Folia Microbiologica

, Volume 43, Issue 2, pp 123–128 | Cite as

Sequence of archaealMethanococcus jannaschii α-amylase contains features of families 13 and 57 of glycosyl hydrolases: A trace of their common ancestor?



Two sequentially different, seemingly unrelated α-amylase families exist, known as family-13 and family-57 glycosyl hydrolases. Despite the common enzyme activity, it has as yet been impossible to detect any sequence similarity between the two families. The detailed analysis of the recently determined sequence of the α-amylase from methanogenic archaeonMethanococcus jannaschii using the sensitiveHydrophobic Cluster Analysis method revealed that this α-amylase contains features of both families of α-amylases. Thus theM. jannaschii α-amylase is similar to thePyrococcus furiosus α-amylase from family 57 while it obviously contains most of the sequence fingerprints characteristic for α-amylase family 13. Importantly, a glutamic acid residue equivalent with the family-13 catalytic glutamate positioned in the β5-strand segment was identified in members of family 57. The results presented in this report indicate that the two families, 13 and 57, are either the products of a very distant common ancestor or have evolved from each other, although at present they can represent two different α-amylase families with evolved different catalytic mechanisms, catalytic machinery and folds.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., Fitzgerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Presley E.A., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Roberts K.M., Kaine B.P., Borodovsky M., Klenk H.P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.: Complete genome sequence of the methanogenic archaeon,Methanococcus jannaschii. Science 273, 1058–1073 (1996). (Details available at the URL:, or in GenBank: U67601)Google Scholar
  2. Dong G., Vieille C., Zeikus J.G.: Cloning, sequencing, and expression of the gene encoding amylopullulanase fromPyrococcus furiosus and biochemical characterization of the recombinant enzyme.Appl. Environ. Microbiol. 63, 3577–3584 (1997).PubMedGoogle Scholar
  3. Fukusumi S., Kamizono A., Horinouchi S., Beppu T.: Cloning and nucleotide sequence of a heat-stable amylase gene from an anaerobic thermophile,Dictyoglomus thermophilum.Eur. J. Biochem. 174, 15–21 (1988).PubMedCrossRefGoogle Scholar
  4. Gaboriaud C., Bissery V., Benchetrit T., Mornon J.P.: Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences.FEBS Lett. 224, 149–155 (1987).PubMedCrossRefGoogle Scholar
  5. Gray M.W.: The third form of life.Nature 383, 299–300 (1996).PubMedCrossRefGoogle Scholar
  6. Henrissat B.: A classification of glycosyl hydrolases based on amino acid sequence similarities.Biochem. J. 280, 309–316 (1991).PubMedGoogle Scholar
  7. Henrissat B., Bairoch A.: Updating the sequence-based classification of glycosyl hydrolases.Biochem. J. 316, 695–696 (1996).PubMedGoogle Scholar
  8. Horinouchi S., Fukusumi S., Ohshima T., Beppu T.: Cloning and expression inEscherichia coli of two additional amylase genes of a strictly anaerobic thermophile,Dictyoglomus thermophilum, and their nucleotide sequences with extremely low guanine-plus-cytosine contents.Eur. J. Biochem. 176, 243–253 (1988).PubMedCrossRefGoogle Scholar
  9. Janeček Š.: Parallel β/α-barrels of α-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase, versus the barrel of β-amylase: evolutionary distance is a reflection of unrelated sequences.FEBS Lett. 353, 119–123 (1994).PubMedCrossRefGoogle Scholar
  10. Janeček Š.: α-Amylase family: molecular biology and evolution.Progr. Biophys. Mol. Biol. 67, 67–97 (1997).CrossRefGoogle Scholar
  11. Janeček Š., MacGregor E.A., Svensson B.: Characteristic differences in the primary structure allow discrimination of cyclodextrin glucanotransferases from α-amylases.Biochem. J. 305, 685–686 (1995).PubMedGoogle Scholar
  12. Jeon B., Taguchi H., Sakai H., Ohshima T., Wakagi T., Matsuzawa H.: 4-α-Glucanotransferase from a hyperthermophilic archaeonThermococcus litoralis.Eur. J. Biochem. 248, 171–178 (1997).PubMedCrossRefGoogle Scholar
  13. Knapp S., Rüdiger A., Antranikian G., Jorgensen P.L., Ladenstein R.: Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic, archaeonPyrococcus woesei.Proteins: Struct., Funct., Genet. 23, 595–597 (1995).CrossRefGoogle Scholar
  14. Laderman K.A., Asada K., Uemori T., Mukai H., Taguchi Y., Kato I., Anfinsen C.B.: α-Amylase from the hyperthermophilic archaebacteriumPyrococcus furiosus Cloning and sequencing of the gene and expression inEscherichia coli.J. Biol. Chem. 268, 24402–24407 (1993).PubMedGoogle Scholar
  15. Lemesle-Varloot L., Henrissat B., Gaboriaud C., Bissery V., Morgat A., Mornon J.P.: Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences.Biochimie 72, 555–574 (1990).PubMedCrossRefGoogle Scholar
  16. Matsuura Y., Kusunoki M., Harada W., Kakudo M.: Structure and possible catalytic residues of Taka-amylase A.J. Biochem. 95, 697–702 (1984).PubMedGoogle Scholar
  17. Metz R.J., Allen L.N., Cao T.M., Zeman N.W.: Nucleotide sequence of an amylase gene fromBacillus megaterium.Nucl. Acids Res. 16, 5203 (1988).PubMedCrossRefGoogle Scholar
  18. Nitschke L., Heeger K., Bender H., Schulz G.E.: Molecular cloning, nucleotide sequence and expression inEscherichia coli of the β-cyclodextrin glycosyltransferase gene fromBacillus circulans strain no. 8.Appl. Microbiol. Biotechnol. 33, 542–546 (1990).PubMedCrossRefGoogle Scholar
  19. Olsen G.J., Woese C.R.: Lessons from an archael genome: what are we learning fromMethanococcus jannaschii? Trends Genet. 12, 377–379 (1996).PubMedCrossRefGoogle Scholar
  20. Qian M., Haser R., Buisson G., Duée E., Payan F.: The active center of a mammalian α-amylase. Structure of the complex of a pancreatic α-amylase with a carbohydrate inhibitor refined to 2.2-Å resolution.Biochemistry 33, 6284–6294 (1994).PubMedCrossRefGoogle Scholar
  21. Strokopytov B., Penninga D., Rozeboom H.J., Kalk K.H., Dukhuizen L., Dukstra B.W.: X-Ray structure of cyclodextrin glycosyltransferase complexed with acarbose. Implications for the catalytic mechanism of glycosidases.Biochemistry 34, 2234–2240 (1995).PubMedCrossRefGoogle Scholar
  22. Svensson B.: Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability.Plant Mol. Biol. 25, 141–157 (1994).PubMedCrossRefGoogle Scholar
  23. Tachibana Y., Fujiwara S., Takagi M., Imanaka T.: Cloning and expression of the 4-α-glucanotransferase gene from the hyperthermophilic archaeonPyrococcus sp. KOD1, and characterization of the enzyme.J. Ferment. Bioeng. 83, 540–548 (1997).CrossRefGoogle Scholar
  24. Thompson J.D., Higgins D.G., Gibson T.J.:CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions specific gap penalties and weight matrix choice.Nucl. Acids Res. 22, 4673–4680 (1994).PubMedCrossRefGoogle Scholar
  25. Woese C.R., Kandler O., Wheells M.L.: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya.Proc. Nat. Acad. Sci. USA,87, 4576–4579 (1990).PubMedCrossRefGoogle Scholar

Copyright information

© Folia Microbiologica 1998

Authors and Affiliations

  1. 1.Institute of MicrobiologySlovak Academy of SciencesBratislavaSlovakia

Personalised recommendations