Structural Dynamics of Lytic Polysaccharide Monooxygenase during Catalysis

. 2020 Feb 05 ; 10 (2) : . [epub] 20200205

Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid32033404

Grantová podpora
LM2015043 Ministry of Education, Youth and Science - International
W1224 Austrian Science Fund - International
J-4154 Austrian Science Fund - International
16-34818L Grantová Agentura České Republiky - International
I 2385-N28 Austrian Science Fund - International
LQ1604 Ministry of Education, Youth and Science - International
W 1224 Austrian Science Fund FWF - Austria
CZ.1.05/1.1.00/02.0109 European Regional Development Fund - International
SVV260427/2019 Univerzita Karlova v Praze - International

Lytic polysaccharide monooxygenases (LPMOs) are industrially important oxidoreductases employed in lignocellulose saccharification. Using advanced time-resolved mass spectrometric techniques, we elucidated the structural determinants for substrate-mediated stabilization of the fungal LPMO9C from Neurosporacrassa during catalysis. LPMOs require a reduction in the active-site copper for catalytic activity. We show that copper reduction in NcLPMO9C leads to structural rearrangements and compaction around the active site. However, longer exposure to the reducing agent ascorbic acid also initiated an uncoupling reaction of the bound oxygen species, leading to oxidative damage, partial unfolding, and even fragmentation of NcLPMO9C. Interestingly, no changes in the hydrogen/deuterium exchange rate were detected upon incubation of oxidized or reduced LPMO with crystalline cellulose, indicating that the LPMO-substrate interactions are mainly side-chain mediated and neither affect intraprotein hydrogen bonding nor induce significant shielding of the protein surface. On the other hand, we observed a protective effect of the substrate, which slowed down the autooxidative damage induced by the uncoupling reaction. These observations further complement the picture of structural changes during LPMO catalysis.

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Chylenski P., Bissaro B., Sørlie M., Røhr A.K., Várnai A., Horn S.J., Eijsink V.G.H. Lytic polysaccharide monooxygenases in enzymatic processing of lignocellulosic biomass. ACS Catal. 2019;9:4970–4991. doi: 10.1021/acscatal.9b00246. DOI

Vaaje-Kolstad G., Westereng B., Horn S.J., Liu Z., Zhai H., Sørlie M., Eijsink V.G.H. An oxidative enzyme boosting the enzymatic conversion of recalcitrant polysaccharides. Science. 2010;330:219–222. doi: 10.1126/science.1192231. PubMed DOI

Levasseur A., Drula E., Lombard V., Coutinho P.M., Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol. Biofuels. 2013;6:1–14. doi: 10.1186/1754-6834-6-41. PubMed DOI PMC

Vu V.V., Beeson W.T., Span E.A., Farquhar E.R., Marletta M.A. A family of starch-active polysaccharide monooxygenases. Proc. Natl. Acad. Sci. USA. 2014;111:13822–13827. doi: 10.1073/pnas.1408090111. PubMed DOI PMC

Couturier M., Ladevèze S., Sulzenbacher G., Ciano L., Fanuel M., Moreau C., Villares A., Cathala B., Chaspoul F., Frendsen K.E., et al. Lytic xylan oxidases from wood-decay fungi unlock biomass degradation. Nat. Chem. Biol. 2018;14:306–310. doi: 10.1038/nchembio.2558. PubMed DOI

Sabbadin F., Hemsworth G.R., Ciano L., Henrissat B., Dupree P., Tryfona T., Marques R.D.S., Sweeney S.T., Besser K., Elias L., et al. An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion. Nat. Commun. 2018;9:756. doi: 10.1038/s41467-018-03142-x. PubMed DOI PMC

Isaksen T., Westereng B., Aachmann F.L., Agger J.W., Kracher D., Kittl R., Ludwig R., Haltrich D., Eijsink V.G.H., Horn S.J. A C4-oxidizing lytic polysaccharide monooxygenase cleaving both cellulose and cello-oligosaccharides. J. Biol. Chem. 2014;289:2632–2642. doi: 10.1074/jbc.M113.530196. PubMed DOI PMC

Quinlan R.J., Sweeney M.D., Lo Leggio L., Otten H., Poulsen J.N., Johansen K.S., Krogh K.B.R.M., Jørgensen C.I., Tovborg M., Anthonsen A., et al. Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components. Proc. Natl. Acad. Sci. USA. 2011;108:15079–15084. doi: 10.1073/pnas.1105776108. PubMed DOI PMC

Westereng B., Ishida T., Vaaje-Kolstad G., Wu M., Eijsink V.G.H., Igarashi K., Samejima M., Ståhlberg J., Horn S.J., Sandgren M. The putative endoglucanase PcGH61D from Phanerochaete chrysosporium is a metal-dependent oxidative enzyme that cleaves cellulose. PLoS ONE. 2011;6:e27807. doi: 10.1371/journal.pone.0027807. PubMed DOI PMC

