{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T17:17:41Z","timestamp":1790875061707,"version":"4.1.0"},"reference-count":45,"publisher":"Portland Press Ltd.","issue":"1","content-domain":{"domain":["portlandpress.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2008,2,15]]},"abstract":"<jats:p>GH 11 (glycoside hydrolase family 11) xylanases are predominant enzymes in the hydrolysis of heteroxylan, an abundant structural polysaccharide in the plant cell wall. To gain more insight into the protein\u2013ligand interactions of the glycone as well as the aglycone subsites of these enzymes, catalytically incompetent mutants of the Bacillus subtilis and Aspergillus niger xylanases were crystallized, soaked with xylo-oligosaccharides and subjected to X-ray analysis. For both xylanases, there was clear density for xylose residues in the \u22121 and \u22122 subsites. In addition, for the B. subtilis xylanase, there was also density for xylose residues in the \u22123 and +1 subsite showing the spanning of the \u22121\/+1 subsites. These results, together with the observation that some residues in the aglycone subsites clearly adopt a different conformation upon substrate binding, allowed us to identify the residues important for substrate binding in the aglycone subsites. In addition to substrate binding in the active site of the enzymes, the existence of an unproductive second ligand-binding site located on the surface of both the B. subtilis and A. niger xylanases was observed. This extra binding site may have a function similar to the separate carbohydrate-binding modules of other glycoside hydrolase families.<\/jats:p>","DOI":"10.1042\/bj20071128","type":"journal-article","created":{"date-parts":[[2008,2,20]],"date-time":"2008-02-20T10:41:44Z","timestamp":1203504104000},"page":"71-79","update-policy":"https:\/\/doi.org\/10.1042\/crossmark_policy","source":"Crossref","is-referenced-by-count":71,"title":["Crystallographic analysis shows substrate binding at the \u22123 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-\u03b2-xylanases"],"prefix":"10.1042","volume":"410","author":[{"given":"Elien","family":"Vandermarliere","sequence":"first","affiliation":[{"name":"Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven, Herestraat 49, O&N II, bus 822, 3000 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tine\u00a0M.","family":"Bourgois","sequence":"additional","affiliation":[{"name":"Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, bus 2462, 3001 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sigrid","family":"Rombouts","sequence":"additional","affiliation":[{"name":"Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, bus 2462, 3001 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"van\u00a0Campenhout","sequence":"additional","affiliation":[{"name":"Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, bus 2462, 3001 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guido","family":"Volckaert","sequence":"additional","affiliation":[{"name":"Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, bus 2462, 3001 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei\u00a0V.","family":"Strelkov","sequence":"additional","affiliation":[{"name":"Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven, Herestraat 49, O&N II, bus 822, 3000 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan\u00a0A.","family":"Delcour","sequence":"additional","affiliation":[{"name":"Laboratory of Food Chemistry and Biochemistry, Department of Molecular and Microbial Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, bus 2463, 3001 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"Rabijns","sequence":"additional","affiliation":[{"name":"Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven, Herestraat 49, O&N II, bus 822, 3000 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe\u00a0M.","family":"Courtin","sequence":"additional","affiliation":[{"name":"Laboratory of Food Chemistry and Biochemistry, Department of Molecular and Microbial Systems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, bus 2463, 3001 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"288","published-online":{"date-parts":[[2008,1,29]]},"reference":[{"key":"2021112213501950800_B1","first-page":"447","article-title":"Hemicelluloses","volume-title":"The Carbohydrates \u2013 Chemistry and Biochemistry","author":"Whistler","year":"1990"},{"key":"2021112213501950800_B2","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/978-94-011-1687-9_8","article-title":"Biodegradation of lignin and hemicelluloses","volume-title":"Biochemistry of Microbial Degradation","author":"Jeffries","year":"1994"},{"key":"2021112213501950800_B3","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/S0014-5793(98)00265-8","article-title":"A scheme for designating enzymes that hydrolyse the polysaccharides in the cell walls of plants","volume":"425","author":"Henrissat","year":"1998","journal-title":"FEBS Lett."