Probing structural determinants specifying high thermostability in Bacillus licheniformis α-amylase 1 1Edited by A. R. Fersht

Aghajari, 1998, Structures of the psychrophilic Alteromonas haloplanctis α-amylase give insights into cold adaptation at a molecular level, Structure, 6, 1503, 10.1016/S0969-2126(98)00149-X Allen, 1998, Stabilization of Aspergillus awamori glucoamylase by proline substitution and combining stabilizing mutations, Protein Eng., 11, 10.1093/protein/11.9.783 Boel, 1990, Calcium binding in α-amylases, Biochemistry, 29, 6244, 10.1021/bi00478a019 Bogin, 1998, Enhanced thermal stability of Clostridium beijerinckii alcohol dehydrogenase after strategic substitution of amino acid residues with prolines from the homologous thermophilic Thermoanaerobacter brockii alcohol dehydrogenase, Protein Sci., 7, 1156, 10.1002/pro.5560070509 Boles, 1995, A rapid and highly efficient method for PCR-based site-directed mutagenesis using only one new primer, Curr. Genet., 28, 197, 10.1007/BF00315788 Bortoli-German, 1995, Informational suppression to investigate structural functional and evolutionary aspects of the Erwinia chrysanthemi cellulase EGZ, J. Mol. Biol., 246, 82, 10.1006/jmbi.1994.0068 Buisson, 1987, Three dimensional structure of porcine pancreatic α-amylase at 2.9 Å resolution. Role of calcium in structure and activity, EMBO J., 6, 3909, 10.1002/j.1460-2075.1987.tb02731.x Capasso, 1996, Deamidation in proteins, J. Mol. Biol., 257, 492, 10.1006/jmbi.1996.0179 Chan, 1995, Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase, Science, 267, 1463, 10.1126/science.7878465 Conrad, 1995, Hybrid Bacillus amyloliquefaciens × Bacillus licheniformis α-amylases. Construction, properties and sequence determinants, Eur. J. Biochem., 230, 481 Danson, 1996, Enzyme thermostability and thermoactivity, Protein Eng., 9, 629, 10.1093/protein/9.8.629 Dao-pin, 1991, Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme, Biochemistry, 30, 11521, 10.1021/bi00113a006 Declerck, 1990, Use of amber suppressors to investigate the thermostability of Bacillus licheniformis α-amylase. Amino acid replacements at 6 histidine residues reveal a critical position at His-133, J. Biol. Chem., 265, 15481, 10.1016/S0021-9258(18)55421-1 Declerck, 1995, Hyperthermostable mutants of Bacillus licheniformis α-amylase, Protein Eng., 8, 1029, 10.1093/protein/8.10.1029 Declerck, 1997, Hyperthermostable mutants of Bacillus licheniformis α-amylase, Protein Eng., 10, 541, 10.1093/protein/10.5.541 Dong, 1997, Cloning, sequencing, and expression of the gene encoding extracellular α-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme, Appl. Environ. Microbiol., 63, 3569, 10.1128/AEM.63.9.3569-3576.1997 Dumas, 1994, Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering, EMBO J., 13, 2483, 10.1002/j.1460-2075.1994.tb06535.x Gray, 1986, Structural genes encoding the thermophilic α-amylases of Bacillus stearothermophilus and Bacillus licheniformis, J. Bacteriol., 166, 635, 10.1128/jb.166.2.635-643.1986 Harris, 1997, Structural basis of the properties of an industrially relevant thermophilic xylanase, Proteins: Struct. Funct. Genet., 29, 77, 10.1002/(SICI)1097-0134(199709)29:1<77::AID-PROT6>3.0.CO;2-C Hendsch, 1994, Do salt bridges stabilize proteins? A continuum electrostatic analysis, Protein Sci., 3, 211, 10.1002/pro.5560030206 Hennig, 1995, 2.0 Å structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus, Structure, 3, 1295, 10.1016/S0969-2126(01)00267-2 Henrissat, 1997, Structural and sequence-based classification of glycoside hydrolases, Curr. Opin. Struct. Biol., 7, 637, 10.1016/S0959-440X(97)80072-3 Hwang, 1997, Crystal structure of thermostable α-amylase from Bacillus licheniformis refined at 1.7 Å resolution, Mol. Cells, 7, 251 Igarashi, 1998, Improved thermostability of a Bacillus α-amylase by deletion of an arginine-glycine residue is caused by enhanced calcium binding, Biochem. Biophys. Res. Commun., 248, 372, 10.1006/bbrc.1998.8970 Janecek, 1993, Does the increased hydrophobicity of the interior and hydrophilicity of the exterior of an enzyme structure reflect its increased thermostability?, Int. J. Biol. Macromol., 15, 317, 10.1016/0141-8130(93)90033-I Janecek, 1992, α-Amylases and approaches leading to their enhanced stability, FEBS Letters, 304, 1, 10.1016/0014-5793(92)80575-2 Jorgensen, 