{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T01:36:07Z","timestamp":1783042567024,"version":"3.54.6"},"reference-count":53,"publisher":"National Academy of Sciences","issue":"4","license":[{"start":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T00:00:00Z","timestamp":1674000000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"DOE Biological and Environmental Research","award":["DE-AC36-08GO28308"],"award-info":[{"award-number":["DE-AC36-08GO28308"]}]},{"DOI":"10.13039\/100011735","name":"DOE Bioenergy Technologies Office","doi-asserted-by":"crossref","award":["DE-AC36-08GO28308"],"award-info":[{"award-number":["DE-AC36-08GO28308"]}],"id":[{"id":"10.13039\/100011735","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Research England for Expanding Excellence in England","award":["E3"],"award-info":[{"award-number":["E3"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CHE-1764328"],"award-info":[{"award-number":["CHE-1764328"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"DOE Biological and Environmental Research","award":["ERKP971"],"award-info":[{"award-number":["ERKP971"]}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2023,1,24]]},"abstract":"<jats:p>\n                    Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon\u2013carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of\n                    <jats:italic>erythro<\/jats:italic>\n                    -1,2-diguaiacylpropane-1,3-diol (\n                    <jats:italic>erythro<\/jats:italic>\n                    -DGPD), a ring-opened lignin-derived \u03b2-1 dimer, was reported in\n                    <jats:italic>Novosphingobium aromaticivorans<\/jats:italic>\n                    . The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts\n                    <jats:italic>erythro<\/jats:italic>\n                    -DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the\n                    <jats:italic>N. aromaticivorans<\/jats:italic>\n                    LdpA and another homolog identified in\n                    <jats:italic>Sphingobium<\/jats:italic>\n                    sp. SYK-6, for which activity was confirmed in\u00a0vivo. For both enzymes, we first demonstrated that formaldehyde is the C\n                    <jats:sub>1<\/jats:sub>\n                    reaction product, and we further demonstrated that both enantiomers of\n                    <jats:italic>erythro<\/jats:italic>\n                    -DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2212246120","type":"journal-article","created":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T13:49:27Z","timestamp":1674049767000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":25,"title":["Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation"],"prefix":"10.1073","volume":"120","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8793-2331","authenticated-orcid":false,"given":"Eugene","family":"Kuatsjah","sequence":"first","affiliation":[{"name":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5709-8665","authenticated-orcid":false,"given":"Michael","family":"Zahn","sequence":"additional","affiliation":[{"name":"Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO12DT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6981-7022","authenticated-orcid":false,"given":"Xiangyang","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1478-6625","authenticated-orcid":false,"given":"Ryo","family":"Kato","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6607-0955","authenticated-orcid":false,"given":"Daniel J.","family":"Hinchen","sequence":"additional","affiliation":[{"name":"Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO12DT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail O.","family":"Konev","sequence":"additional","affiliation":[{"name":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Katahira","sequence":"additional","affiliation":[{"name":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6137-8969","authenticated-orcid":false,"given":"Christian","family":"Orr","sequence":"additional","affiliation":[{"name":"Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8995-7324","authenticated-orcid":false,"given":"Armin","family":"Wagner","sequence":"additional","affiliation":[{"name":"Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yike","family":"Zou","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan J.","family":"Haugen","sequence":"additional","affiliation":[{"name":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5114-742X","authenticated-orcid":false,"given":"Kelsey J.","family":"Ramirez","sequence":"additional","affiliation":[{"name":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2302-8180","authenticated-orcid":false,"given":"Joshua K.","family":"Michener","sequence":"additional","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7237-0030","authenticated-orcid":false,"given":"Andrew R.","family":"Pickford","sequence":"additional","affiliation":[{"name":"Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO12DT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8792-1675","authenticated-orcid":false,"given":"Naofumi","family":"Kamimura","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9194-7483","authenticated-orcid":false,"given":"Eiji","family":"Masai","sequence":"additional","affiliation":[{"name":"Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K. N.","family":"Houk","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6750-1462","authenticated-orcid":false,"given":"John E.","family":"McGeehan","sequence":"additional","affiliation":[{"name":"Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO12DT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3480-212X","authenticated-orcid":false,"given":"Gregg