Tan T., Kracher D., Gandini R., Sygmund C., Kittl R., Haltrich D., Hällberg B.M., Ludwig R., Divne C. Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation. Nat. Commun. 2015;6:7542. doi: 10.1038/ncomms8542. PubMed DOI PMC

Harris P.V., Welner D., McFarland K.C., Re E., Poulsen J.N., Brown K., Salbo R., Ding H., Vlasenko E., Merino S., et al. Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: Structure and function of a large, enigmatic family. Biochemistry. 2010;49:3305–3316. doi: 10.1021/bi100009p. PubMed DOI

Danneels B., Tanghe M., Joosten H., Gundinger T., Spadiut O., Stals I., Desmet T. A quantitative indicator diagram for lytic polysaccharide monooxygenases reveals the role of aromatic surface residues in HjLPMO9A regioselectivity. PLoS ONE. 2017;12:e0178446. doi: 10.1371/journal.pone.0178446. PubMed DOI PMC

Frandsen K.E.H., Poulsen J.N., Tandrup T., Lo Leggio L. Unliganded and substrate bound structures of the cellooligosaccharide active lytic polysaccharide monooxygenase Ls AA9A at low pH. Carbohydr. Res. 2017;448:187–190. doi: 10.1016/j.carres.2017.03.010. PubMed DOI

Li X., Beeson W.T., Phillips C.M., Marletta M.A., Cate J.H.D. Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases. Structure. 2012;20:1051–1061. doi: 10.1016/j.str.2012.04.002. PubMed DOI PMC

Kracher D., Scheiblbrandner S., Felice A.K., Breslmayr E., Preims M., Ludwicka K., Haltrich D., Eijsink V.G., Ludwig R. Extracellular electron transfer systems fuel cellulose oxidative degradation. Science. 2016;352:1098–1101. doi: 10.1126/science.aaf3165. PubMed DOI

Frommhagen M., Mutte S.K., Westphal A.H., Koetsier M.J., Hinz S.W.A., Visser J., Vincken J.P., Weijers D., van Berkel W.J.H., Gruppen H., et al. Boosting LPMO-driven lignocellulose degradation by polyphenol oxidase-activated lignin building blocks. Biotechnol. Biofuels. 2017;10:121. doi: 10.1186/s13068-017-0810-4. PubMed DOI PMC

Loose J.S., Forsberg Z., Kracher D., Scheiblbrandner S., Ludwig R., Eijsink V.G., Vaaje-Kolstad G. Activation of bacterial lytic polysaccharide monooxygenases with cellobiose dehydrogenase. Protein Sci. 2016;25:2175–2186. doi: 10.1002/pro.3043. PubMed DOI PMC

Phillips C.M., Beeson W.T., Cate J.H., Marletta M.A. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem. Biol. 2011;6:1399–1406. doi: 10.1021/cb200351y. PubMed DOI

Courtade G., Wimmer R., Røhr Å.K., Preims M., Felice A.K., Dimarogona M., Vaaje-Kolstad G., Sørlie M., Sandgren M., Ludwig R., et al. Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase. Proc. Natl. Acad. Sci. USA. 2016;113:5922–5927. doi: 10.1073/pnas.1602566113. PubMed DOI PMC

Aachmann F.L., Sorlie M., Skjak-Braek G., Eijsink V.G.H., Vaaje-Kolstad G. NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions. Proc. Natl. Acad. Sci. USA. 2012;109:18779–18784. doi: 10.1073/pnas.1208822109. PubMed DOI PMC

Kracher D., Andlar M., Furtmüller P.G., Ludwig R. Active-site copper reduction promotes substrate binding of fungal lytic polysaccharide monooxygenase and reduces stability. J. Biol. Chem. 2018;293:1676–1687. doi: 10.1074/jbc.RA117.000109. PubMed DOI PMC

Hangasky J.A., Marletta M.A. A random-sequential kinetic mechanism for polysaccharide monooxygenases. Biochemistry. 2018;57:3191–3199. doi: 10.1021/acs.biochem.8b00129. PubMed DOI

Beeson W.T., Phillips C.M., Cate J.H.D., Marletta M.A. Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases. J. Am. Chem. Soc. 2012;134:890–892. doi: 10.1021/ja210657t. PubMed DOI

Bissaro B., Røhr Å.K., Müller G., Chylenski P., Skaugen M., Forsberg Z., Horn S.J., Vaaje-Kolstad G., Eijsink V.G.H. Oxidative cleavage of polysaccharides by monocopper enzymes depends on H2O2. Nat. Chem. Biol. 2017;13:1123–1128. doi: 10.1038/nchembio.2470. PubMed DOI