},{"key":"2021112213501950800_B4","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1016\/S0969-2126(94)00112-X","article-title":"Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites","volume":"2","author":"Harris","year":"1994","journal-title":"Structure"},{"key":"2021112213501950800_B5","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1002\/j.1460-2075.1994.tb06536.x","article-title":"Three-dimensional structure of endo-1,4-\u03b2-xylanase II from Trichoderma reesei: two conformational states in the active site","volume":"13","author":"T\u00f6rr\u00f6nen","year":"1994","journal-title":"EMBO J."},{"key":"2021112213501950800_B6","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/S0168-1656(97)00096-5","article-title":"Endo-\u03b2-1,4-xylanase families: differences in catalytic properties","volume":"57","author":"Biely","year":"1997","journal-title":"J. Biotechnol."},{"key":"2021112213501950800_B7","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1016\/j.carres.2005.02.031","article-title":"Endoxylanase substrate selectivity determines degradation of wheat water-extractable and water-unextractable arabinoxylan","volume":"340","author":"Moers","year":"2005","journal-title":"Carbohydr. Res."},{"key":"2021112213501950800_B8","doi-asserted-by":"crossref","first-page":"11777","DOI":"10.1074\/jbc.M311947200","article-title":"Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C","volume":"279","author":"Pell","year":"2004","journal-title":"J. Biol. Chem."},{"key":"2021112213501950800_B9","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1042\/bj2880117","article-title":"Site-directed mutagenesis at aspartate and glutamate residues of xylanase from Bacillus pumilis","volume":"288","author":"Ko","year":"1992","journal-title":"Biochem. J."},{"key":"2021112213501950800_B10","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1021\/cr00105a006","article-title":"Catalytic mechanism of enzymic glycosyl transfer","volume":"90","author":"Sinnott","year":"1990","journal-title":"Chem. Rev."},{"key":"2021112213501950800_B11","doi-asserted-by":"crossref","first-page":"5226","DOI":"10.1016\/S0021-9258(19)67776-8","article-title":"Comparison of the periplasmic receptors for L-arabinose, D-glucose\/D-galactose and D-ribose: structural and functional similarity","volume":"266","author":"Vyas","year":"1991","journal-title":"J. Biol. Chem."},{"key":"2021112213501950800_B12","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1042\/bj3210557","article-title":"Nomenclature for sugar-binding subsites in glycosyl hydrolases","volume":"321","author":"Davies","year":"1997","journal-title":"Biochem. J."},{"key":"2021112213501950800_B13","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1006\/jmbi.2000.3722","article-title":"Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase","volume":"299","author":"Joshi","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2021112213501950800_B14","doi-asserted-by":"crossref","first-page":"5346","DOI":"10.1021\/bi982946f","article-title":"Sugar ring distortion in the glycosyl-enzyme intermediate of a family GH 11 xylanase","volume":"38","author":"Sidhu","year":"1999","journal-title":"Biochemistry"},{"key":"2021112213501950800_B15","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1002\/pro.5560030312","article-title":"Mutational and crystallographic analysis of the active site residues of the Bacillus circulans xylanase","volume":"3","author":"Wakarchuk","year":"1994","journal-title":"Protein Sci."},{"key":"2021112213501950800_B16","doi-asserted-by":"crossref","first-page":"9617","DOI":"10.1021\/bi953052n","article-title":"Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei","volume":"35","author":"Havukainen","year":"1996","journal-title":"Biochemistry"},{"key":"2021112213501950800_B17","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1016\/S1074-5521(99)80066-0","article-title":"Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase","volume":"6","author":"Sabini","year":"1999","journal-title":"Chem. Biol."},{"key":"2021112213501950800_B18","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1107\/S0907444901010873","article-title":"Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display 2,5B conformations at the active centre","volume":"57","author":"Sabini","year":"2001","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021112213501950800_B19","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1111\/j.1742-4658.2005.04659.x","article-title":"Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography","volume":"272","author":"J\u00e4nis","year":"2005","journal-title":"FEBS J."},{"key":"2021112213501950800_B20","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1110\/ps.03556104","article-title":"Acidophilic adaptation of family 11 endo-\u03b2-1,4-xylanases: modeling and mutational analysis","volume":"13","author":"De\u00a0Lemos\u00a0Esteves","year":"2004","journal-title":"Protein Sci."},{"key":"2021112213501950800_B21","doi-asserted-by":"crossref","first-page":"13475","DOI":"10.1021\/bi980864l","article-title":"Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies","volume":"37","author":"Gruber","year":"1998","journal-title":"Biochemistry"},{"key":"2021112213501950800_B22","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0168-1656(02)00002-0","article-title":"The endoxylanases from family 11: computer analysis of protein sequences reveals important structural and phylogenetic relationships","volume":"95","author":"Sapag","year":"2002","journal-title":"J. Biotechnol."},{"key":"2021112213501950800_B23","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S0378-1119(03)00454-2","article-title":"Identification of Gal80p-interacting proteins by Saccharomyces cerevisiae whole genome phage display","volume":"307","author":"Hertveldt","year":"2003","journal-title":"Gene"},{"key":"2021112213501950800_B24","doi-asserted-by":"crossref","first-page":"438","DOI":"10.2144\/97223bm13","article-title":"Megaprimer method of PCR-based mutagenesis: the concentration of megaprimer is a critical factor","volume":"22","author":"Smith","year":"1997","journal-title":"BioTechniques"},{"key":"2021112213501950800_B25","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.jbiotec.2004.08.013","article-title":"Functional display of family 11 endoxylanases on the surface of phage M13","volume":"115","author":"Beli\u00ebn","year":"2005","journal-title":"J. Biotechnol."},{"key":"2021112213501950800_B26","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0076-6879(97)76066-X","article-title":"Processing of X-ray diffraction data collected in oscillation mode","volume":"276","author":"Otwinowski","year":"1997","journal-title":"Methods Enzymol."},{"key":"2021112213501950800_B27","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1107\/S0907444994003112","article-title":"The CCP4 suite: programs for protein crystallography","volume":"50","author":"Collaborative Computational Project Number 4","year":"1994","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021112213501950800_B28","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1107\/S0907444905001617","article-title":"Likelihood-enhanced fast translation functions","volume":"61","author":"McCoy","year":"2005","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021112213501950800_B29","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1107\/S0021889897006766","article-title":"Molrep: an automated program for molecular replacement","volume":"30","author":"Vagin","year":"1997","journal-title":"J. Appl. Crystallogr."},{"key":"2021112213501950800_B30","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1006\/jmbi.1996.0556","article-title":"Three-dimensional structure of endo-1,4-\u03b2-xylanase I from Aspergillus niger: molecular basis for its low pH optimum","volume":"263","author":"Krengel","year":"1996","journal-title":"J. Mol. Biol."},{"key":"2021112213501950800_B31","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1107\/S0907444996012255","article-title":"Refinement of molecular structures by the maximum-likelihood method","volume":"53","author":"Murshudov","year":"1997","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021112213501950800_B32","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1107\/S0907444904019158","article-title":"Coot: model-building tools for molecular graphics","volume":"60","author":"Emsley","year":"2004","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021112213501950800_B33","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1107\/S0907444998006684","article-title":"SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with atomic model","volume":"55","author":"Vaguine","year":"1999","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2021112213501950800_B34","doi-asserted-by":"crossref","first-page":"W590","DOI":"10.1093\/nar\/gkh477","article-title":"SuperPose: a simple server for sophisticated structural superposition","volume":"32","author":"Maiti","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2021112213501950800_B35"},{"key":"2021112213501950800_B36","unstructured":"Sansen\n              S.\n            \n          \n          Towards a Better Understanding of Xylanase Inhibition by TAXI-type Proteins: A Crystallographic Study\n          Ph.D. Thesis\n          2005\n          Leuven, Belgium\n          Katholieke Universiteit Leuven"},{"key":"2021112213501950800_B37","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1002\/(SICI)1097-0134(19980601)31:4<434::AID-PROT9>3.0.CO;2-H","article-title":"Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study","volume":"31","author":"Muili","year":"1998","journal-title":"Proteins"},{"key":"2021112213501950800_B38","doi-asserted-by":"crossref","first-page":"44035","DOI":"10.1074\/jbc.M205657200","article-title":"Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger","volume":"277","author":"Tahir","year":"2002","journal-title":"J. Biol. Chem."},{"key":"2021112213501950800_B39","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1021\/bi00003a019","article-title":"Structural comparison of two major endo-1,4-xylanases from Trichoderma reesei","volume":"34","author":"T\u00f6rr\u00f6nen","year":"1995","journal-title":"Biochemistry"},{"key":"2021112213501950800_B40","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1006\/jmbi.1993.1509","article-title":"Crystallization and preliminary X-ray analysis of two major xylanases from Trichodermi reesei","volume":"233","author":"T\u00f6rr\u00f6nen","year":"1993","journal-title":"J. Mol. Biol."},{"key":"2021112213501950800_B41","doi-asserted-by":"crossref","first-page":"90","DOI":"10.3998\/ark.5550190.0007.d10","article-title":"Itineraries of enzymatically and non-enzymatically catalyzed substitutions at O-glycopyranosidic bonds","volume":"13","author":"Nerinckx","year":"2006","journal-title":"ARKIVOC"},{"key":"2021112213501950800_B42","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1007\/s00253-006-0764-0","article-title":"Substrate and product hydrolysis specificity in family 11 glycoside hydrolases: an analysis of Penicillium funiculosum and Penicillium griseofulvum xylanases","volume":"74","author":"Berrin","year":"2006","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"2021112213501950800_B43","doi-asserted-by":"crossref","first-page":"4797","DOI":"10.1021\/bi052193e","article-title":"Oligosaccharide binding in family 8 glycosidases: crystal structures of active site mutants of the \u03b2-1,4-xylanase pXyl from Pseudoalteromonas haloplanktis TAH3a in complex with substrate and product","volume":"45","author":"De\u00a0Vos","year":"2006","journal-title":"Biochemistry"},{"key":"2021112213501950800_B44","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.jmb.2007.07.057","article-title":"A secondary xylan-binding site enhances the catalytic activity of a single-domain family 11 glycoside hydrolase","volume":"373","author":"Ludwiczek","year":"2007","journal-title":"J. Mol. Biol."},{"key":"2021112213501950800_B45","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.enzmictec.2006.12.019","article-title":"Alteration of Bacillus subtilis XynA endoxylanase substrate selectivity by site-directed mutagenesis","volume":"41","author":"Moers","year":"2007","journal-title":"Enzyme Microbiol. Technol."}],"container-title":["Biochemical Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/portlandpress.com\/biochemj\/article-pdf\/410\/1\/71\/652170\/bj4100071.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/portlandpress.com\/biochemj\/article-pdf\/410\/1\/71\/652170\/bj4100071.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,22]],"date-time":"2021-11-22T15:44:16Z","timestamp":1637595856000},"score":1,"resource":{"primary":{"URL":"https:\/\/portlandpress.com\/biochemj\/article\/410\/1\/71\/43496\/Crystallographic-analysis-shows-substrate-binding"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,1,29]]},"references-count":45,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,2,15]]}},"URL":"https:\/\/doi.org\/10.1042\/bj20071128","relation":{},"ISSN":["0264-6021","1470-8728"],"issn-type":[{"value":"0264-6021","type":"print"},{"value":"1470-8728","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,29]]}}}