The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure

Journal of Bacteriology

Volumn 186, Issue 15, 2004, Pages 5129-5137

  Patel, Hiten M ^a   Kraszewski, Jessica L ^b,c   Mukhopadhyay, Biswarup ^b,c  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^c VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL COENZYME A; ARGININE; ASPARAGINE; ASPARTIC ACID; CARBON DIOXIDE; LYSINE; OXALOACETIC ACID; PHOSPHOENOLPYRUVATE CARBOXYLASE; PYRUVATE CARBOXYLASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; GEL FILTRATION CHROMATOGRAPHY; GENE; METHANOBACTERIALES; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; ARCHAEA; METHANOBACTERIACEAE; MODELS, MOLECULAR; PHOSPHOENOLPYRUVATE CARBOXYLASE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

ARCHAEA; BACTERIA (MICROORGANISMS); CLOSTRIDIUM; CLOSTRIDIUM PERFRINGENS; ESCHERICHIA COLI; EUKARYOTA; LEUCONOSTOC; LEUCONOSTOC MESENTEROIDES; METHANOBACTERIALES; METHANOPYRUS KANDLERI; METHANOTHERMOBACTER; METHANOTHERMOBACTER THERMAUTOTROPHICUS; OENOCOCCUS OENI;

EID: 3242763774     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.15.5129-5137.2004     Document Type: Article

References (62)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, 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. Boone, D. R., W. B. Whitman, and P. Rouviere. 1993. Diversity and taxonomy of methanogens. In J. G. Ferry (ed.), Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman and Hall, New York, N.Y.
3. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
4. Bult, C. J., O. White, G. J. Olsen, L. Zhou, R. D. Fleischmann, G. G. Sutton, J. A. Blake, L. M. FitzGerald, R. A. Clayton, J. D. Gocayne, A. R. Kerlavage, B. A. Dougherty, J. F. Tomb, M. D. Adams, C. I. Reich, R. Overbeek, E. F. Kirkness, K. G. Weinstock, J. M. Merrick, A. Glodek, J. L. Scott, N. S. Geoghagen, and J. C. Venter. 1996. Complete genome sequence of the methanogenic archaeon Methanococcus janaschii. Science 273:1058-1073.
5. Canovas, J. L., and H. L. Kornberg. 1966. Properties and regulation of phosphopyruvate carboxylase activity in Escherichia coli. Proc. R. Soc. Lond. B 165:189-205.
6. Canovas, J. L., and H. L. Kornberg. 1965. Fine control of phosphopyruvate carboxylase activity in Escherichia coli. Biochim. Biophys. Acta 96:169-172.
7. Cantor, C. R., and P. R. Schimmel. 1980. Techniques for the study of biological structure and function: biophysical chemistry, vol. 2. W. H. Freeman Co., New York, N.Y.
8. Chinen, A., I. Uchiyama, and I. Kobayashi. 2000. Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene 259:109-121.
9. Deppenmeier, U., A. Johann, T. Hartsch, R. Merkl, R. A. Schmitz, R. Martinez-Arias, A. Henne, A. Wiezer, S. Baumer, C. Jacobi, H. Bruggemann, T. Lienard, A. Christmann, M. Bomeke, S. Steckel, A. Bhattacharyya, A. Lykidis, R. Overbeek, H. P. Klenk, R. P. Gunsalus, H. J. Fritz, and G. Gottschalk. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4:453-461.
10. 13C nuclear magnetic resonance. J. Bacteriol. 156:316-326.
11. 2 assimilation by Methanothrix concilii. J. Bacteriol. 162:905-908.
12. Felsenstein, J. 2001. PHYLIP, Phylogeny Inference Package, version 3.6a2.1. Department of Genetics, University of Washington, Seattle.
13. Fitz-Gibbon, S. T., H. Ladner, U. J. Kim, K. O. Stetter, M. I. Simon, and J. H. Miller. 2002. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA 99:984-989.
14. 2 fixation pathway in Methanobacterium thermoautotrophicum. Zentbl. Bakteriol. Hyg. Abt. 1 Orig. C3 177:277-288.
15. Fuchs, G., and E. Stupperich. 1978. Evidence for an incomplete reductive carboxylic acid cycle in Methanobacterium thermoautotrophicum. Arch. Microbiol. 118:121-125.
16. Fuchs, G., E. Stupperich, and R. K. Thauer. 1978. Acetate assimilation and the synthesis of alanine, aspartate and glutamate in Methanobacterium thermoautotrophicum. Arch. Microbiol. 117:61-66.