Bissaro B., Streit B., Isaksen I., Eijsink V.G.H., Beckham G.T., DuBois J.L., Røhr Å.K. Molecular mechanism of the chitinolytic peroxygenase reaction. Proc. Natl. Acad. Sci. USA. 2020;117:1504–1513. doi: 10.1073/pnas.1904889117. PubMed DOI PMC

Kim S., Stahlberg J., Sandgren M., Paton R.S., Beckham G.T. Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism. Proc. Natl. Acad. Sci. USA. 2014;111:149–154. doi: 10.1073/pnas.1316609111. PubMed DOI PMC

Bennati-Granier C., Garajova S., Champion C., Grisel S., Haon M., Zhou S., Fanuel M., Ropartz D., Rogniaux H., Gimbert I., et al. Substrate specificity and regioselectivity of fungal AA9 lytic polysaccharide monooxygenases secreted by Podospora anserina. Biotechnol. Biofuels. 2015;8:90. doi: 10.1186/s13068-015-0274-3. PubMed DOI PMC

Walton P.H., Davies G.J. On the catalytic mechanisms of lytic polysaccharide monooxygenases. Curr. Opin. Chem. Biol. 2016;31:195–207. doi: 10.1016/j.cbpa.2016.04.001. PubMed DOI

Kuusk S., Bissaro B., Kuusk P., Forsberg Z., Eijsink V.G.H., Sørlie M., Väljamäe P. Kinetics of H2O2 -driven degradation of chitin by a bacterial lytic polysaccharide monooxygenase. J. Biol. Chem. 2018;293:523–531. doi: 10.1074/jbc.M117.817593. PubMed DOI PMC

Hangasky J.A., Iavarone A.T., Marletta M.A. Reactivity of O2 versus H2O2 with polysaccharide monooxygenases. Proc. Natl. Acad. Sci. USA. 2018;115:4915–4920. doi: 10.1073/pnas.1801153115. PubMed DOI PMC

Müller G., Chylenski P., Bissaro B., Eijsink V.G.H., Horn S.J. The impact of hydrogen peroxide supply on LPMO activity and overall saccharification efficiency of a commercial cellulase cocktail. Biotechnol. Biofuels. 2018;11:209. doi: 10.1186/s13068-018-1199-4. PubMed DOI PMC

Loose J.S.M., Arntzen M.Ø., Bissaro B., Ludwig R., Eijsink V.G.H., Vaaje-Kolstad G. Multipoint precision binding of substrate protects lytic polysaccharide monooxygenases from self-destructive off-pathway processes. Biochemistry. 2018;57:4114–4124. doi: 10.1021/acs.biochem.8b00484. PubMed DOI

Scarpa M., Stevanato R., Viglino P., Rigo A. Superoxide ion as active intermediate in the autoxidation of ascorbate by molecular oxygen. Effect of superoxide dismutase. J. Biol. Chem. 1983;258:6695–6697. PubMed

Bissaro B., Várnai A., Røhr Å.K., Eijsink V.G.H. Oxidoreductases and reactive oxygen species in conversion of lignocellulosic biomass. Microbiol. Mol. Biol. Rev. 2018;82:e00029-18. doi: 10.1128/MMBR.00029-18. PubMed DOI PMC

Kittl R., Kracher D., Burgstaller D., Haltrich D., Ludwig R. Production of four Neurospora crassa lytic polysaccharide monooxygenases in Pichia pastoris monitored by a fluorimetric assay. Biotechnol. Biofuels. 2012;5:79. doi: 10.1186/1754-6834-5-79. PubMed DOI PMC

Span E.A., Suess D.L.M., Deller M.C., Britt R.D., Marletta M.A. The role of the secondary coordination sphere in a fungal polysaccharide monooxygenase. ACS Chem. Biol. 2017;12:1095–1103. doi: 10.1021/acschembio.7b00016. PubMed DOI PMC

Gregory R.C., Hemsworth G.R., Turkenburg J.P., Hart S.J., Walton P.H., Davies G.J. Activity, stability and 3-D structure of the CuII form of a chitin-active lytic polysaccharide monooxygenase from Bacillus amyloliquefaciens. Dalt. Trans. 2016;45:16904–16912. doi: 10.1039/C6DT02793H. PubMed DOI

Sugimoto H., Nakajima Y., Motoyama A., Katagiri E., Watanabe T., Suzuki K. Unfolding of CBP21, a lytic polysaccharide monooxygenase, without dissociation of its copper ion cofactor. Biopolymers. 2019;111:e23339. doi: 10.1002/bip.23339. PubMed DOI

Kadek A., Mrazek H., Halada P., Rey M., Schriemer D.C., Man P. Aspartic protease nepenthesin-1 as a tool for digestion in hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 2014;86:4287–4294. doi: 10.1021/ac404076j. PubMed DOI

