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Crystal structures of a mutant maltotetraose-forming exo-amylase cocrystallized with maltopentaose.

Yoshioka Y, Hasegawa K, Matsuura Y, Katsube Y, Kubota M
J Mol Biol 271 619-28 (1997)
Related entries: 1jda, 1jdc, 2amg

Cited: 21 times
EuropePMC logo PMID: 9281429

Abstract

The three-dimensional structures of the catalytic residue Glu219-->Gln mutant of Pseudomonas stutzeri maltotetraose-forming exo-alpha-amylase, and its complex with carbohydrate obtained by cocrystallization with maltopentaose were determined. Two crystal forms were obtained for the complexed enzyme, and a bound maltotetraose was found in each. The structures were analyzed at 2.2 A and 1.9 A resolution, respectively for the uncomplexed and complexed mutant. These structures were compared with the wild-type enzyme structure. In the complexed crystals, the maltotetraose was firmly bound, extensively interacting with the amino acid environments in the active cleft. The non-reducing end glucose unit was hydrogen bonded to the side-chain of Asp160 and the main-chain nitrogen of Gly158, which seem to be predominantly required for the recognition of the non-reducing end of the substrate that determines the exo-wise degradation of this enzyme. The reducing end glucose unit of bound maltotetraose showed clear deformation, adopting a half-chair conformation with extensive hydrogen bonds to surrounding polypeptides. The C1-atom of this deformed glucose unit lies very close to Asp193OD1 with a distance of 2.6 A. The catalytic residue Asp294 is firmly hydrogen-bonded to the O2 and O3-hydroxyl groups of the deformed reducing end glucose unit. Upon binding of the carbohydrate, small but significant induced fits were observed in the regions of Asp294, Phe156, Ile157, and Asp160. Possible roles of the three catalytic residues are also discussed.

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  1. Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. MacGregor EA, Janecek S, Svensson B. Biochim Biophys Acta 1546 1-20 (2001)
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  1. Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution. Katsuya Y, Mezaki Y, Kubota M, Matsuura Y. J Mol Biol 281 885-897 (1998)
  2. Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase. Hondoh H, Kuriki T, Matsuura Y. J Mol Biol 326 177-188 (2003)
  3. Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose. Fujimoto Z, Takase K, Doui N, Momma M, Matsumoto T, Mizuno H. J Mol Biol 277 393-407 (1998)
  4. Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM. Mol Microbiol 95 209-230 (2015)
  5. Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: implications for substrate specificity and catalysis. Roujeinikova A, Raasch C, Sedelnikova S, Liebl W, Rice DW. J Mol Biol 321 149-162 (2002)
  6. Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism. Golubev AM, Nagem RA, Brandão Neto JR, Neustroev KN, Eneyskaya EV, Kulminskaya AA, Shabalin KA, Savel'ev AN, Polikarpov I. J Mol Biol 339 413-422 (2004)
  7. Substrate recognition mechanism of alpha-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans. Hondoh H, Saburi W, Mori H, Okuyama M, Nakada T, Matsuura Y, Kimura A. J Mol Biol 378 913-922 (2008)
  8. Crystal structure of glycosyltrehalose trehalohydrolase from the hyperthermophilic archaeum Sulfolobus solfataricus. Feese MD, Kato Y, Tamada T, Kato M, Komeda T, Miura Y, Hirose M, Hondo K, Kobayashi K, Kuroki R. J Mol Biol 301 451-464 (2000)
  9. Analysis of the key active subsites of glycoside hydrolase 13 family members. Kumar V. Carbohydr Res 345 893-898 (2010)
  10. Roles of catalytic residues in alpha-amylases as evidenced by the structures of the product-complexed mutants of a maltotetraose-forming amylase. Hasegawa K, Kubota M, Matsuura Y. Protein Eng 12 819-824 (1999)
  11. Crystal structure of the pig pancreatic alpha-amylase complexed with malto-oligosaccharides. Payan F, Qian M. J Protein Chem 22 275-284 (2003)
  12. Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity. Mori H, Bak-Jensen KS, Svensson B. Eur J Biochem 269 5377-5390 (2002)
  13. The crystal structure of Thermotoga maritima maltosyltransferase and its implications for the molecular basis of the novel transfer specificity. Roujeinikova A, Raasch C, Burke J, Baker PJ, Liebl W, Rice DW. J Mol Biol 312 119-131 (2001)
  14. A canonical EF-loop directs Ca(2+) -sensitivity in phospholipase C-η2. Popovics P, Lu J, Nadia Kamil L, Morgan K, Millar RP, Schmid R, Blindauer CA, Stewart AJ. J Cell Biochem 115 557-565 (2014)
  15. Bacillus licheniformis trehalose-6-phosphate hydrolase structures suggest keys to substrate specificity. Lin MG, Chi MC, Naveen V, Li YC, Lin LL, Hsiao CD. Acta Crystallogr D Struct Biol 72 59-70 (2016)
  16. DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of alpha-maltotetraose. Schnupf U, Willett JL, Bosma W, Momany FA. Carbohydr Res 344 362-373 (2009)
  17. Enhanced Yield of Bioactivities from Onion (Allium cepa L.) Skin and Their Antioxidant and Anti-α-Amylase Activities. Gois Ruivo da Silva M, Skrt M, Komes D, Poklar Ulrih N, Pogačnik L. Int J Mol Sci 21 (2020)
  18. DFT conformation and energies of amylose fragments at atomic resolution. Part 2: 'Band-flip' and 'kink' forms of alpha-maltotetraose. Schnupf U, Willett JL, Momany FA. Carbohydr Res 344 374-383 (2009)


Related citations provided by authors (1)

  1. Crystal structure of a maltotetraose-forming exo-amylase from Pseudomonas stutzeri.. Morishita Y, Hasegawa K, Matsuura Y, Katsube Y, Kubota M, Sakai S J Mol Biol 267 661-72 (1997)

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