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Biochemistry & Molecular Biology

Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability

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Pages 989-997 | Received 14 Dec 2013, Accepted 04 Feb 2014, Published online: 18 Jun 2014

References

  • Henrissat B, Davies G. Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol. 1997;7:637–644.10.1016/S0959-440X(97)80072-3
  • Buisson G, Duee E, Haser R, Payan F. Three dimensional structure of porcine pancreatic α-amylase at 2.9 Å resolution. Role of calcium in structure and activity. EMBO J. 1987;6:3909–3916.
  • Kadziola A, Abe J, Svensson B, Haser R. Crystal and molecular structure of barley α-amylase. J. Mol. Biol. 1994;239:104–121.10.1006/jmbi.1994.1354
  • Machius M, Wiegand G, Huber R. Crystal structure of calcium-depleted Bacillus licheniformis α-amylase at 2.2 Å resolution. J. Mol. Biol. 1995;246:545–559.10.1006/jmbi.1994.0106
  • Matsuura Y, Kusunoki M, Harada W, Tanaka N, Iga Y, Yasuoka N, Toda H, Narita K, Kakudo M. Molecular structure of taka-amylase A. I. Backbone chain folding at 3 A resolution. J. Biochem. 1980;87:1555–1558.
  • Ramasubbu N, Paloth V, Luo Y, Brayer GD, Levine MJ. Structure of human salivary α-amylase at 1.6 Å resolution: implications for its role in the oral cavity. Acta Crystallogr. D. 1996;52:435–446.10.1107/S0907444995014119
  • Ramasubbu N, Ragunath C, Mishra PJ. Probing the role of a mobile loop in substrate binding and enzyme activity of human salivary amylase. J. Mol. Biol. 2003;325:1061–1076.10.1016/S0022-2836(02)01326-8
  • Stefan J. How many conserved sequence regions are there in the α-amylase family? Biologia. 2002;57:S29–S41.
  • Martin M, Stefan J. The invariant residues in the α-amylase family: just the catalytic triad. Biologia. 2003;58:S1127–S1132.
  • Machius M, Declerck N, Huber R, Wiegand G. Activation of Bacillus licheniformis α-amylase through a disorder → order transition of the substrate-binding site mediated by a calcium–sodium–calcium metal triad. Structure. 1998;6:281–292.10.1016/S0969-2126(98)00032-X
  • Savchenko A, Vieille C, Kang S, Zeikus JG. Pyrococcus furiosus α-amylase is stabilized by calcium and zinc. Biochemistry. 2002;41:6193–6201.10.1021/bi012106s
  • Vallee BL, Stein EA, Sumerwell WN, Fischer EH. Metal content of α-amylases of various origins. J. Biol. Chem. 1959;234:2901–2905.
  • Akazawa T, Mitsui T, Hayashi M, Preiss J. 11 – Recent progress in alpha-amylase biosynthesis. San Diego, CA: Academic Press; 1988. p. 465–492.
  • Beck E, Ziegler P. Biosynthesis and degradation of starch in higher plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1989;40:95–117.10.1146/annurev.pp.40.060189.000523
  • Fincher GB. Molecular and cellular biology associated with endosperm mobilization in germinating cereal grains. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1989;40:305–346.10.1146/annurev.pp.40.060189.001513
  • Jacobsen JV, Beach LR. Control of transcription of α-amylase and rRNA genes in barley aleurone protoplasts by gibberellin and abscisic acid. Nature. 1985;316:275–277.10.1038/316275a0
  • Bethke PC, Schuurink R, Jones RL. Hormonal signalling in cereal aleurone. J. Exp. Bot. 1997;48:1337–1356.10.1093/jxb/48.7.1337
  • Chen PW, Chiang CM, Tseng TH, Yu SM. Interaction between rice MYBGA and the gibberellin response element controls tissue-specific sugar sensitivity of α-amylase genes. Plant Cell. 2006;18:2326–2340.10.1105/tpc.105.038844
  • Mitsui T, Itoh K. The α-amylase multigene family. Trends Plant Sci. 1997;2:255–261.10.1016/S1360-1385(97)86347-9
  • Mitsui T, Yamaguchi J, Akazawa T. Physicochemical and serological characterization of rice α-amylase isoforms and identification of their corresponding genes. Plant Physiol. 1996;110:1395–1404.10.1104/pp.110.4.1395
  • Nanjo Y, Asatsuma S, Itoh K, Hori H, Mitsui T. Proteomic identification of α-amylase isoforms encoded by RAmy3B/3C from germinating rice seeds. Biosci. Biotechnol. Biochem. 2004;68:112–118.10.1271/bbb.68.112
