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Crystal structure of Aspergillus niger isopullulanase, a member of glycoside hydrolase family 49.

Mizuno M, Koide A, Yamamura A, Akeboshi H, Yoshida H, Kamitori S, Sakano Y, Nishikawa A, Tonozuka T
J Mol Biol 376 210-20 (2008)
Related entries: 1wmr, 2z8g

Cited: 9 times
EuropePMC logo PMID: 18155243

Abstract

An isopullulanase (IPU) from Aspergillus niger ATCC9642 hydrolyzes alpha-1,4-glucosidic linkages of pullulan to produce isopanose. Although IPU does not hydrolyze dextran, it is classified into glycoside hydrolase family 49 (GH49), major members of which are dextran-hydrolyzing enzymes. IPU is highly glycosylated, making it difficult to obtain its crystal. We used endoglycosidase H(f) to cleave the N-linked oligosaccharides of IPU, and we here determined the unliganded and isopanose-complexed forms of IPU, both solved at 1.7-A resolution. IPU is composed of domains N and C joined by a short linker, with electron density maps for 11 or 12 N-acetylglucosamine residues per molecule. Domain N consists of 13 beta-strands and forms a beta-sandwich. Domain C, where the active site is located, forms a right-handed beta-helix, and the lengths of the pitches of each coil of the beta-helix are similar to those of GH49 dextranase and GH28 polygalacturonase. The entire structure of IPU resembles that of a GH49 enzyme, Penicillium minioluteum dextranase (Dex49A), despite a difference in substrate specificity. Compared with the active sites of IPU and Dex49A, the amino acid residues participating in subsites +2 and +3 are not conserved, and the glucose residues of isopanose bound to IPU completely differ in orientation from the corresponding glucose residues of isomaltose bound to Dex49A. The shape of the catalytic cleft characterized by the seventh coil of the beta-helix and a loop from domain N appears to be critical in determining the specificity of IPU for pullulan.

Reviews citing this publication (1)

  1. Characteristics, protein engineering and applications of microbial thermostable pullulanases and pullulan hydrolases. Nisha M, Satyanarayana T. Appl Microbiol Biotechnol 100 5661-5679 (2016)

Articles citing this publication (8)

  1. Mapping the polysaccharide degradation potential of Aspergillus niger. Andersen MR, Giese M, de Vries RP, Nielsen J. BMC Genomics 13 313 (2012)
  2. The atmospheric and room-temperature plasma (ARTP) method on the dextranase activity and structure. Wang X, Lu M, Wang S, Fang Y, Wang D, Ren W, Zhao G. Int J Biol Macromol 70 284-291 (2014)
  3. Heterologous expression and characterization of processing α-glucosidase I from Aspergillus brasiliensis ATCC 9642. Miyazaki T, Matsumoto Y, Matsuda K, Kurakata Y, Matsuo I, Ito Y, Nishikawa A, Tonozuka T. Glycoconj J 28 563-571 (2011)
  4. A glycoside hydrolase family 31 dextranase with high transglucosylation activity from Flavobacterium johnsoniae. Gozu Y, Ishizaki Y, Hosoyama Y, Miyazaki T, Nishikawa A, Tonozuka T. Biosci Biotechnol Biochem 80 1562-1567 (2016)
  5. In vitro and in silico characterization of a novel dextranase from Pochonia chlamydosporia. Sufiate BL, Soares FEF, Moreira SS, Gouveia AS, Cardoso EF, Braga FR, de Araújo JV, de Queiroz JH. 3 Biotech 8 167 (2018)
  6. The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of α-1,3-galactosidic linkages in λ-carrageenan and blood group antigens. McGuire BE, Hettle AG, Vickers C, King DT, Vocadlo DJ, Boraston AB. J Biol Chem 295 18426-18435 (2020)
  7. The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase. Miyazaki T, Yashiro H, Nishikawa A, Tonozuka T. J Biochem 157 225-234 (2015)
  8. Inhibiting S-palmitoylation arrests metastasis by relocating Rap2b from plasma membrane in colorectal cancer. Zhu J, Cao X, Chen Z, Lai B, Xi L, Zhang J, Zhu S, Qi S, Liang Y, Cao F, Zhou B, Song Y, Jiang S, Wang T, Kang X, Kong E. Cell Death Dis 15 675 (2024)


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