1
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Wieduwilt EK, Lo Leggio L, Hedegård ED. A frontier-orbital view of the initial steps of lytic polysaccharide monooxygenase reactions. Dalton Trans 2024; 53:5796-5807. [PMID: 38445349 DOI: 10.1039/d3dt04275h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that oxidatively cleave the strong C-H bonds in recalcitrant polysaccharide substrates, thereby playing a crucial role in biomass degradation. Recently, LPMOs have also been shown to be important for several pathogens. It is well established that the Cu(II) resting state of LPMOs is inactive, and the electronic structure of the active site needs to be altered to transform the enzyme into an active form. Whether this transformation occurs due to substrate binding or due to a unique priming reduction has remained speculative. Starting from four different crystal structures of the LPMO LsAA9A with well-defined oxidation states, we use a frontier molecular orbital approach to elucidate the initial steps of the LPMO reaction. We give an explanation for the requirement of the unique priming reduction and analyse electronic structure changes upon substrate binding. We further investigate how the presence of the substrate could facilitate an electron transfer from the copper active site to an H2O2 co-substrate. Our findings could help to control experimental LPMO reactions.
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Affiliation(s)
- Erna Katharina Wieduwilt
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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2
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Munzone A, Eijsink VGH, Berrin JG, Bissaro B. Expanding the catalytic landscape of metalloenzymes with lytic polysaccharide monooxygenases. Nat Rev Chem 2024; 8:106-119. [PMID: 38200220 DOI: 10.1038/s41570-023-00565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have an essential role in global carbon cycle, industrial biomass processing and microbial pathogenicity by catalysing the oxidative cleavage of recalcitrant polysaccharides. Despite initially being considered monooxygenases, experimental and theoretical studies show that LPMOs are essentially peroxygenases, using a single copper ion and H2O2 for C-H bond oxygenation. Here, we examine LPMO catalysis, emphasizing key studies that have shaped our comprehension of their function, and address side and competing reactions that have partially obscured our understanding. Then, we compare this novel copper-peroxygenase reaction with reactions catalysed by haem iron enzymes, highlighting the different chemistries at play. We conclude by addressing some open questions surrounding LPMO catalysis, including the importance of peroxygenase and monooxygenase reactions in biological contexts, how LPMOs modulate copper site reactivity and potential protective mechanisms against oxidative damage.
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Affiliation(s)
- Alessia Munzone
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France.
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3
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Dan M, Zheng Y, Zhao G, Hsieh YSY, Wang D. Current insights of factors interfering the stability of lytic polysaccharide monooxygenases. Biotechnol Adv 2023; 67:108216. [PMID: 37473820 DOI: 10.1016/j.biotechadv.2023.108216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/30/2023] [Accepted: 07/16/2023] [Indexed: 07/22/2023]
Abstract
Cellulose and chitin are two of the most abundant biopolymers in nature, but they cannot be effectively utilized in industry due to their recalcitrance. This limitation was overcome by the advent of lytic polysaccharide monooxygenases (LPMOs), which promote the disruption of biopolymers through oxidative mechanism and provide a breakthrough in the action of hydrolytic enzymes. In the application of LPMOs to biomass degradation, the key to consistent and effective functioning lies in their stability. The efficient transformation of biomass resources using LPMOs depends on factors that interfere with their stability. This review discussed three aspects that affect LPMO stability: general external factors, structural factors, and factors in the enzyme-substrate reaction. It explains how these factors impact LPMO stability, discusses the resulting effects, and finally presents relevant measures and considerations, including potential resolutions. The review also provides suggestions for the application of LPMOs in polysaccharide degradation.
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Affiliation(s)
- Meiling Dan
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yuting Zheng
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Guohua Zhao
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden; School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Damao Wang
- College of Food Science, Southwest University, Chongqing 400715, China.
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4
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Askarian F, Tsai CM, Cordara G, Zurich RH, Bjånes E, Golten O, Vinther Sørensen H, Kousha A, Meier A, Chikwati E, Bruun JA, Ludviksen JA, Choudhury B, Trieu D, Davis S, Edvardsen PKT, Mollnes TE, Liu GY, Krengel U, Conrad DJ, Vaaje-Kolstad G, Nizet V. Immunization with lytic polysaccharide monooxygenase CbpD induces protective immunity against Pseudomonas aeruginosa pneumonia. Proc Natl Acad Sci U S A 2023; 120:e2301538120. [PMID: 37459522 PMCID: PMC10372616 DOI: 10.1073/pnas.2301538120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/30/2023] [Indexed: 07/20/2023] Open
Abstract
Pseudomonas aeruginosa (PA) CbpD belongs to the lytic polysaccharide monooxygenases (LPMOs), a family of enzymes that cleave chitin or related polysaccharides. Here, we demonstrate a virulence role of CbpD in PA pneumonia linked to impairment of host complement function and opsonophagocytic clearance. Following intratracheal challenge, a PA ΔCbpD mutant was more easily cleared and produced less mortality than the wild-type parent strain. The x-ray crystal structure of the CbpD LPMO domain was solved to subatomic resolution (0.75Å) and its two additional domains modeled by small-angle X-ray scattering and Alphafold2 machine-learning algorithms, allowing structure-based immune epitope mapping. Immunization of naive mice with recombinant CbpD generated high IgG antibody titers that promoted human neutrophil opsonophagocytic killing, neutralized enzymatic activity, and protected against lethal PA pneumonia and sepsis. IgG antibodies generated against full-length CbpD or its noncatalytic M2+CBM73 domains were opsonic and protective, even in previously PA-exposed mice, while antibodies targeting the AA10 domain were not. Preexisting antibodies in PA-colonized cystic fibrosis patients primarily target the CbpD AA10 catalytic domain. Further exploration of LPMO family proteins, present across many clinically important and antibiotic-resistant human pathogens, may yield novel and effective vaccine antigens.