T.","family":"Beckham","sequence":"additional","affiliation":[{"name":"Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2023,1,18]]},"reference":[{"key":"e_1_3_3_1_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1246843"},{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2016.02.030"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1410657111"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biotechadv.2016.10.001"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/1758-2229.12597"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.joule.2019.05.011"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biotechadv.2019.02.016"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1039\/C7CS00566K"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymben.2021.11.011"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2015.06.009"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1039\/9781788010351-00290"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA117.001268"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1039\/C8GC03504K"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2018.11.011"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA118.006548"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1039\/c1np00042j"},{"key":"e_1_3_3_17_2","first-page":"1319","article-title":"Purification and some properties of the enzyme catalyzing the C\u03b3-elimination of a diarylpropane-type lignin model from Pseudomonas paucimobilis TMY1009","volume":"55","author":"Kishi K.","year":"1991","unstructured":"K. Kishi, N. Habu, M. Samejima, T. Yoshimoto, Purification and some properties of the enzyme catalyzing the C\u03b3-elimination of a diarylpropane-type lignin model from Pseudomonas paucimobilis TMY1009. Agric. Biol. Chem. 55, 1319\u20131323 (1991).","journal-title":"Agric. Biol. Chem."},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymben.2021.02.003"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ibiod.2021.105208"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2021.100758"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0411"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.24971"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(94)00095-6"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2010.08.043"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-82660-z"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1080\/02773818708085258"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1107\/S2059798316001078"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3749"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M007452200"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.200700724"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA119.009428"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1608917113"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.7b00251"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.14099"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1039\/D0OB02204G"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1021\/cs400637t"},{"key":"e_1_3_3_37_2","first-page":"2659","article-title":"3-hexulose phosphate synthase from a new facultative methylotroph, Mycobacterium gastri MB 19","volume":"52","author":"Kato N.","year":"1988","unstructured":"N. Kato, N. Miyamoto, M. Shimao, C. Sakazawa, 3-hexulose phosphate synthase from a new facultative methylotroph, Mycobacterium gastri MB 19. Agric. Biol. Chem. 52, 2659\u20132661 (1988).","journal-title":"Agric. Biol. Chem."},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.202200269"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioorg.2014.09.001"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmc.2007.11.041"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jafc.7b04430"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1021\/np980003d"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.3183\/npprj-1991-06-03-p136-139"},{"key":"e_1_3_3_44_2","first-page":"161","article-title":"A 2D NMR investigation of the heterogeneity of distribution of diarylpropane structures in extracted Pinus radiata lignins","volume":"50","author":"Ede R. M.","year":"1996","unstructured":"R. M. Ede, J. Ralph, K. M. Torr, B. S. W. Dawson, A 2D NMR investigation of the heterogeneity of distribution of diarylpropane structures in extracted Pinus radiata lignins. Holzforschung 50, 161\u2013164 (1996).","journal-title":"Holzforschung"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-458X(199604)34:4<261::AID-OMR864>3.0.CO;2-J"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/0031-9422(91)83747-9"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1515\/hfsg.1990.44.2.95"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00225306"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00880-09"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.6.1768-1775.2003"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02391-15"},{"key":"e_1_3_3_52_2","unstructured":"K. Lundquist S. Li \"Structural analysis of lignin and lignin degradation products\" in 10th International Symposium on Wood and Pulping Chemistry Main Symposium Yokohama Japan June 7\u201310 1999 Chalmers University of Technology (1999) p. 2."},{"key":"e_1_3_3_53_2","unstructured":"M. J. Frisch Gaussian 16 Rev. C.01. Gaussian Inc. Wallingford CT (2016)."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2212246120","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,21]],"date-time":"2023-09-21T08:48:47Z","timestamp":1695286127000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/10.1073\/pnas.2212246120"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,18]]},"references-count":53,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,1,24]]}},"alternative-id":["10.1073\/pnas.2212246120"],"URL":"https:\/\/doi.org\/10.1073\/pnas.2212246120","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,18]]},"assertion":[{"value":"2022-08-15","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-11-27","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-01-18","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2212246120"}}