Einzeltreffer — DigiBib

Glycoside hydrolase (GH) 30 family xylanases are enzymes of biotechnological interest due to their capacity to degrade recalcitrant hemicelluloses, such as glucuronoxylan (GX). This study focuses on a subfamily 7 GH30, TtXyn30A from Thermothelomyces thermophilus, which acts on GX in an "endo" and "exo" mode, releasing methyl-glucuronic acid branched xylooligosaccharides (XOs) and xylobiose, respectively. The crystal structure of inactive TtXyn30A in complex with 2 3 -(4-O-methyl-α-D-glucuronosyl)-xylotriose (UXX), along with biochemical analyses, corroborate the implication of E233, previously identified as alternative catalytic residue, in the hydrolysis of decorated xylan. At the -1 subsite, the xylose adopts a distorted conformation, indicative of the Michaelis complex of TtXyn30AEE with UXX trapped in the semi-functional active site. The most significant structural rearrangements upon substrate binding are observed at residues W127 and E233. The structures with neutral XOs, representing the "exo" function, clearly show the nonspecific binding at aglycon subsites, contrary to glycon sites, where the xylose molecules are accommodated via multiple interactions. Last, an unproductive ligand binding site is found at the interface between the catalytic and the secondary β-domain which is present in all GH30 enzymes. These findings improve current understanding of the mechanism of bifunctional GH30s, with potential applications in the field of enzyme engineering.

