Mapping of barley α-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft

FEBS Letters

Volumn 580, Issue 21, 2006, Pages 5049-5053

  Kandra, Lili ^a   Hachem, Maher Abou ^b   Gyémánt, Gyöngyi ^a   Kramhøft, Birte ^b   Svensson, Birte ^b  

^a UNIVERSITY OF DEBRECEN   (Hungary)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

2 Chloro 4 nitrophenyl d maltooligosaccharides; Barley amylase; Bond cleavage frequencies; Subsite maps; Subsite mutants

Indexed keywords

AMYLASE; OLIGOSACCHARIDE;

ARTICLE; BARLEY; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; ENZYME BINDING; ENZYME SUBSTRATE; HYDROLYSIS; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL;

ALPHA-AMYLASE; ANIMALS; BINDING SITES; BIOPOLYMERS; CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; HORDEUM; HYDROLYSIS; ISOENZYMES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; OLIGOSACCHARIDES; RABBITS; SUBSTRATE SPECIFICITY;

HORDEUM VULGARE SUBSP. VULGARE;

EID: 33748328058     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.08.028     Document Type: Article

References (28)

1. http://afmb.cnrs-mrs.fr/CAZY/. Carbohydrate Active Enzymes.
2. Davies G.J., Wilson K.S., and Henrissat B. Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem. J. 321 (1997) 557-559
3. Brzozowski A.M., Lawson D.M., Turkenburg J.P., Bisgaard-Frantzen H., Svendsen A., Borchert T.V., Dauter Z., Wilson K.S., and Davies G.J. Structural analysis of a chimeric bacterial α-amylase. High-resolution analysis of native and ligand complexes. Biochemistry 39 (2000) 9099-9107
4. Gyémánt G., Hovánszki G., and Kandra L. Subsite mapping of the binding region of α-amylases with a computer program. Eur. J. Biochem. 269 (2002) 5157-5162
5. Robert X., Haser R., Mori H., Svensson B., and Aghajari N. Oligosaccharide binding by barley alpha-amylase 1. J. Biol. Chem. 280 (2005) 32968-32978
6. Suganuma T., Matsuno R., Ohnishi M., and Hiromi K. A study of the mechanism of action of Taka-amylase A1 on linear oligosaccharides by product analysis and computer simulation. J. Biochem. 84 (1978) 293-316
7. Ajandouz E.H., Abe J., Svensson B., and Marchis-Mouren G. Barley malt α-amylase. Purification, action pattern and subsite mapping of isozyme 1 and two members of the isozyme 2 subfamily using p-nitrophenylated maltooligosaccharide substrates. Biochim. Biophys. Acta 1159 (1992) 193-202
8. MacGregor E.A., MacGregor A.W., Macri L.J., and Morgan J.E. Models for the action of barley alpha-amylase isozymes on linear substrates. Carbohydr. Res. 257 (1994) 249-268
9. MacGregor A.W., Morgan J.E., and MacGregor E.A. The action of germinated barley alpha-amylases on linear maltodextrins. Carbohydr. Res. 227 (1992) 301-313
10. Jones R.L., and Jacobsen J.V. Regulation of synthesis and transport of secreted proteins in cereal aleurone. Int. Rev. Cytol. 126 (1991) 49-68
11. Bak-Jensen K.S., André G., Gottschalk T.E., Paës G., Tran V., and Svensson B. Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley α-amylase 1. J. Biol. Chem. 279 (2004) 10093-10102
12. Mori H., Bak-Jensen K.S., Gottschalk T.E., Motawia M.S., Damager I., Møller B.L., and Svensson B. Modulation of activity and substrate binding modes by mutation of single and double subsites +1/+2 and -5/-6. Eur. J. Biochem. 268 (2001) 6545-6558
13. Kadziola A., Søgaard M., Svensson B., and Haser R. Molecular structure of a barley α-amylase inhibitor complex: implications for starch binding and catalysis. J. Mol. Biol. 278 (1998) 205-217
14. Robert X., Haser R., Gottschalk T.E., Ratajczak F., Driguez H., Svensson B., and Aghajari N. The structure of barley α-amylase 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs. Structure 11 (2003) 973-984
15. Kandra L., Gyémánt G., Remenyik J., Hovánszki G., and Lipták A. Action pattern and subsite mapping of Bacillus licheniformis α-amylase (BLA) with modified maltooligosaccharide substrates. FEBS Lett. 518 (2002) 79-82
16. Kandra L., Gyémánt G., Pál M., Petró M., Remenyik J., and Lipták A. Chemoenzymatic synthesis of 2-chloro-4nitrophenyl β-maltoheptaoside acceptor-products using glycogen phosphorylase b. Carbohydr. Res. 333 (2001) 129-136
17. Farkas E., Jánossy L., Harangi J., Kandra L., and Lipták A. Synthesis of chromogenic substrates of α-amylases on a cyclodextrin basis. Carbohydr. Res. 303 (1997) 407-415
18. Kandra L., Gyémánt G., Remenyik J., Ragunath C., and Ramasubbu N. Subsite mapping of human salivary α-amylase and the mutant Y151M. FEBS Lett. 544 (2003) 194-198
19. Kaplan W., and Littlejohn T.G. Swiss-PDB viewer (deep view). Brief Bioinform. 2 (2001) 195-197
20. Uitdehaag J.C.M., Mosi R., Kalk K.H., van der Veen B.A., Dijkhuizen L., Withers S.G., and Dijkstra B.W. X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the α-amylase family. Nat. Struct. Biol. 6 (1999) 432-436
21. Uitdehaag J.C., van Alebeek G.-J., van der Veen B.A., Dijkhuizen L., and Dijkstra B.W. Structures of maltohexaose and maltoheptaose bound at the donor sites of cyclodextrin glycosyltransferase give insight into the mechanism of transglycosylation activity and cyclodextrin size specificity. Biochemistry 39 (2000) 7772-7780
22. Machovič M., and Janecek S. The invariant residues in the α-amylase family: just the catalytic triad. Biologia 58 (2003) 1127-1132
23. Brayer G.D., Sidhu G., Maurus R., Rydberg E.H., Braun C., Wang Y., Nguyen N.T., Overall C.M., and Withers S.G. Subsite mapping of human pancreatic α-amylase active site through structural, kinetic, and mutagenesis techniques. Biochemistry 39 (2000) 4778-4791
24. Fujimoto Z., Takase K., Doui N., Momma M., Matsumoto T., and Mizuno H. Crystal structure of a catalytic-site mutant α-amylase from Bacillus subtilis complexed with maltopentaose. J. Mol. Biol. 277 (1998) 393-407
25. Ramasubbu N., Ragunath C., Mishra P.J., Thomas L.M., Gyémánt G., and Kandra L. Human salivary α-amylase Trp58 situated at subsite -2 is critical for enzyme activity. Eur. J. Biochem. 217 (2004) 2517-2529
26. Brzozowski A.M., and Davies G.J. Structure of the Aspergillus oryzae α-amylase complexed withe the inhibitor acarbose at 2.0 Å resolution. Biochemistry 36 (1997) 10837-10845
27. Davies G.J., Brzozowski A.M., Dauter Z., Rasmussen M.D., Borchert T.V., and Wilson K.S. Structure of a Bacillus halmapalus family 13 α-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 Å resolution. Acta Crystallogr. D 61 (2005) 190-193
28. Kanai R., Haga K., Akiba T., Yamane K., and Harata K. Biochemical and crystallographic analyses of maltohexaose-producing amylase from alkalophilic Bacillus sp. Biochemistry 43 (2004) 14047-14056