Rey M., Man P., Brandolin G., Forest E., Pelosi L. Recombinant immobilized rhizopuspepsin as a new tool for protein digestion in hydrogen/deuterium exchange mass spectrometry. Rapid Commun. Mass Spectrom. 2009;23:3431–3438. doi: 10.1002/rcm.4260. PubMed DOI

Hsieh E.J., Hoopmann M.R., MacLean B., MacCoss M.J. Comparison of database search strategies for high precursor mass accuracy MS/MS data. J. Proteome Res. 2010;9:1138–1143. doi: 10.1021/pr900816a. PubMed DOI PMC

Trcka F., Durech M., Vankova P., Chmelik J., Martinkova V., Hausner J., Kadek A., Marcoux J., Klumpler T., Vojtesek B., et al. Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding. Mol. Cell. Proteomics. 2019;18:320–337. doi: 10.1074/mcp.RA118.001044. PubMed DOI PMC

Kavan D., Man P. MSTools—Web based application for visualization and presentation of HXMS data. Int. J. Mass Spectrom. 2011;302:53–58. doi: 10.1016/j.ijms.2010.07.030. DOI

Borisova A.S., Isaksen T., Dimarogona M., Kognole A.A., Mathiesen G., Várnai A., Røhr Å.K., Payne C.M., Sørlie M., Sandgren M., et al. Structural and functional characterization of a lytic lolysaccharide monooxygenase with broad substrate specificity. J. Biol. Chem. 2015;290:22955–22969. doi: 10.1074/jbc.M115.660183. PubMed DOI PMC

Singh K.R., Blossom B.M., Russo D.A., van Oort B., Croce R., Jensen P.E., Felbyb C., Bjerrum M.J. Thermal unfolding and refolding of a lytic polysaccharide monooxygenase from Thermoascus aurantiacus. RSC Adv. 2019;9:29734–29742. doi: 10.1039/C9RA05920B. PubMed DOI PMC

Yang M., Hoeppner M., Rey M., Kadek A., Man P., Schriemer D.C. Recombinant nepenthesin II for hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 2015;87:6681–6687. doi: 10.1021/acs.analchem.5b00831. PubMed DOI

Kadek A., Tretyachenko V., Mrazek H., Ivanova L., Halada P., Rey M., Schriemer D.C., Man P. Expression and characterization of plant aspartic protease nepenthesin-1 from Nepenthes gracilis. Protein Expr. Purif. 2014;95:121–128. doi: 10.1016/j.pep.2013.12.005. PubMed DOI

Tsiatsiani L., Akeroyd M., Olsthoorn M., Heck A.J.R. Aspergillus niger prolyl endoprotease for hydrogen–deuterium exchange mass spectrometry and protein structural studies. Anal. Chem. 2017;89:7966–7973. doi: 10.1021/acs.analchem.7b01161. PubMed DOI PMC

Uchida K., Kato Y., Kawakishi S. A novel mechanism for oxidative cleavage of prolyl peptides induced by the hydroxyl radical. Biochem. Biophys. Res. Commun. 1990;169:265–271. doi: 10.1016/0006-291X(90)91463-3. PubMed DOI

Garrison W.M. Reaction mechanisms in the radiolysis of peptides, polypeptides, and proteins. Chem. Rev. 1987;87:381–398. doi: 10.1021/cr00078a006. DOI

Frandsen K.E., Simmons T.J., Dupree P., Poulsen J.C., Hemsworth G.R., Ciano L., Johnston E.M., Tovborg M., Johansen K.S., von Freiesleben P., et al. The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases. Nat. Chem. Biol. 2016;12:298–303. doi: 10.1038/nchembio.2029. PubMed DOI PMC

Vaaje-Kolstad G., Forsberg Z., Loose J.S., Bissaro B., Eijsink V.G. Structural diversity of lytic polysaccharide monooxygenases. Curr. Opin. Struct. Biol. 2017;44:67–76. doi: 10.1016/j.sbi.2016.12.012. PubMed DOI

Beckham G.T., Matthews J.F., Bomble Y.J., Bu L., Adney W.S., Himmel M.E., Nimlos M.R., Crowley M.F. Identification of amino acids responsible for processivity in a Family 1 carbohydrate-binding module from a fungal cellulase. J. Phys. Chem. B. 2010;114:1447–1453. doi: 10.1021/jp908810a. PubMed DOI

Griffo A., Rooijakkers B.J.M., Hähl H., Jacobs K., Linder M.B., Laaksonen P. Binding Forces of Cellulose Binding Modules on Cellulosic Nanomaterials. Biomacromolecules. 2019;20:769–777. doi: 10.1021/acs.biomac.8b01346. PubMed DOI PMC

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