Titel:	Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan.
Autor/in / Beteiligte Person:	Pentari, C ; Kosinas, C ; Nikolaivits, E ; Dimarogona, M ; Topakas, E
Link:	Full Text Finder (Volltext)
Zeitschrift:	Biotechnology and bioengineering, Jg. 121 (2024-07-01), Heft 7, S. 2067-2078
Veröffentlichung:	<2005->: Hoboken, NJ : Wiley ; <i>Original Publication</i>: New York, Wiley., 2024
Medientyp:	academicJournal
ISSN:	1097-0290 (electronic)
DOI:	10.1002/bit.28731
Schlagwort:	Crystallography, X-Ray Models, Molecular Protein Conformation Glycoside Hydrolases chemistry Glycoside Hydrolases metabolism Glycoside Hydrolases genetics Sordariales enzymology Sordariales genetics Catalytic Domain Eurotiales enzymology Substrate Specificity Endo-1,4-beta Xylanases chemistry Endo-1,4-beta Xylanases metabolism Endo-1,4-beta Xylanases genetics Xylans metabolism Xylans chemistry
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article Language: English [Biotechnol Bioeng] 2024 Jul; Vol. 121 (7), pp. 2067-2078. <i>Date of Electronic Publication: </i>2024 Apr 28. MeSH Terms: Xylans* / metabolism ; Xylans* / chemistry ; Crystallography, X-Ray ; Models, Molecular ; Protein Conformation ; Glycoside Hydrolases / chemistry ; Glycoside Hydrolases / metabolism ; Glycoside Hydrolases / genetics ; Sordariales / enzymology ; Sordariales / genetics ; Catalytic Domain ; Eurotiales / enzymology ; Substrate Specificity ; Endo-1,4-beta Xylanases / chemistry ; Endo-1,4-beta Xylanases / metabolism ; Endo-1,4-beta Xylanases / genetics References: Agirre, J., Iglesias‐Fernández, J., Rovira, C., Davies, G. J., Wilson, K. S., & Cowtan, K. D. (2015). Privateer: Software for the conformational validation of carbohydrate structures. Nature Structural & Molecular Biology, 22(11), 833–834. https://doi.org/10.1038/nsmb.3115. ; Albenne, C., Skov, L. K., Tran, V., Gajhede, M., Monsan, P., Remaud‐Siméon, M., & André‐Leroux, G. (2007). Towards the molecular understanding of glycogen elongation by amylosucrase. Proteins: Structure, Function, and Bioinformatics, 66(1), 118–126. https://doi.org/10.1002/prot.21083. ; Alvarez, T. M., Paiva, J. H., Ruiz, D. M., Cairo, J. P. L. F., Pereira, I. O., Paixão, D. A. A., de Almeida, R. F., Tonoli, C. C. C., Ruller, R., Santos, C. R., Squina, F. M., & Murakami, M. T. (2013). Structure and function of a novel cellulase 5 from sugarcane soil metagenome. PLoS One, 8(12), e83635. https://doi.org/10.1371/journal.pone.0083635. ; Biely, P., Singh, S., & Puchart, V. (2018). Towards enzymatic breakdown of complex plant xylan structures: State of the art. Biotechnology Advances, 34(7), 1260–1274. https://doi.org/10.1016/j.biotechadv.2016.09.001. ; Bilyard, M. K., Bailey, H. J., Raich, L., Gafitescu, M. A., Machida, T., Iglésias‐Fernández, J., Lee, S. S., Spicer, C. D., Rovira, C., Yue, W. W., & Davis, B. G. (2018). Palladium‐mediated enzyme activation suggests multiphase initiation of glycogenesis. Nature, 563(7730), 235–240. https://doi.org/10.1038/s41586-018-0644-7. ; Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: All‐atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D: Biological Crystallography, 66(1), 12–21. https://doi.org/10.1107/S0907444909042073. ; Crooks, C., Bechle, N. J., & St John, F. J. (2021). A new subfamily of glycoside hydrolase family 30 with strict xylobiohydrolase function. Frontiers in Molecular Biosciences, 8(September), 714238. https://doi.org/10.3389/fmolb.2021.714238. ; Cuyvers, S., Dornez, E., Delcour, J. A., & Courtin, C. M. (2012). Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases. Critical Reviews in Biotechnology, 32(2), 93–107. https://doi.org/10.3109/07388551.2011.561537. ; Drula, E., Garron, M. L., Dogan, S., Lombard, V., Henrissat, B., & Terrapon, N. (2022). The carbohydrate‐active enzyme database: Functions and literature. Nucleic Acids Research, 50(D1), D571–D577. https://doi.org/10.1093/nar/gkab1045. ; Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010). Features and development of Coot. Acta Crystallographica. Section D: Biological Crystallography, 66(4), 486–501. https://doi.org/10.1107/S0907444910007493. ; Evans, P. R., & Murshudov, G. N. (2013). How