{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:57:07Z","timestamp":1791388627010,"version":"4.3.3"},"reference-count":44,"publisher":"American Chemical Society (ACS)","issue":"39","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100002338","name":"Ministry of Education of the People's Republic of China","doi-asserted-by":"publisher","award":["JYB2025XDXM509"],"award-info":[{"award-number":["JYB2025XDXM509"]}],"id":[{"id":"10.13039\/501100002338","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFC2104500"],"award-info":[{"award-number":["2022YFC2104500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003395","name":"Shanghai Municipal Education Commission","doi-asserted-by":"publisher","award":["23CGA39"],"award-info":[{"award-number":["23CGA39"]}],"id":[{"id":"10.13039\/501100003395","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32301214"],"award-info":[{"award-number":["32301214"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003024","name":"Shanghai Education Development Foundation","doi-asserted-by":"publisher","award":["23CGA3"],"award-info":[{"award-number":["23CGA3"]}],"id":[{"id":"10.13039\/501100003024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Alginate lyases produce alginate oligosaccharides (AOS) whose bioactivities depend on the degree of polymerization (DP). Loop regions and individual residues influence product DP. However, how residues from loops cooperate at subsites to enforce a defined DP remains unresolved. Here, we identified ALG4, a PL7_5 alginate lyase specifically producing trisaccharides (\u0394DP3), and ALG3, a same-subfamily homologue generating \u0394DP2\u2212\u0394DP4 mixtures. Action-pattern analysis showed that ALG4 accommodates three sugar residues at the +1\/+2\/+3 subsites without extension toward +4. Structurally, the Orange Loop and Red Loop converge beyond +3 to form a distal occlusion zone in ALG4, absent in ALG3. Molecular dynamics (MD) simulations and systematic experiments supported a bipartite anchoring mechanism comprising a physical barrier layer (Y112\/E56) and a direct binding layer (R105\/K38) coupled through a hub network. Gain-of-function transplantation of these elements into ALG3 progressively shifted products toward trisaccharides, demonstrating a transferable residue-level design strategy within this homologous enzyme pair.<\/jats:p>","DOI":"10.1021\/acs.jafc.6c10205","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T05:02:15Z","timestamp":1790226135000},"page":"31010-31027","source":"Crossref","is-referenced-by-count":0,"title":["Bipartite Anchoring\nat the +3 Subsite Governs Trisaccharide\nSpecificity in a PL7 Alginate Lyase and Is Transferable to a Homologous\nEnzyme"],"prefix":"10.1021","volume":"74","author":[{"given":"Mengxuan","family":"Zhao","sequence":"first","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiling","family":"Zhang","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengqi","family":"Zhao","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liqiang","family":"Fan","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu","family":"Li","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongjun","family":"Qiu","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Deng","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8523-103X","authenticated-orcid":true,"given":"Liming","family":"Zhao","sequence":"additional","affiliation":[{"name":"East China University of Science and Technology , , ,","place":["Shanghai, China, 200237"]},{"name":"Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) , ,","place":["Shanghai, China, 200237"]},{"name":"East China University of Science and Technology , , 130 Mei Long Road , ,","place":["Shanghai, China, 200237"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,24]]},"reference":[{"issue":"2","key":"2026100711075342500_cit1","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/s41558-024-02238-1","article-title":"Carbon burial in sediments\nbelow seaweed farms matches that of Blue Carbon habitats","volume":"15","author":"Duarte","year":"2025","journal-title":"Nat. Clim. Change"},{"issue":"1","key":"2026100711075342500_cit2","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1038\/s42003-022-03721-1","article-title":"Determination\nof oligosaccharide product distributions\nof PL7 alginate lyases by their structural elements","volume":"5","author":"Zhang","year":"2022","journal-title":"Commun. Biol."},{"issue":"10","key":"2026100711075342500_cit3","doi-asserted-by":"publisher","first-page":"5666","DOI":"10.1021\/acs.jafc.4c09913","article-title":"Molecular engineering\nof alginate lyases and the potential agricultural applications of\ntheir enzymatic products","volume":"73","author":"Ye","year":"2025","journal-title":"J. Agric. 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Polym."