  • Nanjo Y, Asatsuma S, Itoh K, Hori H, Mitsui T, Fujisawa Y. Posttranscriptional regulation of α-amylase II-4 expression by gibberellin in germinating rice seeds. Plant Physiol. Biochem. 2004;42:477–484.10.1016/j.plaphy.2004.04.005
  • Asatsuma S, Sawada C, Itoh K, Okito M, Kitajima A, Mitsui T. Involvement of α-amylase I-1 in starch degradation in rice chloroplasts. Plant Cell Physiol. 2005;46:858–869.10.1093/pcp/pci091
  • Asatsuma S, Sawada C, Kitajima A, Asakura T, Mitsui T. α-Amylase affects starch accumulation in rice grains. J. Appl. Glycosci. 2006;53:187–192.10.5458/jag.53.187
  • Hakata M, Kuroda M, Miyashita T, Yamaguchi T, Kojima M, Sakakibara H, Mitsui T, Yamakawa H. Suppression of α-amylase genes improves quality of rice grain ripened under high temperature. Plant Biotechnol. J. 10:1110–1117.
  • O’Neill SD, Kumagai MH, Majumdar A, Huang N, Sutliff TD, Rodriguez RL. The α-amylase genes in Oryza sativa: Characterization of cDNA clones and mRNA expression during seed germination. Mol. Gen. Genet. 1990;221:235–244.
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc. Nat. Acad. Sci. 1977;74:5463–5467.10.1073/pnas.74.12.5463
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970;227:680–685.10.1038/227680a0
  • Smith PK, Krohn RI, Hermanson GT, Mallia AK, Gartner FH, et al. Measurement of protein using bicinchoninic acid. Anal. Biochem. 1985;150:76–85.10.1016/0003-2697(85)90442-7
  • Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–326.10.1016/S0076-6879(97)76066-X
  • Vagin A, Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 1997;30:1022–1025.10.1107/S0021889897006766
  • Collaborative Computational Project. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D. 1994;50:760–763.
  • Kadziola A, Søgaard M, Svensson B, Haser R. Molecular structure of a barley α-amylase-inhibitor complex: implications for starch binding and catalysis. J. Mol. Biol. 1998;278:205–217.10.1006/jmbi.1998.1683
  • Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. 2004;60:2126–2132.10.1107/S0907444904019158
  • Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D. 1997;53:240–255.10.1107/S0907444996012255
  • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A. 1976;32:922–923.10.1107/S0567739476001873
  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993;26:283–291.10.1107/S0021889892009944
  • DeLano WL. The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific LLC; 2004.
  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242.10.1093/nar/28.1.235
  • Terashima M, Kubo A, Suzawa M, Itoh Y, Katoh S. The roles of the N-linked carbohydrate chain of rice α-amylase in thermostability and enzyme kinetics. Eur. J. Biochem. 1994;226:249–254.10.1111/ejb.1994.226.issue-1
  • Luzzati V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallogr. 1952;5:802–810.10.1107/S0365110X52002161
  • Sibanda BL, Thornton JM. β-Hairpin families in globular proteins. Nature. 1985;316:170–174.10.1038/316170a0
  • Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 1993;233:123–138.10.1006/jmbi.1993.1489
  • Robert X, Haser R, Gottschalk TE, Ratajczak F, Driguez H, Svensson B, Aghajari N. The structure of barley α-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs. Structure. 2003;11:973–984.10.1016/S0969-2126(03)00151-5
  • Gilles C, Astier JP, Marchis-Mouren G, Cambillau C, Payan F. Crystal structure of pig pancreatic α-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose. Eur. J. Biochem. 1996;238:561–569.10.1111/ejb.1996.238.issue-2
  • Kuriki T, Imanaka T. The concept of the α-amylase family: structural similarity and common catalytic mechanism. J. Biosci. Bioeng. 1999;87:557–565.10.1016/S1389-1723(99)80114-5
  • Nielsen MM, Bozonnet S, Seo ES, Mótyán JA, Andersen JM, et al. Two secondary carbohydrate binding sites on the surface of barley α-amylase 1 have distinct functions and display synergy in hydrolysis of starch granules. Biochemistry. 2009;48:7686–7697.10.1021/bi900795a
  • Kitajima A, Asatsuma S, Okada H, Hamada Y, Kaneko K, et al. The rice α-amylase glycoprotein is targeted from the Golgi apparatus through the secretory pathway to the plastids. Plant Cell. 2009;21:2844–2858.10.1105/tpc.109.068288

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