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Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86

Abstract

Although many xylanases have been studied, many of the characteristics of xylanases toward branches in xylan remain unclear. In this study, the substrate specificity of a GH11 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn11B) was elucidated based on its three-dimensional structure. Subsite mapping suggests that SoXyn11B has seven subsites (four subsites on the – side and three subsites on the + side), and it is one longer than the GH10 xylanase from S. olivaceoviridis (SoXyn10A). SoXyn11B has no affinity for the subsites at either end of the scissile glycosidic bond, and the sugar-binding energy at subsite – 2 was the highest, followed by subsite + 2. These properties were very similar to those of SoXyn10A. In contrast, SoXyn11B produced different branched oligosaccharides from bagasse compared with those of SoXyn10A. These branched oligosaccharides were identified as O-β-D-xylopyranosyl-(1→4)-[O-α-L-arabinofuranosyl-(1→3)]-O-β-D-xylopyranosyl-(1→4)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranose (Ara3Xyl4) and O-β-D-xylopyranosyl-(1→4)-[O-4-O-methyl-α-D-glucuronopyranosyl-(l→2)]-β-D-xylopyranosyl-(1→4)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranose (MeGlcA3Xyl4) by nuclear magnetic resonance (NMR) and electrospray ionization mass spectrometry (ESI-MS) and confirmed by crystal structure analysis of SoXyn11B in complex with these branched xylooligosaccharides. SoXyn11B has a β-jerryroll fold structure, and the catalytic cleft is located on the inner β-sheet of the fold. The ligand-binding structures revealed seven subsites of SoXyn11B. The 2- and 3-hydroxy groups of xylose at the subsites + 3, + 2, and – 3 face outwards, and an arabinose or a glucuronic acid side chain can be linked to these positions. These subsite structures appear to cause the limited substrate specificity of SoXyn11B for branched xylooligosaccharides.

Key points

Crystal structure of family 11 β-xylanase from Streptomyces olivaceoviridis was determined.

• Topology of substrate-binding cleft of family 11 β-xylanase from Streptomyces olivaceoviridis was characterized.

• Mode of action of family 11 β-xylanase from Streptomyces olivaceoviridis for substitutions in xylan was elucidated.

Graphical abstract

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Data availability

Protein structure data dissolved in this study have been deposited in Protein Data Bank (http://www.wwpdb.org) with accession code 7DFM, 7DFN, 7DFO.

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Acknowledgements

The authors wish to thank Mitsui Sugar Co., Ltd. for providing us sugarcane bagasse.

Funding

This study was funded in part by Innovation system construction program of Okinawa Science & Technology promotion Center.

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Authors and Affiliations

Authors

Contributions

SK and ZF conceived and designed research. NK, KT, and ST conducted experiments. SK and ZF analyzed data. SK and ZF wrote the manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to Satoshi Kaneko.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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The authors declare no competing interests.

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Fujimoto, Z., Kishine, N., Teramoto, K. et al. Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86. Appl Microbiol Biotechnol 105, 1943–1952 (2021). https://doi.org/10.1007/s00253-021-11098-0

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  • DOI: https://doi.org/10.1007/s00253-021-11098-0

Keywords

  • Xylan
  • Xylanase
  • Substrate specificity
  • Hydrolysis
  • Substituted xylooligosaccharides