},{"key":"2026100711075342500_cit6","doi-asserted-by":"publisher","first-page":"120806","DOI":"10.1016\/j.carbpol.2023.120806","article-title":"Alginate oligosaccharide structures differentially\naffect DSS-induced colitis in mice by modulating gut microbiota","volume":"312","author":"Lu","year":"2023","journal-title":"Carbohydr. Polym."},{"key":"2026100711075342500_cit7","doi-asserted-by":"publisher","first-page":"117124","DOI":"10.1016\/j.carbpol.2020.117124","article-title":"Unsaturated\nmannuronate oligosaccharide ameliorates \u03b2-amyloid pathology\nthrough autophagy in Alzheimer\u2019s disease cell models","volume":"251","author":"Bi","year":"2021","journal-title":"Carbohydr. 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Chem."},{"issue":"25","key":"2026100711075342500_cit17","doi-asserted-by":"publisher","first-page":"7190","DOI":"10.1021\/acs.jafc.1c02473","article-title":"Substrate-binding\nmode and intermediate-product distribution coguided protein design\nof alginate lyase AlyF for altered end-product distribution","volume":"69","author":"Zhang","year":"2021","journal-title":"J. Agric. Food Chem."},{"issue":"8","key":"2026100711075342500_cit18","doi-asserted-by":"publisher","first-page":"110467","DOI":"10.1016\/j.jbc.2025.110467","article-title":"A key loop in the catalytic\npocket of the PL17 family\nof alginate lyases determines minimal substrate recognition","volume":"301","author":"Li","year":"2025","journal-title":"J. Biol. 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Commun."},{"issue":"6","key":"2026100711075342500_cit21","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02399-20","article-title":"Alginate\ndegradation: Insights obtained through\ncharacterization of a thermophilic exolytic alginate lyase","volume":"87","author":"Arntzen","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"issue":"1","key":"2026100711075342500_cit22","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1186\/s13068-019-1600-y","article-title":"Biochemical\ncharacteristics\nand synergistic effect of two novel alginate lyases from Photobacterium sp. FC615","volume":"12","author":"Lu","year":"2019","journal-title":"Biotechnol. Biofuels"},{"key":"2026100711075342500_cit23","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/0008-6215(96)00060-2","article-title":"NMR spectroscopy\nanalysis of oligoguluronates and oligomannuronates prepared by acid\nor enzymatic hydrolysis of homopolymeric blocks of alginic acid","volume":"289","author":"Heyraud","year":"1996","journal-title":"Carbohydr. Res."},{"key":"2026100711075342500_cit24","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.carres.2012.02.014","article-title":"Substrate\nspecificity of the recombinant alginate lyase from the marine bacteria Pseudomonas alginovora","volume":"352","author":"Lundqvist","year":"2012","journal-title":"Carbohydr.\nRes."},{"key":"2026100711075342500_cit25","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance\nmolecular simulations through multi-level parallelism from laptops\nto supercomputers","volume":"1\u20132","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"issue":"8","key":"2026100711075342500_cit26","doi-asserted-by":"publisher","first-page":"1950","DOI":"10.1002\/prot.22711","article-title":"Improved\nside-chain\ntorsion potentials for the Amber ff99SB protein force field","volume":"78","author":"Lindorff-Larsen","year":"2010","journal-title":"Proteins: Struct., Funct., Bioinf."},{"issue":"4","key":"2026100711075342500_cit27","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1002\/jcc.20820","article-title":"GLYCAM06: A generalizable\nbiomolecular force field. Carbohydrates","volume":"29","author":"Kirschner","year":"2008","journal-title":"J.\nComput. Chem."},{"issue":"2","key":"2026100711075342500_cit28","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1021\/acs.jafc.3c06778","article-title":"Action pattern of a novel G-specific alginate lyase: Determination\nof subsite specificity by HPAEC\u2013PAD\/MS","volume":"72","author":"Li","year":"2024","journal-title":"J. Agric. Food Chem."},{"issue":"2","key":"2026100711075342500_cit29","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/j.jmb.2008.05.008","article-title":"Substrate recognition by family 7\nalginate lyase from Sphingomonas sp. A1","volume":"380","author":"Ogura","year":"2008","journal-title":"J. Mol. 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Rep."},{"issue":"4","key":"2026100711075342500_cit32","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1016\/j.bbapap.2010.01.009","article-title":"Mutagenesis and subsite mapping underpin\nthe importance for substrate specificity of the aglycon subsites of\nglycoside hydrolase family 11 xylanases","volume":"1804","author":"Pollet","year":"2010","journal-title":"Biochim.