good are my data and what is the resolution? Acta Crystallographica. Section D: Biological Crystallography, 69(7), 1204–1214. https://doi.org/10.1107/S0907444913000061. ; Fushinobu, S., Ito, K., Konno, M., Wakagi, T., & Matsuzawa, H. (1998). Crystallographic and mutational analyses of an extremely acidophilic and acid‐stable xylanase: Biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Protein Engineering, Design and Selection, 11(12), 1121–1128. https://doi.org/10.1093/protein/11.12.1121. ; Guidi, C., Biarnés, X., Planas, A., & De Mey, M. (2023). Controlled processivity in glycosyltransferases: A way to expand the enzymatic toolbox. Biotechnology Advances, 63, 108081. https://doi.org/10.1016/j.biotechadv.2022.108081. ; Ho, A. L., Kosik, O., Lovegrove, A., Charalampopoulos, D., & Rastall, R. A. (2018). In vitro fermentability of xylo‐oligosaccharide and xylo‐polysaccharide fractions with different molecular weights by human faecal bacteria. Carbohydrate Polymers, 179, 50–58. https://doi.org/10.1016/j.carbpol.2017.08.077. ; Kabsch, W. (2010). XDS. Acta Crystallographica. Section D: Biological Crystallography, 66(2), 125–132. https://doi.org/10.1107/S0907444909047337. ; Katsimpouras, C., Dedes, G., Thomaidis, N. S., & Topakas, E. (2019). A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity. Biotechnology for Biofuels, 12(1), 120. https://doi.org/10.1186/s13068-019-1455-2. ; Krissinel, E., & Henrick, K. (2004). Secondary‐structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica. Section D: Biological Crystallography, 60(12), 2256–2268. https://doi.org/10.1107/S0907444904026460. ; Larson, S. B., Day, J. S., & McPherson, A. (2010). X‐ray crystallographic analyses of pig pancreatic α‐Amylase with limit dextrin, oligosaccharide, and α‐Cyclodextrin. Biochemistry, 49(14), 3101–3115. https://doi.org/10.1021/bi902183w. ; Li, X., Dilokpimol, A., Kabel, M. A., & de Vries, R. P. (2022). Fungal xylanolytic enzymes: Diversity and applications. Bioresource Technology, 344(PB), 126290. https://doi.org/10.1016/j.biortech.2021.126290. ; Li, X., Kouzounis, D., Kabel, M. A., de Vries, R. P., & Dilokpimol, A. (2022). Glycoside Hydrolase family 30 harbors fungal subfamilies with distinct polysaccharide specificities. New Biotechnology, 67(April 2021), 32–41. https://doi.org/10.1016/j.nbt.2021.12.004. ; Linares‐Pasten, J. A., Aronsson, A., & Karlsson, E. N. (2017). Structural considerations on the use of Endo‐Xylanases for the production of prebiotic xylooligosaccharides from biomass. Current Protein & Peptide Science, 19(1), 48–67. https://doi.org/10.2174/1389203717666160923155209. ; Lv, T., Feng, J., Jia, X., Wang, C., Li, F., Peng, H., Xiao, Y., Liu, L., & He, C. (2024). Structural insights into curdlan degradation via a glycoside hydrolase containing a disruptive carbohydrate‐binding module. Biotechnology for Biofuels and Bioproducts, 17(1), 45. https://doi.org/10.1186/s13068-024-02494-5. ; Mazurkewich, S., Poulsen, J. C. N., Lo Leggio, L., & Larsbrink, J. (2019). Structural and biochemical studies of the glucuronoyl esterase OtCE15A illuminate its interaction with lignocellulosic components. Journal of Biological Chemistry, 294(52), 19978–19987. https://doi.org/10.1074/jbc.RA119.011435. ; McCoy, A. J., Grosse‐Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007). Phaser crystallographic software. Journal of Applied Crystallography, 40(4), 658–674. https://doi.org/10.1107/S0021889807021206. ; Mewis, K., Lenfant, N., Lombard, V., & Henrissat, B. (2016). Dividing the large glycoside hydrolase family 43 into subfamilies: A motivation for detailed enzyme characterization. Applied and Environmental Microbiology, 82(6), 1686–1692. https://doi.org/10.1128/AEM.03453-15. ; Morais, M. A. B., Coines, J., Domingues, M. N., Pirolla, R. A. S., Tonoli, C. C. C., Santos, C. R., Correa, J. B. L., Gozzo, F. C., Rovira, C., & Murakami, M. T. (2021). Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X‐ray and QM/MM simulations. Nature Communications, 12(1), 367. https://doi.org/10.1038/s41467-020-20620-3. ; Morais, M. A. B., Nin‐Hill, A., & Rovira, C. (2023). Glycosidase mechanisms: Sugar conformations and reactivity in endo‐ and exo‐acting enzymes. Current Opinion in Chemical Biology, 74, 102282. https://doi.org/10.1016/j.cbpa.2023.102282. ; Mueller, U., Förster, R., Hellmig, M., Huschmann, F. U., Kastner, A., Malecki, P., Pühringer, S., Röwer, M., Sparta, K., Steffien, M., Ühlein, M., Wilk, P., & Weiss, M. S. (2015). The macromolecular crystallography beamlines at BESSY II of the Helmholtz‐Zentrum Berlin: Current status and perspectives. The European Physical Journal Plus, 130(7), 141. https://doi.org/10.1140/epjp/i2015-15141-2. ; Murshudov, G. N., Vagin, A. A., & Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum‐likelihood method. Acta Crystallographica. Section D: Biological Crystallography, 53(3), 240–255. https://doi.org/10.1107/S0907444996012255. ; Nakamichi, Y., Fouquet, T., Ito, S., Matsushika, A., & Inoue, H. (2019). Mode of action of GH30‐7 Reducing‐End Xylose‐Releasing exoxylanase A (Xyn30A) from the filamentous fungus talaromyces cellulolyticus. Applied and Environmental Microbiology, 85(13), 1–17. https://doi.org/10.1128/AEM.00552-19. ; Nakamichi, Y., Fouquet, T., Ito, S., Watanabe, M., Matsushika, A., & Inoue, H. (2019). Structural and functional characterization of a bifunctional GH30‐7 xylanase B from the filamentous fungus Talaromyces cellulolyticus. Journal of Biological Chemistry, 294(11), 4065–4078. https://doi.org/10.1074/jbc.RA118.007207. ; Nakamichi, Y., Watanabe, M., Fujii, T., Inoue, H., & Morita, T. (2023). Crystal structure of reducing‐end xylose‐releasing exoxylanase in subfamily 7 of glycoside hydrolase family 30. Proteins: Structure, Function, and Bioinformatics, 91(9), 1341–1350. https://doi.org/10.1002/prot.26505. ; Nakamichi, Y., Watanabe, M., Matsushika, A., & Inoue, H. (2020). Substrate recognition by a bifunctional GH30‐7 xylanase B from Talaromyces cellulolyticus. FEBS Open Bio, 10(6), 1180–1189. https://doi.org/10.1002/2211-5463.12873. ; Nikolaivits, E., Pentari, C., Kosinas, C., Feiler, C. G., Spiliopoulou, M., Weiss, M. S., Dimarogona, M., & Topakas, E. (2021). Unique features of the bifunctional GH30 from Thermothelomyces thermophila revealed by structural and mutational studies. Carbohydrate Polymers, 273(August), 118553. https://doi.org/10.1016/j.carbpol.2021.118553. ; Nordberg Karlsson, E., Schmitz, E., Linares‐Pastén, J. A., & Adlercreutz, P. (2018). Endo‐xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties. Applied Microbiology and Biotechnology, 102(21), 9081–9088. https://doi.org/10.1007/s00253-018-9343-4. ; Pentari, C., Zerva, A., Dimarogona, M., & Topakas, E. (2023). The xylobiohydrolase activity of a GH30 xylanase on natively acetylated xylan may hold the key for the degradation of recalcitrant xylan. Carbohydrate Polymers, 305, 120527. https://doi.org/10.1016/j.carbpol.2022.120527. ; Pentari, C., Zerva, A., Kosinas, C., Karampa, P., Puchart, V., Dimarogona, M., & Topakas, E. (2024). The role of CE16 exo‐deacetylases in hemicellulolytic enzyme mixtures revealed by the biochemical and structural study of the novel TtCE16B esterase. Carbohydrate Polymers, 327(December 2023), 121667. https://doi.org/10.1016/j.carbpol.2023.121667. ; Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera?A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084. ; Puchart, V., Šuchová, K., & Biely, P. (2021). Xylanases of glycoside hydrolase family 30—An overview. Biotechnology Advances, 47(February), 107704. https://doi.org/10.1016/j.biotechadv.2021.107704. ; Rogowski, A., Baslé, A., Farinas, C. S., Solovyova, A., Mortimer, J. C., Dupree, P., Gilbert, H. J., & Bolam, D. N. (2014). Evidence that GH115 α‐Glucuronidase activity, which is required to degrade plant biomass, is dependent on conformational flexibility. Journal of Biological Chemistry, 289(1), 53–64. https://doi.org/10.1074/jbc.M113.525295. ; Sagong, H.‐Y., Kim, S., Lee, D., Hong, H., Lee, S. H., Seo, H., & Kim, K.