive tricarboxylic acid cycle in an obligately autotrophic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus. Arch. Microbiol. 141, 198-203
13. Arai, H., Kanbe, H., Ishii, M., and Igarashi, Y. (2010) Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6. J. Bacteriol. 192, 2651-2652
14. Kameya, M., Arai, H., Ishii, M., and Igarashi, Y. (2010) Purification of three aminotransferases from Hydrogenobacter thermophilus TK-6. Novel types of alanine or glycine aminotransferase. Enzymes and catalysis. FEBS J. 277, 1876-1885
15. Rigden, D. J. (2008) The histidine phosphatase superfamily. Structure and function. Biochem. J. 409, 333-348
16. Suzuki, M., Cui, Z. J., Ishii, M., and Igarashi, Y. (2001) Nitrate respiratory metabolism in an obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6. Arch. Microbiol. 175, 75-78 (Pubitemid 32202033)
17. Shapiro, B. M., and Stadtman, E. R. (1971) Glutamine synthetase (Escherichia coli). Methods Enzymol. 17A, 910-922
18. Kameya, M., Arai, H., Ishii, M., and Igarashi, Y. (2006) Purification and properties of glutamine synthetase from Hydrogenobacter thermophilus TK-6. J. Biosci. Bioeng. 102, 311-315 (Pubitemid 44751631)
19. D'Alessio, G., and Josse, J. (1975) Phosphoglycerate kinase and phosphoglyceromutase from Escherichia coli. Methods Enzymol. 41, 139-144
20. Yokoyama, S., Hirota, H., Kigawa, T., Yabuki, T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y., Nishimura, Y., Kyogoku, Y., Miki, K., Masui, R., and Kuramitsu, S. (2000) Structural genomics projects in Japan. Nat. Struct. Biol. 7, 943-945
21. Seki, M., Carninci, P., Nishiyama, Y., Hayashizaki, Y., and Shinozaki, K. (1998) High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. Plant J. 15, 707-720
22. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., Muramatsu, M., Hayashizaki, Y., Kawai, J., Carninci, P., Itoh, M., Ishii, Y., Arakawa, T., Shibata, K., Shinagawa, A., and Shinozaki, K. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296, 141-145 (Pubitemid 34280073)
23. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011) MEGA5. Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739
24. Edgar, R. C. (2004) MUSCLE. Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797
25. Whelan, S., and Goldman, N. (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Mol. Biol. Evol. 18, 691-699 (Pubitemid 32372940)
26. Rigden, D. J., Bagyan, I., Lamani, E., Setlow, P., and Jedrzejas, M. J. (2001) A cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase. Protein. Sci. 10, 1835-1846 (Pubitemid 32848780)
27. Rigden, D. J., Walter, R. A., Phillips, S. E., and Fothergill-Gilmore, L. A. (1999) Sulfate ions observed in the 2.12 Å structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism. J. Mol. Biol. 286, 1507-1517 (Pubitemid 29121731)
28. Kuznetsova, E., Proudfoot, M., Gonzalez, C. F., Brown, G., Omelchenko, M. V., Borozan, I., Carmel, L., Wolf, Y. I., Mori, H., Savchenko, A. V., Arrowsmith, C. H., Koonin, E. V., Edwards, A. M., and Yakunin, A. F. (2006) Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J. Biol. Chem. 281, 36149-36161 (Pubitemid 46041349)
29. 2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae. Evidence for two ways of citrate cleavage. Environ. Microbiol. 9, 81-92
30. Bourgis, F., Botha, F. C., Mani, S., Hiten, F. N., Rigden, D. J., and Verbruggen, N. (2005) Characterization and functional investigation of an Arabidopsis cDNA encoding a homologue to the d-PGMase superfamily. J. Exp. Bot. 56, 1129-1142 (Pubitemid 40518586)
31. Hills, T., Srivastava, A., Ayi, K., Wernimont, A. K., Kain, K., Waters, A. P., Hui, R., and Pizarro, J. C. (2011) Characterization of a new phosphatase from Plasmodium. Mol. Biochem. Parasitol. 179, 69-79
32. Chiba, Y., Terada, T., Kameya, M., Shimizu, K., Arai, H., Ishii, M., and Igarashi, Y. (2012) Mechanism for folate-independent aldolase reaction catalyzed by serine hydroxymethyltransferase. FEBS J. 279, 504-514
33. Ogawa, H., Gomi, T., and Fujioka, M. (2000) Serine hydroxymethyltransferase and threonine aldolase. Are they identical? Int. J. Biochem. Cell Biol. 32, 289-301 (Pubitemid 30069971)
34. Szebenyi, D. M., Musayev, F. N., di Salvo, M. L., Safo, M. K., and Schirch, V. (2004) Serine hydroxymethyltransferase. Role of Glu-75 and evidence that serine is cleaved by a retroaldol mechanism. Biochemistry 43, 6865-6876
35. Florio, R., di Salvo, M. L., Vivoli, M., and Contestabile, R. (2011) Serine hydroxymethyltransferase. A model enzyme for mechanistic, structural, and evolutionary studies. Biochim. Biophys. Acta 1814, 1489-1896
36. Bartrons, R., and Carreras, J. (1982) Purification and characterization of phosphoglycerate mutase isozymes from pig heart. Biochim. Biophys. Acta 708, 167-177
37. Prince, V. E., and Pickett, F. B. (2002) Splitting pairs. The diverging fates of duplicated genes. Nat. Rev. Genet. 3, 827-837 (Pubitemid 35303515)
38. Ohno, S. (1970) Evolution by Gene Duplication, Springer, New York
39. Oshima, K., Kakizawa, S., Arashida, R., Ishii, Y., Hoshi, A., Hayashi, Y., Kagiwada, S., and Namba, S. (2007) Presence of two glycolytic gene clusters in a severe pathogenic line of Candidatus Phytoplasma asteris. Mol. Plant Pathol. 8, 481-489 (Pubitemid 46985629)
40. Thaller, M. C., Schippa, S., Bonci, A., Cresti, S., and Rossolini, G. M. (1997) Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product. FEMS Microbiol. Lett. 146, 191-198 (Pubitemid 27057721)