Bioinformatics Analysis of Oligosaccharide Phosphorylation Effect on the Stabilization of the β-Amylase Ligand Complex

REFERENCES

• Hizukuri , S. 1986 . Polymodal distribution of the chain lengths of amylopectin, and its significance Carbohydr . Res. , 147 : 342 – 347 .
   Google Scholar
• Samojedny , D. and Orzechowski , S . 2007 . New look at starch degradation in Arabidopsis thaliana L. chloroplasts . Post. Biochem. , 53 : 74 – 83 .
   PubMedGoogle Scholar
• Zeeman , S. C. , Delatte , T. , Messerli , G. , Umhang , M. , Stettler , M. , Mettler , T. , Steb , S. , Reinhold , H. and Kötting , O . 2007 . Starch breakdown: recent discoveries suggest distinct pathways and novel mechanisms . Functional Plant Biol. , 34 : 465 – 473 .
   PubMed Web of Science ®Google Scholar
• Tester , R. F. , Karkalas , J. Q.I. and Starch , X. 2004 . structure and digestibility: enzyme-structure relationship . World's Poultry Sci. J. , 60 : 186 – 195 .
   Web of Science ®Google Scholar
• Yu , T. S. , Zeeman , S. C. , Thorneycroft , D. , Fulton , D. C. , Dunstan , H. , Lue , W. L. , Hegemann , B. , Tung , S. Y. , Umemoto , T. , Chapple , A. , Tsai , D. L. , Wang , S. M. , Smith , A. M. , Chen , J. and Smith , S. M. 2005 . Alpha-amylase is not required for breakdown of transitory starch in Arabidopsis leaves . J Biol Chem. , 280 : 9773 – 9779 .
   PubMed Web of Science ®Google Scholar
• Edner , Ch. , Li , J. , Albrecht , T. , Mahlow , S. , Hejazi , M. , Hussain , H. , Kaplan , F. , Guy , Ch. , Smith , S. M. , Steup , M. and Ritte , G. 2007 . Water dikinase activity stimulates breakdown of starch granules by plastidial β -amylases . Plant Physiol. , 145 : 17 – 28 .
   PubMed Web of Science ®Google Scholar
• Ritte , G. , Heydenreich , M. , Mahlow , S. , Haebel , S. , Kotting , O. and Steup , M. 2006 . Phosphorylation of C6- and C3-positions of glucosyl residues in starch is catalysed by distinct dikinases . FEBS Lett. , 580 : 4872 – 4876 .
   Google Scholar
• Blennow , A. , Bay-Smidt , A. M. , Olsen , C. E. and Moller , B. L. 2000 . The distribution of covalently bound phosphate in the starch granule in relation to starch crystallinity . Int J. Biol. Macromol. , 27 : 211 – 218 .
   PubMed Web of Science ®Google Scholar
• Ritte , G. , Scharf , A. , Eckermann , N. , Haebel , S. and Steup , M. 2004 . Phosphorylation of transitory starch is increased during degradation . Plant Physiol. , 135 : 2068 – 2077 .
   PubMed Web of Science ®Google Scholar
• Tabata , S. and Hizukuri , S. 1971 . Studies on starch phosphate . Part 2. Isolation of glucose-3-phosphate and maltose phosphate by acid hydrolysis of potato starch. Starch , 23 : 267 – 272 .
   Google Scholar
• Kötting , O. , Pusch , K. , Tiessen , A. , Geigenberger , P. , Steup , M. and Ritte , G. 2005 . Identification of a novel enzyme required for starch metabolism in Arabidopsis leaves . The phosphoglucan, water dikinase. Plant Physiol. , 137 : 242 – 252 .
   PubMedGoogle Scholar
• Engelsen , S. B. , Madsen , A. , Blennow , A. , Motawia , M. S. , M⊘ller , B. L. and Larsen , S. 2003 . The phosphorylation site in double helical amylopectin as investigated by a combined approach using chemical synthesis, crystallography and molecular modelling . FEBS Lett. , 541 : 137 – 144 .
   Google Scholar
• Kang , Y. N. , Adachi , M. , Utsumi , S. and Mikami , B. 2004 . The roles of Glu186 and Glu380 in the catalytic reaction of soybean β -amylase . J. Mol. Biol. , 339 : 1129 – 1140 .
