Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase

Journal of Molecular Biology

Volumn 326, Issue 1, 2003, Pages 177-188

  Hondoh, Hironori ^a   Kuriki, Takashi ^b   Matsuura, Yoshiki ^a  

^a OSAKA UNIVERSITY   (Japan)

^b EZAKI GLICO CO LTD   (Japan)

Author keywords

Bacillus stearothermophilus; Crystal structure; Neopullulanase; Substrate complex structure; Substrate specificity

Indexed keywords

AMYLASE; CARBOHYDRATE DERIVATIVE; DEXTRANASE; ENZYME; GLUCAN 1,4 ALPHA GLUCOSIDASE; ISOPANOSE; MALTOTETROSE; NEOPULLULANASE; PANOSE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME SPECIFICITY; GEOBACILLUS STEAROTHERMOPHILUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE;

GEOBACILLUS STEAROTHERMOPHILUS;

EID: 0037423706     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01402-X     Document Type: Article

References (36)

1. Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 280:1991;309-316.
2. Svensson B. Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol. Biol. 25:1994;141-157.
3. Kuriki T., Okada S., Imanaka T. New type of pullulanase from Bacillus stearothermophilus and molecular cloning and expression of the gene in Bacillus subtilis. J. Bacteriol. 170:1988;1554-1559.
4. Imanaka T., Kuriki T. Pattern of action of Bacillus stearothermophilus neopullulanase on pullulan. J. Bacteriol. 171:1989;369-374.
5. Takata H., Kuriki T., Okada S., Takesada Y., Iizuka M., Minamiura N., et al. Action of neopullulanase: neopullulanase catalyzes both hydrolysis and transglycosylation at α-(1,4) and α-(1,6)-glucosidic linkages. J. Biol. Chem. 267:1992;18447-18452.
6. Kamasaka H., Sugimoto K., Takata H., Nishimura T., Kuriki T. Bacillus stearothermophilus neopullulanase selective hydrolysis of amylose to maltose in the presence of amylopectin. Appl. Environ. Microbiol. 68:2002;1658-1664.
7. Tonozuka T., Ohtsuka M., Mogi S., Sakai H., Ohta T., Sakano Y. A neopullulanase-type α-amylase gene from Thermoactinomyces vulgaris R-47. Biosci. Biotechnol. Biochem. 57:1993;395-401.
8. Park K.-H., Kim T.-J., Cheong T.-K., Kim J.-W., Oh B.-H., Svensson B. Structure, specificity and function of cyclomaltodextrinase, a multispecific enzyme of the α-amylase family. Biochim. Biophys. Acta. 1478:2000;165-185.
9. Lee H.-S., Kim M.-S., Cho H.-S., Kim J.-I., Kim T.-J., Choi J.-H., et al. Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other. J. Biol. Chem. 277:2002;21891-21897.
10. Kamitori S., Kondo S., Okuyama K., Yokota T., Shimura Y., Tonozuka T., et al. Crystal structure of Thermoactinomyces vulgaris R-47 α-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 Å resolution. J. Mol. Biol. 287:1999;907-921.
11. Kim J.-S., Cha S.-S., Kim H.-J., Kim T.-J., Ha N.-C., Oh S.-T., et al. Crystal structure of a maltogenic amylase provides insights into a catalytic versatility. J. Biol. Chem. 274:1999;26279-26286.
12. Braden B.C., Souchon H., Eisele J.L., Bentley G.A., Bhat T.N., Navaza J., et al. Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. J. Mol. Biol. 243:1994;767-781.
13. Noon W.H., Kong Y., Ma J. Molecular dynamics analysis of a buckyball-antibody complex. Proc. Natl Acad. Sci. USA. 99:2002;6466-6470.
14. Yoshioka Y., Hasegawa K., Matsuura Y., Katsube Y., Kubota M. Crystal structure of a mutant maltotetraose-forming exo-amylase cocrystallized with maltopentaose. J. Mol. Biol. 271:1997;619-628.