17. Fujita, N., T. Miwa, S. Ishijima, K. Izui, and H. Katsuki. 1984. The primary structure of phosphoenolpyruvate carboxylase of Escherichia coli. Nucleotide sequence of the ppc gene and deduced amino acid sequence. J. Biochem. (Tokyo) 95:909-916.
18. Galagan, J. E., C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, R. D. Barber, I. Cann, D. E. Graham, D. A. Grahame, A. M. Guss, R. Hedderich, C. Ingram-Smith, H. C. Kuettner, J. A. Krzycki, J. A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J. N. Reeve, K. Smith, T. A. Springer, L. A. Umayam, O. White, R. H. White, E. Conway de Macario, J. G. Ferry, K. F. Jarrell, H. Jing, A. J. Macario, I. Paulsen, M. Pritchett, K. R. Sowers, R. V. Swanson, S. H. Zinder, E. Lander, W. W. Metcalf, and B. Birren. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532-542.
19. Graham, D. E., R. Overbeek, G. J. Olsen, and C. R. Woese. 2000. An archaeal genomic signature. Proc. Natl. Acad. Sci. USA 97:3304-3308.
20. Huber, R., M. Kurr, H. W. Jannasch, and K. O. Stetter. 1989. A novel group of abyssal methanogenic archaebacteria (Methanopyrus) growing at 110°C. Nature (London) 342:833-834.
21. Izui, K. 1970. Kinetic studies on the allosteric nature of phosphoenolpyruvate carboxylase from Escherichia coli. J. Biochem. (Tokyo) 68:227-238.
22. Izui, K., S. Ishijima, Y. Yamaguchi, F. Katagiri, T. Murata, K. Shigesada, T. Sugiyama, and H. Katsuki. 1986. Cloning and sequence analysis of cDNA encoding active phosphoenolpyruvate carboxylase of the C4-pathway from maize. Nucleic Acids Res. 14:1615-1628.
23. Jones, W. J., J. A. Leigh, F. Mayer, C. R. Woese, and R. S. Wolfe. 1983. Methanococcus jannaschii sp. nov., an extreme thermophilic methanogen from a submarine hydrothermal vent. Arch. Microbiol. 136:254-261.
24. Kai, Y., H. Matsumura, T. Inoue, K. Terada, Y. Nagara, T. Yoshinaga, A. Kihara, K. Tsumura, and K. Izui. 1999. Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition. Proc. Natl. Acad. Sci. USA 96:823-828.
25. Kai, Y., H. Matsumura, and K. Izui. 2003. Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms. Arch. Biochem. Biophys. 414:170-179.
26. Kawarabayasi, Y., Y. Hino, H. Horikawa, K. Jin-no, M. Takahashi, M. Sekine, S. Baba, A. Ankai, H. Kosugi, A. Hosoyama, S. Fukui, Y. Nagai, K. Nishijima, R. Otsuka, H. Nakazawa, M. Takamiya, Y. Kato, T. Yoshizawa, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, K. Aoki, S. Masuda, M. Yanagil, M. Nishimura, A. Yamagishi, T. Oshima, and H. Kikuchi. 2001. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7. DNA Res. 8:123-140.
27. Kawarabayasi, Y., Y. Hino, H. Horikawa, S. Yamazaki, Y. Haikawa, K. Jin-no, M. Takahashi, M. Sekine, S. Baba, A. Ankai, H. Kosugi, A. Hosoyama, S. Fukui, Y. Nagai, K. Nishijima, H. Nakazawa, M. Takamiya, S. Masuda, T. Funahashi, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, H. Kikuchi, et al. 1999. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 6:83-101, 145-152.
28. Kawarabayasi, Y., M. Sawada, H. Horikawa, Y. Haikawa, Y. Hino, S. Yamamoto, M. Sekine, S. Baba, H. Kosugi, A. Hosoyama, Y. Nagai, M. Sakai, K. Ogura, R. Otsuka, H. Nakazawa, M. Takamiya, Y. Ohfuku, T. Funahashi, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, K. Aoki, and H. Kikuchi. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5:55-76.
29. Kawashima, T., N. Amano, H. Koike, S. Makino, S. Higuchi, Y. Kawashima-Ohya, K. Watanabe, M. Yamazaki, K. Kanehori, T. Kawamoto, T. Nunoshiba, Y. Yamamoto, H. Aramaki, K. Makino, and M. Suzuki. 2000. Archaeal adaptation to higher temperatures revealed by genomic sequence of Themoplasma volcanium. Proc. Natl. Acad. Sci. USA 97:14257-14262.
30. Kelley, L. A., R. M. MacCallum, and M. J. Sternberg. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299:499-520.
31. Kenealy, W. R., and J. G. Zeikus. 1982. Characterization and function of phosphoenolpyruvate carboxylase in Methanobacterium thermoautotrophicum. FEMS Microbiol. 14:7-10.