   Google Scholar
• Thoma , J. A. and Koshland , D. E. 1960 . Competitive inhibition by substrate during enzyme action . Evidence for induced-fit theory. J. Am. Chem. Soc. , 82 : 3329 – 3333 .
   Google Scholar
• Rockey , W. M. , Laederach , A. and Reilly , P. 2000 . Automated docking of alpha-(1→ 4)-and alpha-(1→ 6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site . J. Proteins , 40 : 299 – 309 .
   Google Scholar
• Laederach , A. , Dowd , M. K. , Coutinho , P. M. and Reilly , P. J. 1999 . Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean beta-amylase active site . Proteins , 37 : 166 – 175 .
   Google Scholar
• Adachi , M. , Mikami , B. , Katsube , T. and Utsumi , S. 1998 . Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin . J. Biol. Chem. , 273 : 19859 – 19865 .
   Google Scholar
• Akira , H. , Adachi , M. , Atsushi , S. , Kang , Y. N. , Shigeru , U. and Bunzo , M. 2004 . Structural and enzymatic analysis of soybean β -amylase mutants with increased pH optimum . J. Biol. Chem. , 279 : 7282 – 7295 .
   Google Scholar
• Oyama , T. , Miyake , H. , Kusunoki , M. and Nitta , Y . 2003 . Crystal structures of β -amylase from Bacillus cereus var. mycoides in complexes with substrate analogs and affinity-labeling reagents . J. Biochem. , 133 : 467 – 474 .
   PubMed Web of Science ®Google Scholar
• Ye , Z. , Miyake , H. , Tatsumi , M. , Nishimura , S. and Nitta , Y . 2004 . Two additional carbohydrate-binding sites of β-amylase from Bacillus cereus var. mycoides are involved in hydrolysis and raw starch-binding . J. Biochem. , 135 : 355 – 363 .
   PubMed Web of Science ®Google Scholar
• Pettersen , E. F. , Goddard , T. D. , Huang , C. C. , Couch , G. S. , Greenblatt , D. M. , Meng , E. C. and Ferrin , T. E. 2004 . UCSF chimera - a visualization system for exploratory research and analysis . J. Comput. Chem. , 25 : 1605 – 1612 .
   PubMed Web of Science ®Google Scholar
• Meng , E. C. , Pettersen , E. F. , Couch , G. S. , Huang , C. C. and Ferrin , T. E. 2006 . Tools for integrated sequence-structure analysis with UCSF Chimera . BMC Bioinformatics , 7 : 339
   PubMed Web of Science ®Google Scholar
• Schwede , T. , Diemand , A. , Guex , N. and Peitsch , M. C. 2000 . Protein structure computing in the genomic era . Res. Microbiol. , 151 : 107 – 112 .
   Google Scholar
• Schwede , T. , Kopp , J. , Guex , N. and Peitsch , M. C. 2003 . SWISS-MODEL: an automated protein homology-modeling server . Nucl. Acids Res. , 31 : 3381 – 3385 .
   PubMed Web of Science ®Google Scholar
• Peitsch , M. C. , Schwede , T. and Guex , N. 2000 . Automated protein modelling—the proteome in 3D . Pharmacogenomics , 1 : 257 – 266 .
   Google Scholar
• Moustakas , D. T. , Lang , T. , Pegg , S. , Pettersen , E. , Kuntz , I. D. , Brooijamans , N. and Rizzo , R. C. 2006 . Development and validation of a modular, extensible docking program: DOCK 5 . J. Comput. Aided Mol. Des. , 20 : 601 – 619 .
   PubMed Web of Science ®Google Scholar
• Richards , F. M. 1977 . Areas, volumes, packing, and protein structure . Ann. Rev. Biophys. Bioeng. , 6 : 151 – 176 .
   PubMedGoogle Scholar
• Connolly , M. 1981 . Protein surfaces and interiors , Ph.D. Thesis Berkeley : University of California .
   Google Scholar
• Kuntz , I. D. , Blaney , J. M. , Oatley , S. J. , Langridge , R. and Ferrin , T. E. 1982 . A geometric approach to macromolecule-ligand interactions . J. Mol. Biol. , 161 : 269 – 288 .
   PubMed Web of Science ®Google Scholar
• Viks⊘-Nielsen , A. , Blennow , A. , Nielsen , T. H. and M⊘ller , B. L. 1998 . Phosphorylated α(1,4) glucans as substrate for potato starch-branching enzyme . Plant Physiol. , 117 : 869 – 875 .
   Google Scholar