15. Fujimoto Z., Takase K., Doui N., Momma M., Matsumoto T., et al. Crystal structure of a catalytic-site mutant α-amylase from Bacillus subtilis complexed with maltopentaose. J. Mol. Biol. 277:1998;393-407.
16. Katsuya Y., Mezaki Y., Kubota M., Matsuura Y. Three-dimensional structure of Pseudomonas isoamylase at 2.2 Å resolution. J. Mol. Biol. 281:1998;885-897.
17. Uitdehaag J.C.M., Mosi R., Kalk K.H., van der Veen B.A., Dijkhuizen L., Withers S.G., et al. X-Ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the α-amylase family. Nature Struct. Biol. 6:1999;432-436.
18. Hasegawa K., Kubota M., Matsuura Y. Roles of catalytic residues in α-amylases as evidenced by the structures of the product-complexed mutants of a maltotetraose-forming amylase. Protein Eng. 12:1999;819-824.
19. Yokota T., Tonozuka T., Shimura Y., Ichikawa K., Kamitori S., Sakano Y. Structures of Thermoactinomyces vulgaris R-47 α-amylase II complexed with substrate analogues. Biosci. Biotechnol. Biochem. 65:2001;619-626.
20. Kuriki T., Takata H., Okada S., Imanaka T. Analysis of the active center of Bacillus stearothermophilus neopullulanase. J. Bacteriol. 173:1991;6147-6152.
21. Igarashi K., Hatada Y., Hagihara H., Saeki K., Takaiwa M., Uemura T., et al. Enzymatic properties of a novel liquefying α-amylase from alkaliphilic Bacillus isolate and entire nucleotide and amino acid sequences. Appl. Environ. Microbiol. 64:1998;3282-3289.
22. Ohdan K., Kuriki T., Kaneko H., Shimada J., Takada T., Fujimoto Z., et al. Characteristics of two forms of α-amylases and structural implication. Appl. Environ. Microbiol. 65:1999;4652-4658.
23. Klein C., Hollender J., Bender H., Schulz G.E. Catalytic center of cyclodextrin glycosyltransferase derived from X-ray structure analysis combined with site-directed mutagenesis. Biochemistry. 31:1992;8740-8746.
24. Kubota M., Matsuura Y., Sakai S., Katsube Y. Molecular structure of Bacillus stearothermophilus cyclodextrin glucanotransferase and analysis of the substrate binding site. Denpun Kagaku. 38:1991;141-146.
25. Strokopytov B., Knegtel R.M.A., Penninga D., Rozeboom H.J., Kalk K.H., Dijkhuizen L., Dijkstra B.W. Structure of cyclodextrin glycosyltransferase complexed with a maltononaose inhibitor at 2.6 Å resolution. Implications for product specificity. Biochemistry. 35:1996;4241-4249.
26. Sakano Y., Kogure M., Kobayashi T., Tamura M., Suekane M. Enzymic preparation of panose and isopanose from pullulan. Carbohydr. Res. 61:1978;175-179.
27. Kuriki T., Kaneko H., Yanase M., Takata H., Shimada J., Handa S., et al. Controlling substrate preference and transglycosylation activity of neopullulanase by manipulating steric constraint and hydrophobicity in active center. J. Biol. Chem. 271:1996;17321-17329.
28. Rossmann M.G., van Beek C.G. Data processing. Acta Crystallog. sect. D. 55:1999;1631-1640.
29. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
30. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
31. Brünger A.T., Adams P.D., Clore G.M., Delano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921.
32. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
33. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242.
34. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
35. Merritt E.A., Murphy M.E.P. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallog. sect. D. 50:1994;869-873.
36. Esnouf R.M. An extensively modified version of molscript that includes generally enhanced colouring capabilities. J. Mol. Graph. 15:1997;132-134.