1997, Cloning, sequencing, characterization, and expression of an extracellular α-amylase from the hyperthermophilic archaeon Pyrococcus furiosus in Escherichia coli and Bacillus subtilis, J. Biol. Chem., 272, 16335, 10.1074/jbc.272.26.16335 Joyet, 1992, Hyperthermostable variants of a highly thermostable α-amylase, Biotechnology, 10, 1579, 10.1038/nbt1292-1579 Kleina, 1990, Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors, J. Mol. Biol., 212, 295, 10.1016/0022-2836(90)90126-7 Kleina, 1990, Construction of Escherichia coli amber suppressor tRNA genes. II. Synthesis of additional tRNA genes and improvement of suppressor efficiency, J. Mol. Biol., 213, 705, 10.1016/S0022-2836(05)80257-8 Korndorfer, 1995, The crystal structure of holo- glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 Å resolution, J. Mol. Biol., 246, 511, 10.1006/jmbi.1994.0103 Kunkel, 1985, Rapid and efficient site-specific mutagenesis without phenotypic selection, Proc. Natl Acad. Sci. USA, 82, 488, 10.1073/pnas.82.2.488 Kuroki, 1989, Design and creation of a Ca2+ binding site in human lysozyme to enhance structural stability, Proc. Natl Acad. Sci. USA, 86, 6903, 10.1073/pnas.86.18.6903 Machius, 1995, Crystal structure of calcium-depleted Bacillus licheniformis α-amylase at 2.2 Å resolution, J. Mol. Biol., 246, 545, 10.1006/jmbi.1994.0106 Machius, 1998, 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, 6, 281, 10.1016/S0969-2126(98)00032-X Masson, 1986, Expression of synthetic suppressor tRNA genes under the control of a synthetic promoter, Gene, 47, 179, 10.1016/0378-1119(86)90061-2 Matthews, 1987, Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding, Proc. Natl Acad. Sci. USA, 84, 6663, 10.1073/pnas.84.19.6663 Miller, 1991, Use of nonsense suppression to generate altered proteins, Methods Enzymol., 208, 543, 10.1016/0076-6879(91)08028-G Miller, 1989, Protein engineering with synthetic Escherichia coli amber suppressor genes, Genome, 31, 905, 10.1139/g89-161 Normanly, 1986, Construction of two Escherichia coli amber suppressor genes, Proc. Natl Acad. Sci. USA, 83, 6548, 10.1073/pnas.83.17.6548 Normanly, 1990, Construction of Escherichia coli amber suppressor tRNA genes. III. Determination of tRNA specificity, J. Mol. Biol., 213, 719, 10.1016/S0022-2836(05)80258-X Salminen, 1996, An unusual route to thermostability disclosed by the comparison of Thermus thermophilus and Escherichia coli inorganic pyrophosphatases, Protein Sci., 5, 1014, 10.1002/pro.5560050604 Smith, 1999, Calcium-mediated thermostability in the subtilisin superfamily, J. Mol. Biol., 294, 1027, 10.1006/jmbi.1999.3291 Suckow, 1996, Genetic studies of the Lac repressor. XV. 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure, J. Mol. Biol., 261, 509, 10.1006/jmbi.1996.0479 Suzuki, 1989, Amino acid residues stabilizing a Bacillus α-amylase against irreversible thermoinactivation, J. Biol. Chem., 264, 18933, 10.1016/S0021-9258(19)47247-5 Teplyakov, 1990, Crystal structure of thermitase at 1.4 Å resolution, J. Mol. Biol., 214, 261, 10.1016/0022-2836(90)90160-N Tomazic, 1988, Mechanisms of irreversible thermal inactivation of Bacillus α-amylases, J. Biol. Chem., 263, 3086, 10.1016/S0021-9258(18)69038-6 Tomazic, 1988, Why is one Bacillus α-amylase more resistant against irreversible thermoinactivation than another?, J. Biol. Chem., 263, 3092, 10.1016/S0021-9258(18)69039-8 Vallée, 1959, Metal content of α-amylases of various origins, J. Biol. Chem., 234, 2901, 10.1016/S0021-9258(18)69691-7 Vetriani, 1998, Protein thermostability above 100°C, Proc. Natl Acad. Sci. USA, 95, 12300, 10.1073/pnas.95.21.12300 Vihinen, 1989, Microbial amylytic enzymes, Crit. Rev. Biochem. Mol. Biol., 24, 000, 10.3109/10409238909082556 Wimley, 1996, Direct measurement of salt-bridge solvation energies using a peptide model system, Proc. Natl Acad. Sci. USA, 93, 2985, 10.1073/pnas.93.7.2985 Wright, 1991, Sequence and structure determinants of the nonenzymatic deamidation of asparagine and glutamine residues in proteins, Protein Eng., 4, 283, 10.1093/protein/4.3.283 Yip, 1995, The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures, Structure, 3, 1147, 10.1016/S0969-2126(01)00251-9 Yuuki, 1985, Complete nucleotide sequence of a gene coding for heat- and pH-stable α-amylase of Bacillus licheniformis, J. Biochem., 98, 1147, 10.1093/oxfordjournals.jbchem.a135381