32. Klenk, H. P., R. A. Clayton, J. F. Tomb, O. White, K. E. Nelson, K. A. Ketchum, R. J. Dodson, M. Gwinn, E. K. Hickey, J. D. Peterson, D. L. Richardson, A. R. Kerlavage, D. E. Graham, N. C. Kyrpides, R. D. Fleischmann, J. Quackenbush, N. H. Lee, G. G. Sutton, S. Gill, E. F. Kirkness, B. A. Dougherty, K. McKenney, M. D. Adams, B. Loftus, J. C. Venter, et al. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.
33. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
34. Matte, A., L. W. Tari, H. Goldie, and E. L. T. Delbaer. 1997. Structure and mechanism of phosphoenolpyruvate carboxylkinase. J. Biochem. 272:8105-8108.
35. Medina, V., R. Pontarollo, D. Glaeske, H. Tabel, and H. Goldie. 1990. Sequence of the pckA gene of Escherichia coli K-12: relevance to genetic and allosteric regulation and homology of E. coli phosphoenolpyruvate carboxykinase with the enzymes from Trypanosoma brucei and Saccharomyces cerevisiae. J. Bacteriol. 172:7151-7156.
36. Metcalf, W. W., J. K. Zhang, E. Apolinario, K. R. Sowers, and R. S. Wolfe. 1997. A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors. Proc. Natl. Acad. Sci. USA 94:2626-2631.
37. Mukhopadhyay, B., E. M. Concar, and R. S. Wolfe. 2001. A GTP-dependent vertebrate-type phosphoenolpyruvate carboxykinase from Mycobacterium smegmatis. J. Biol. Chem. 276:16137-16145.
38. Mukhopadhyay, B., and L. Daniels. 1989. Aerobic purification of N5,N10-methylenetetrahydromethanopterin dehydrogenase, separated from N5,N10-methylenetetrahydromethanopterin cyclohydrolase, from Methanobacterium thermoautotrophicum strain Marburg. Can J. Microbiol. 35:499-507.
39. Mukhopadhyay, B., V. J. Patel, and R. S. Wolfe. 2000. A stable archaeal pyruvate carboxylase from the hyperthermophile Methanococcus jannaschii. Arch. Microbiol. 174:406-414.
40. Mukhopadhyay, B., and E. Purwantini. 2000. Pyruvate carboxylase from Mycobacterium smegmatis: stabilization, rapid purification, molecular and biochemical characterization and regulation of the cellular level. Biochim. Biophys. Acta 1475:191-206.
41. Mukhopadhyay, B., E. Purwantini, C. Kreder, and R. Wolfe. 2001. Oxaloacetate synthesis in the methanarchaeon Methanosarcina barkeri: pyruvate carboxylase genes and a putative Escherichia coli-type bifunctional biotin protein ligase gene (bpl/birA) exhibit a unique organization. J. Bacteriol. 183:3804-3810.
42. Mukhopadhyay, B., S. F. Stoddard, and R. S. Wolfe. 1998. Purification, regulation, and molecular and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain AH. J. Biol. Chem. 273:5155-5166.
43. Ng, W. V., S. P. Kennedy, G. G. Mahairas, B. Berquist, M. Pan, H. D. Shukla, S. R. Lasky, N. S. Baliga, V. Thorsson, J. Sbrogna, S. Swartzell, D. Weir, J. Hall, T. A. Dahl, R. Welti, Y. A. Goo, B. Leithauser, K. Keller, R. Cruz, M. J. Danson, D. W. Hough, D. G. Maddocks, P. E. Jablonski, M. P. Krebs, C. M. Angevine, H. Dale, T. A. Isenbarger, R. F. Peck, M. Pohlschroder, J. L. Spudich, K. W. Jung, M. Alam, T. Freitas, S. Hou, C. J. Daniels, P. P. Dennis, A. D. Omer, H. Ebhardt, T. M. Lowe, P. Liang, M. Riley, L. Hood, and S. DasSarma. 2000. Genome sequence of Halobacterium species NRC-1. Proc. Natl. Acad. Sci. USA 97:12176-12181.
44. Nielsen, H., J. Engelbrecht, S. Brunak, and G. V. Heijne. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
45. Robb, F. T., D. L. Maeder, J. R. Brown, J. DiRuggiero, M. D. Stump, R. K. Yeh, R. B. Weiss, and D. M. Dunn. 2001. Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Methods Enzymol. 330:134-157.
46. Ruepp, A., W. Graml, M. L. Santos-Martinez, K. K. Koretke, C. Volker, H. W. Mewes, D. Frishman, S. Stocker, A. N. Lupas, and W. Baumeister. 2000. The genomic sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407:508-513.
47. Sako, Y., K. Takai, A. Uchida, and Y. Ishida. 1996. Purification and characterization of phosphoenolpyruvate carboxylase from the hyperthermophilic archaeon Methanothermus sociabilis. FEBS Lett. 392:148-152.
48. Sako, Y., K. Takai, T. Nishizaka, and Y. Ishido. 1997. Biochemical relationship of phosphoenol pyruvate carboxylases (PEPCs) from thermophilic archaea. FEMS Michobiol. 153:159-165.
49. Saunders, N. F., T. Thomas, P. M. Curmi, J. S. Mattick, E. Kuczek, R. Slade, J. Davis, P. D. Franzmann, D. Boone, K. Rusterholtz, R. Feldman, C. Gates, S. Bench, K. Sowers, K. Kadner, A. Aerts, P. Dehal, C. Detter, T. Glavina, S. Lucas, P. Richardson, F. Larimer, L. Hauser, M. Land, and R. Cavicchioli. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13:1580-1588.
50. She, Q., R. K. Singh, F. Confalonieri, Y. Zivanovic, G. Allard, M. J. Awayez, C. C. Chan-Weiher, I. G. Clausen, B. A. Curtis, A. De Moors, G. Erauso, C. Fletcher, P. M. Gordon, I. Heikamp-de Jong, A. C. Jeffries, C. J. Kozera, N. Medina, X. Peng, H. P. Thi-Ngoc, P. Redder, M. E. Schenk, C. Theriault, N. Tolstrup, R. L. Charlebois, W. F. Doolittle, M. Duguet, T. Gaasterland, R. A. Garrett, M. A. Ragan, C. W. Sensen, and J. Van der Oost. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98:7835-7840.
51. Shieh, J. S., and W. B. Whitman. 1987. Pathway of acetate assimilation in autotrophic and heterotrophic methanococci. J. Bacteriol. 169:5327-5329.
52. Shimizu, T., K. Ohtani, H. Hirakawa, K. Ohshima, A. Yamashita, T. Shiba, N. Ogasawara, M. Hattori, S. Kuhara, and H. Hayashi. 2002. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc. Natl. Acad. Sci. USA 99:996-1001.
53. Simpson, P. G., and W. B. Whitman. 1993. Anabolic pathways in methanogens, p. 445-472. In J. G. Ferry (ed.), Methanogenesis: ecology, physiology, biochemistry, and genetics. Chapman and Hall, New York, N.Y.
54. Slesarev, A. I., K. V. Mezhevaya, K. S. Makarova, N. N. Polushin, O. V. Shcherbinina, V. V. Shakhova, G. I. Belova, L. Aravind, D. A. Natale, I. B. Rogozin, R. L. Tatusov, Y. I. Wolf, K. O. Stetter, A. G. Malykh, E. V. Koonin, and S. A. Kozyavkin. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 99:4644-4649.
55. Smith, D. R., L. A. Doueette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert, D. Harrison, L. Hoang, P. Keagle, W. Lumm, B. Pothier, D. Qiu, R. Spadafora, R. Vicaire, Y. Wang, J. Wierzbowski, R. Gibson, N. Jiwani, A. Caruso, D. Bush, and J. N. Reeve. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum AH: functional analysis and comparative genomics. J. Bacteriol. 179:7135-7155.
56. Teraoka, H., K. Izui, and H. Katsuki. 1974. Phosphoenolpyruvate carboxylase of Escherichia coli. Multiple conformational states elicited by allosteric effectors. Biochemistry 13:5121-5128.
57. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
58. Wasserfallen, A., J. Nolling, P. Pfister, J. Reeve, and E. Conway de Macario. 2000. Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermobacter thermautotrophicus comb. nov., Methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp. nov. Int. J. Syst. Evol. Microbiol. 50:43-53.
59. Weimer, P. J., and J. G. Zeikus. 1979. Acetate assimilation pathway of Methanosarcina barkeri. J. Bacteriol. 137:332-339.
60. Westhoff, P., and U. Gowik. 2004. Evolution of c4 phosphoenolpyruvate carboxylase. Genes and proteins: a case study with the genus Flaveria. Ann. Bot. (London) 93:13-23.
61. Zeikus, J. G., G. Fuchs, W. Kenealy, and R. K. Thauer. 1977. Oxidoreductases involved in cell carbon synthesis of Methanobacterium thermoautotrophicum. J. Bacteriol. 132:604-613.
62. Zeikus, J. G., and R. S. Wolfe. 1972. Methanobacterium thermoautotrophicus sp. nov., an anaerobic, autotrophic, extreme thermophile. J. Bacteriol. 109:707-715.