\nBiophys. Acta, Proteins Proteomics"},{"issue":"11","key":"2026100711075342500_cit33","doi-asserted-by":"publisher","first-page":"1557","DOI":"10.1093\/glycob\/cwab073","article-title":"Exploring molecular\ndeterminants\nof polysaccharide lyase family 6\u20131 enzyme activity","volume":"31","author":"Violot","year":"2021","journal-title":"Glycobiology"},{"issue":"3","key":"2026100711075342500_cit34","doi-asserted-by":"publisher","first-page":"111227","DOI":"10.1016\/j.jbc.2026.111227","article-title":"Dissecting\na two-domain alginate lyase of family PL6\nreveals a mechanistic basis for substrate specificity and enzyme activity","volume":"302","author":"Madsen","year":"2026","journal-title":"J. Biol. Chem."},{"key":"2026100711075342500_cit35","doi-asserted-by":"publisher","first-page":"109022","DOI":"10.1016\/j.carres.2024.109022","article-title":"How alginate\nlyase\nproduces quasi-monodisperse oligosaccharides: A normal-mode-based\ndocking and molecular dynamics simulation study","volume":"536","author":"Xu","year":"2024","journal-title":"Carbohydr. Res."},{"issue":"4","key":"2026100711075342500_cit36","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1021\/ar300024d","article-title":"Carbohydrate\u2013aromatic\ninteractions","volume":"46","author":"Asensio","year":"2013","journal-title":"Acc. Chem. Res."},{"issue":"1","key":"2026100711075342500_cit37","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/s13068-016-0455-8","article-title":"Engineering\nbroad-spectrum digestion\nof polyuronides from an exolytic polysaccharide lyase","volume":"9","author":"MacDonald","year":"2016","journal-title":"Biotechnol. Biofuels"},{"issue":"5","key":"2026100711075342500_cit38","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.70150","article-title":"Recent advances\nin alginate lyase engineering for efficient\nconversion of alginate to value-added products","volume":"18","author":"Shin","year":"2025","journal-title":"Microb. Biotechnol."},{"key":"2026100711075342500_cit39","doi-asserted-by":"publisher","first-page":"1272","DOI":"10.1016\/j.ijbiomac.2020.11.009","article-title":"Construction and biochemical\ncharacterization of a novel hybrid alginate lyase with high activity\nby module recombination to prepare alginate oligosaccharides","volume":"166","author":"Hu","year":"2021","journal-title":"Int. J. Biol. Macromol."},{"key":"2026100711075342500_cit40","doi-asserted-by":"publisher","first-page":"102370","DOI":"10.1016\/j.sbi.2022.102370","article-title":"Computational design of novel protein\u2013protein\ninteractions \u2013 An overview on methodological approaches and\napplications","volume":"74","author":"Marchand","year":"2022","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2026100711075342500_cit41","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/0008-6215(94)84085-7","article-title":"Isolation and characterization\nof alginate-derived oligosaccharides with root growth-promoting activities","volume":"258","author":"Natsume","year":"1994","journal-title":"Carbohydr. Res."},{"issue":"11","key":"2026100711075342500_cit42","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1016\/j.nutres.2006.09.015","article-title":"In vivo prebiotic\nproperties of alginate oligosaccharides prepared through enzymatic\nhydrolysis of alginate","volume":"26","author":"Wang","year":"2006","journal-title":"Nutr. Res."},{"issue":"3","key":"2026100711075342500_cit43","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1080\/10408398.2021.1946008","article-title":"Process and applications\nof alginate oligosaccharides with emphasis on health beneficial perspectives","volume":"63","author":"Zhang","year":"2023","journal-title":"Crit. Rev. Food Sci. Nutr."},{"issue":"28","key":"2026100711075342500_cit44","doi-asserted-by":"publisher","first-page":"7703","DOI":"10.1080\/10408398.2021.1916736","article-title":"Recent advances\nin marine algae oligosaccharides: Structure,\nanalysis, and potential prebiotic activities","volume":"62","author":"Xie","year":"2022","journal-title":"Crit. Rev. Food Sci. Nutr."}],"container-title":["Journal of Agricultural\nand Food Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jafc.6c10205","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/39\/31010\/68632279\/acs.jafc.6c10205.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jafcau\/article-pdf\/74\/39\/31010\/68632279\/acs.jafc.6c10205.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:37:08Z","timestamp":1791387428000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jafcau\/article\/74\/39\/31010\/5437289\/Bipartite-Anchoring-at-the-3-Subsite-Governs"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,24]]},"references-count":44,"journal-issue":{"issue":"39","published-online":{"date-parts":[[2026,9,24]]},"published-print":{"date-parts":[[2026,10,7]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jafc.6c10205","relation":{},"ISSN":["0021-8561","1520-5118"],"issn-type":[{"value":"0021-8561","type":"print"},{"value":"1520-5118","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,24]]}}}