‐J. (2022). Structural and functional characterization of an auxiliary domain‐containing PET hydrolase from Burkholderiales bacterium. Journal of Hazardous Materials, 429, 128267. https://doi.org/10.1016/j.jhazmat.2022.128267. ; Southall, S. M., Simpson, P. J., Gilbert, H. J., Williamson, G., & Williamson, M. P. (1999). The starch‐binding domain from glucoamylase disrupts the structure of starch. FEBS Letters, 447(1), 58–60. https://doi.org/10.1016/S0014-5793(99)00263-X. ; St John, F. J., Crooks, C., Kim, Y., Tan, K., & Joachimiak, A. (2022). The first crystal structure of a xylobiose‐bound xylobiohydrolase with high functional specificity from the bacterial glycoside hydrolase family 30, subfamily 10. FEBS Letters, 596(18), 2449–2464. https://doi.org/10.1002/1873-3468.14454. ; St John, F. J., Hurlbert, J. C., Rice, J. D., Preston, J. F., & Pozharski, E. (2011). Ligand bound structures of a glycosyl hydrolase family 30 glucuronoxylan xylanohydrolase. Journal of Molecular Biology, 407(1), 92–109. https://doi.org/10.1016/j.jmb.2011.01.010. ; Tenkanen, M., Vršanská, M., Siika‐aho, M., Wong, D. W., Puchart, V., Penttilä, M., Saloheimo, M., & Biely, P. (2013). Xylanase XYN IV from trichoderma reesei showing exo‐ and endo‐xylanase activity. The FEBS journal, 280(1), 285–301. https://doi.org/10.1111/febs.12069. ; Vandermarliere, E., Bourgois, T. M., Rombouts, S., van Campenhout, S., Volckaert, G., Strelkov, S. V., Delcour, J. A., Rabijns, A., & Courtin, C. M. (2008). Crystallographic analysis shows substrate binding at the −3 to +1 active‐site subsites and at the surface of glycoside hydrolase family 11 endo‐1,4‐β‐xylanases. Biochemical Journal, 410(1), 71–79. https://doi.org/10.1042/BJ20071128. ; Ye, Z. (2004). Two additional carbohydrate‐binding sites of β‐amylase from bacillus cereus var. mycoides are involved in hydrolysis and raw starch‐binding. Journal of Biochemistry, 135(3), 355–363. https://doi.org/10.1093/jb/mvh043. ; Zerva, A., Pentari, C., Grisel, S., Berrin, J.‐G., & Topakas, E. (2020). A new synergistic relationship between xylan‐active LPMO and xylobiohydrolase to tackle recalcitrant xylan. Biotechnology for Biofuels, 13(1), 142. https://doi.org/10.1186/s13068-020-01777-x. ; Šuchová, K., Chyba, A., Hegyi, Z., Rebroš, M., & Puchart, V. (2022). Yeast GH30 xylanase from sugiyamaella lignohabitans is a glucuronoxylanase with auxiliary xylobiohydrolase activity. Molecules, 27(3), 751. https://doi.org/10.3390/molecules27030751. ; Šuchová, K., Puchart, V., Spodsberg, N., Mørkeberg Krogh, K. B. R., & Biely, P. (2020). A novel GH30 xylobiohydrolase from Acremonium alcalophilum releasing xylobiose from the non‐reducing end. Enzyme and Microbial Technology, 134, 109484. https://doi.org/10.1016/j.enzmictec.2019.109484. ; Šuchová, K., Puchart, V., Spodsberg, N., Mørkeberg Krogh, K. B. R., & Biely, P. (2021). Catalytic diversity of GH30 xylanases. Molecules, 26(15), 4528. https://doi.org/10.3390/molecules26154528. Grant Information: 20209 Horizon 2020; 81074 Research Committee of the University of Patras; 00328 Hellenic Foundation for Research and Innovation (HFRI) Contributed Indexing: Keywords: GH30; bifunctional enzyme; crystal structure; glucuronoxylan; xylobiose Substance Nomenclature: 0 (Xylans) ; 37317-38-7 (glucuronoxylan) ; EC 3.2.1.- (Glycoside Hydrolases) ; EC 3.2.1.8 (Endo-1,4-beta Xylanases) SCR Organism: Thermothelomyces thermophilus Entry Date(s): Date Created: 20240428 Date Completed: 20240612 Latest Revision: 20240625 Update Code: 20240625

Klicken Sie ein Format an und speichern Sie dann die Daten oder geben Sie eine Empfänger-Adresse ein und lassen Sie sich per Email zusenden.

BibTeX Citavi, JabRef, u.a.
(Literaturverwaltung)

PDF kein Volltext!
(Merkzettel, Notizen)

RIS Endnote, Citavi u.a.
(Literaturverwaltung)

MODS
(XML zur Weiterverarbeitung)

oder

Wählen Sie das für Sie passende Zitationsformat und kopieren Sie es dann in die Zwischenablage, lassen es sich per Mail zusenden oder speichern es als PDF-Datei.

Gewünschter Zitations-Stil:

oder

Bitte prüfen Sie, ob die Zitation formal korrekt ist, bevor Sie sie in einer Arbeit verwenden. Benutzen Sie gegebenenfalls den "Exportieren"-Dialog, wenn Sie ein Literaturverwaltungsprogramm verwenden und die Zitat-Angaben selbst formatieren wollen.

Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan.