The invariant residues in the α-amylase family: Just the catalytic triad

Biologia - Section Cellular and Molecular Biology

Volumn 58, Issue 6, 2003, Pages 1127-1132

  Machovič, Martin ^a   Janeček, Štefan ^a,b  

^a UNIVERSITY OF SS CYRIL AND METHODIUS   (Slovakia)

^b INSTITUTE OF CHEMISTRY   (Slovakia)

Author keywords

amylase family; 4 glucanotransferase; Catalytic triad; Glycoside hydrolase family 77; Invariantly conserved residues

Indexed keywords

BORRELIA; BORRELIA BURGDORFERI; SPIROCHAETALES;

EID: 0346306302     PISSN: 13356399     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (50)

1. ALTSCHUL, S. F., MADDEN, T. L., SCHÄFFER, A. A., ZHANG, J., ZHANG, Z., MILLER, W. & LIPMAN, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. AMEMURA, A., CHAKRABORTY, R., FUJITA, M., NOUMI, T. & FUTAI, M. 1988. Cloning and nucleotide sequence of the isoamylase gene from Pseudomonas amyloderamosa SB-15. J. Biol. Chem. 263: 9271-9275.
3. BAECKER, P. A., GREENBERG, E. & PREISS, J. 1986. Biosynthesis of bacterial glycogen. Primary structure of Escherichia coli 1,4-α-D-glucan: 1,4-α-D-glucan 6-α-D-(1,4-α-D-glucano)-transferase as deduced from the nucleotide sequence of the glgB gene. J. Biol. Chem. 261: 8738-8743.
4. BAIROCH, A. & APWEILER, R. 2000. The SWISS-PROT protein sequence database and its supple-ment TrEMBL in 2000. Nucleic Acids Res. 28: 45-48.
5. BENSON, D. A., KARSCH-MIZRACHI, I., LIPMAN, D. J., OSTELL, J., RAPP, B. A. & WHEELER, D. L. 2000. GenBank. Nucleic Acids Res. 28: 15-18.
6. BERMAN, H. M., BATTISTUZ, T., BHAT, T. N., ... & ZARDECKI, C. 2002. The protein data bank. Acta Crystallogr. D58: 899-907.
7. COUTINHO, P. M. & HENRISSAT, B. 1999. Carbohydrate-Active Enzymes server at URL: http:// afmb.cnrs-mrs.fr/~cazy/CAZY/index.html.
8. D'AMICO, S., GERDAY, C. & FELLER, G. 2000. Structural similarities and evolutionary relationships in chloride-dependent α-amylases. Gene 253: 95-105.
9. DEVULAPALLE, K. S., GOODMAN, S. D., GAO, Q., HEMSLEY, A. & MOOSER, G. 1997. Knowledge-based model of a glucosyltransferase from the oral bacterial group of mutans streptococci. Protein Sci. 6: 2489-2493.
10. DIDERICHSEN, B. & CHRISTIANSEN, L. 1988. Cloning of a maltogenic α-amylase from Bacillus stearothermophilus. FEMS Microbiol. Lett. 56: 53-60.
11. FERRETTI, J. J., GILPIN, M. L. & RUSSELL, R. R. 1987. Nucleotide sequence of a glucosyltransferase gene from Streptococcus sobrinus MFe28. J. Bacteriol. 169: 4271-4278.
12. FRASER, C. M., CASJENS, S., HUANG, W. M., ... & VENTER, J. C. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390: 580-586.
13. FUJITA, M., TORIGAE, K., NAKADA, T., TSUSAKI, K., KUBOTA, M., SAKAI, S. & TSUJISAKA, Y. 1989. Cloning and nucleotide sequence of the gene (amyP) for maltotetraose-forming amylase from Pseudomonas stutzeri MO-19. J. Bacteriol. 171: 1333-1339.
14. GODA, S. K., EISSA, O., AKHTAR, M. & MINTON, N.P. 1997. Molecular analysis of a Clostridium butyricum NCIMB 7423 gene encoding 4-α-glucano-transferase and characterization of the recombinant enzyme produced in Escherichia coli. Microbiology 143: 3287-3294.
15. GUEX, N., DIEMAND, A. & PEITSCH, M. C. 1999. Protein modelling for all. Trends Biochem. Sci. 24: 364-367.
16. GUEX, N. & PEITSCH, M. C. 1997. SWISS-MODEL and the SWISS-PDBviewer: an environment for comparative protein modelling. Electrophoresis 18: 2714-2723.
17. HEINRICH, P., HUBER, W. & LIEBL, W. 1994. Expression in Escherichia coli and structure of the gene encoding 4-α-glucanotransferase from Thermotoga maritima. Classification of maltodextrin glycosyltransferses into two distantly related enzyme subfamilies. System. Appl. Microbiol. 17: 297-305.
18. 8-barrel domains. Biochem. J. 288: 1069-1070.
19. JANEČEK, Š. 1994a. 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.
20. JANEČEK, Š. 1994b. Sequence similarities and evolutionary relationships of microbial, plant and animal α-amylases. Eur. J. Biochem. 224: 519-524.
21. 8-barrel glycosyl hydrolases suggested by the similarity of their fifth conserved sequence region. FEBS Lett. 377: 6-8.
22. JANEČEK, Š. 2002. How many conserved sequence regions are there in the α-amylase family? Biologia, Bratislava 57 (Suppl. 11): 29-41.
23. KIM, T. J., KIM, M. J., KIM, B. C., KIM, J. C., CHEONG, T. K., KIM, J. W. & PARK, K. H. 1999. Modes of action of acarbose hydrolysis and transglycosylation catalyzed by a thermostable maltogenic amylase, the gene for which was cloned from a Thermus strain. Appl. Environ. Microbiol. 65: 1644-1951.
24. KIM, T.-J., SHIN, J.-H., OH, J.-H., KIM, M.-J., LEE, S.-B., RYU, S., KWON, K., KIM, J.-W., CHOI, E.-H., ROBYT, J. F. & PARK, K.-H. 1998. Analysis of the gene encoding cyclomaltodextrinase from alkalophilic Bacillus sp. I-5 and characterization of enzymatic properties. Arch. Biochem. Biophys. 353: 221-227.
25. KOBAYASHI, K., KATO, M., MIURA, Y., KETTOKU, M., KOMEDA, T. & IWAMATSU, A. 1996. Gene cloning and expression of new trehalose-producing enzymes from the hyperthermophilic archaeum Sulfolobus solfataricus KM1. Biosci. Biotech. Biochem. 60: 1882-1885.
26. KURIKI, T. & IMANAKA, T. 1989. Nucleotide sequence of the neopullulanase gene from Bacillus stearothermophilus. J. Gen. Microbiol. 135: 1521-1528.
27. LIBESSART, N. & PREISS, J. 1998. Arginine residue 384 at the catalytic center is important for branching enzyme II from maize endosperm. Arch. Biochem. Biophys. 360: 135-141.
28. MACGREGOR, E.A., JANEČEK, Š. & SVENSSON, B. 2001. Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim. Biophys. Acta 1546: 1-20.
29. MACGREGOR, E. A., JESPERSEN, H. M. & SVENSSON, B. 1996. A circularly permuted α-amylase-type α/β-barrel structure in glucan-synthesizing glucosyltransferases. FEBS Lett. 378: 263-266.
30. MATSUURA, Y., KUSUNOKI, M., HARADA, W. & KAKUDO, M. 1984. Structure and possible catalytic residues of Taka-amylase A. J. Biochem. 95: 697-702.
31. MCCARTER, J. D. & WITHERS, S. G. 1994. Mechanisms of enzymatic glycoside hydrolysis. Curr. Opin. Struct. Biol. 4: 885-892.
32. MEISSNER, H. & LIEBL, W. 1998. Thermotoga maritima maltosyltransferase, a novel type of maltodextrin glycosyltransferase acting on starch and malto-oligosaccharides. Eur. J. Biochem. 250: 1050-1058.
33. NAKAJIMA, R., IMANAKA, T. & AIBA, S. 1986. Comparison of amino acid sequences of eleven different α-amylases. Appl. Microbiol. Biotechnol. 23: 355-360.
34. NITSCHKE, L., HEEGER, K., BENDER, H. & SCHULZ, G. E. 1990. Molecular cloning, nucleotide sequence and expression in Escherichia coli of the β-cyclodextrin glycosyltransferase gene from Bacillus circulans strain no. 8. Appl. Microbiol. Biotechnol. 33: 542-546.
35. POTOCKI DE MONTALK, G., REMAUD-SIMEON, M., WILLEMOT, R.M., PLANCHOT, V. & MONSAN, P. 1999. Sequence analysis of the gene encoding amylosucrase from Neisseria polysaccahrea and characterization of the recombinant enzyme. J. Bacteriol. 181: 375-381.
36. PRZYLAS, I., TERADA, Y., FUJII, K., TAKAHA, T., SAENGER, W. & STRATER, N. 2000a. X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans. Eur. J. Biochem. 267: 6903-6913.
37. PRZYLAS, I., TOMOO, K., TERADA, Y., TAKAHA, T., FUJII, K., SAENGER, W. & STRÄTER, N. 2000b. Crystal structure of amylomaltase from Thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans. J. Mol. Biol. 296: 873-886.
38. PUGSLEY, A. P. & DUBREUIL, C. 1988. Molecular characterization of malQ, the structural gene for the Escherichia coli enzyme amylomaltase. Mol. Microbiol. 2: 473-479.
39. PUJADAS, G. & PALAU, J. 1999. TIM barrel fold: structural, functional and evolutionary characteristics in natural and designed molecules. Biologia, Bratislava 54: 231-254.
40. STRÄTER, N., PRZYLAS, I., SAENGER, W., TERADA, Y., FUJI, K. & TAKAHA, T. 2002. Structural basis of the synthesis of large cycloamyloses by amylomaltase. Biologia, Bratislava 57 (Suppl. 11): 93-99.
41. SØGAARD, M., KADZIOLA, A., HASER, R. & SVENSSON, B. 1993. Site-directed mutagenesis of histidine 93, aspartic acid 180, glutamic acid 205, histidine 290, and aspartic acid 291 at the active site and tryptophan 279 at the raw starch binding site in barley α-amylase 1. J. Biol. Chem. 268: 22480-22484.
42. SVENSSON, B. 1994. Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol. Biol. 25: 141-157.
43. TAKAHA, T., YANASE, M., OKADA, S. & SMITH, S. M. 1993. Disproportionating enzyme (4-α-glucanotransferase; EC 2.4.1.25) of potato. Purification, molecular cloning, and potential role in starch metabolism. J. Biol. Chem. 268: 1391-1396.
44. TERADA, Y., FUJII, K., TAKAHA, T. & OKADA, S. 1999. Thermus aquaticus ATCC 33923 amylomaltase gene cloning and expression and enzyme characterization: production of cycloamylose. Appl. Environ. Microbiol. 65: 910-915.
45. TODA, H., KONDO, K., & NARITA, K. 1982. The complete amino acid sequence of Taka-amylase A. Proc. Japan Acad. B58: 208-212.
46. TONOZUKA, T., MOGI, S., SHIMURA, Y., IBUKA, A., SAKAI, H., MATSUZAWA, H., SAKANO, Y. & OHTA, T. 1995. Comparison of primary structures and substrate specificities of two pullulan-hydrolyzing α-amylases, TVA I and TVA II, from Thermoactinomyces vulgaris R-47. Biochim. Biophys. Acta 1252: 35-42.
47. TONOZUKA, T., OHTSUKA, M., MOGI, S. I., SAKAI, H., OHTA, T. & SAKANO, Y. 1993. A neopullulanase-type α-amylase gene from Thermoactinomyces vulgaris R-47 Biosci. Biotech. Biochem. 57: 395-401.
48. VIHINEN, M., OLLIKKA, P., NISKANEN, J., MEYER, P., SUOMINEN, I., KARP, M., HOLM, L., KNOWLES, J. & MÄNTSÄLÄ, P. 1990. Site-directed mutagenesis of a thermostable α-amylase from Bacillus stearothermophilus: putative role of three conserved residues. J. Biochem. 107: 267-272.
49. WATANABE, K., KITAMURA, K., IHA, H. & SUZUKI, Y. 1990. Primary structure of the oligo-1,6-glucosidase of Bacillus cereus ATCC7064 deduced from the nucleotide sequence of the gene. Eur. J. Biochem. 192: 609-620.
50. WATTEBLED, F., RAL, J. P., DAUVILLEE, D., MYERS, A. M., JAMES, M. G., SCHLICHTING, R., GIERSCH, C., BALL, S. G. & D'HULST, C. 2003. STA11, a Chlamydomonas reinhardtii locus required for normal starch granule biogenesis, encodes disproportionating enzyme. Further evidence for a function of α-1,4 glucanotransferases during starch granule biosynthesis in green algae. Plant Physiol. 132: 137-145.