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Affiliation(s)
- Fatemeh Askarian
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Chih-Ming Tsai
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | | | - Raymond H. Zurich
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Elisabet Bjånes
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Ole Golten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432Ås, Norway
| | | | - Armin Kousha
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Angela Meier
- Division of Critical Care, Department of Anesthesiology, University of California San Diego, La Jolla, CA92037
| | - Elvis Chikwati
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, N-1432Ås, Norway
| | - Jack-Ansgar Bruun
- Proteomics and Metabolomics Core Facility, Department of Medical Biology, The Arctic University of Norway, N-9037Tromsø, Norway
| | | | - Biswa Choudhury
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA92093
| | - Desmond Trieu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
- School of Pharmacy, University of California San Francisco, San Francisco, CA94143
| | - Stanley Davis
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | | | - Tom Eirik Mollnes
- Research Laboratory, Nordland Hospital, N-8005Bodø, Norway
- Department of Immunology, University of Oslo Hospital, N-0424Oslo, Norway
- Center of Molecular Inflammation Research, Norwegian University of Science and Technology, N-7491Trondheim, Norway
| | - George Y. Liu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
| | - Ute Krengel
- Department of Chemistry, University of Oslo, N-0315Oslo, Norway
| | - Douglas J. Conrad
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA92037
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432Ås, Norway
| | - Victor Nizet
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA92093
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
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5
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Revisiting the role of electron donors in lytic polysaccharide monooxygenase biochemistry. Essays Biochem 2023; 67:585-595. [PMID: 36748351 PMCID: PMC10154616 DOI: 10.1042/ebc20220164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
The plant cell wall is rich in carbohydrates and many fungi and bacteria have evolved to take advantage of this carbon source. These carbohydrates are largely locked away in polysaccharides and so these organisms deploy a range of enzymes that can liberate individual sugars from these challenging substrates. Glycoside hydrolases (GHs) are the enzymes that are largely responsible for bringing about this sugar release; however, 12 years ago, a family of enzymes known as lytic polysaccharide monooxygenases (LPMOs) were also shown to be of key importance in this process. LPMOs are copper-dependent oxidative enzymes that can introduce chain breaks within polysaccharide chains. Initial work demonstrated that they could activate O2 to attack the substrate through a reaction that most likely required multiple electrons to be delivered to the enzyme. More recently, it has emerged that LPMO kinetics are significantly improved if H2O2 is supplied to the enzyme as a cosubstrate instead of O2. Only a single electron is required to activate an LPMO and H2O2 cosubstrate and the enzyme has been shown to catalyse multiple turnovers following the initial one-electron reduction of the copper, which is not possible if O2 is used. This has led to further studies of the roles of the electron donor in LPMO biochemistry, and this review aims to highlight recent findings in this area and consider how ongoing research could impact our understanding of the interplay between redox processes in nature.
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6
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Hagemann MM, Hedegård ED. Molecular Mechanism of Substrate Oxidation in Lytic Polysaccharide Monooxygenases: Insight from Theoretical Investigations. Chemistry 2023; 29:e202202379. [PMID: 36207279 PMCID: PMC10107554 DOI: 10.1002/chem.202202379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that today comprise a large enzyme superfamily, grouped into the distinct members AA9-AA17 (with AA12 exempted). The LPMOs have the potential to facilitate the upcycling of biomass waste products by boosting the breakdown of cellulose and other recalcitrant polysaccharides. The cellulose biopolymer is the main component of biomass waste and thus comprises a large, unexploited resource. The LPMOs work through a catalytic, oxidative reaction whose mechanism is still controversial. For instance, the nature of the intermediate performing the oxidative reaction is an open question, and the same holds for the employed co-substrate. Here we review theoretical investigations addressing these questions. The applied theoretical methods are usually based on quantum mechanics (QM), often combined with molecular mechanics (QM/MM). We discuss advantages and disadvantages of the employed theoretical methods and comment on the interplay between theoretical and experimental results.
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Affiliation(s)
- Marlisa M Hagemann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Erik D Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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7
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Abstract
Lytic polysaccharide monooxygenases (LPMOs) are unique redox enzymes capable of disrupting the crystalline surfaces of industry-relevant recalcitrant polysaccharides, such as chitin and cellulose. Historically, LPMOs were thought to be slow enzymes relying on O2 as the co-substrate, but it is now clear that these enzymes prefer H2O2, allowing for fast depolymerization of polysaccharides through a peroxygenase reaction. Thus, quantifying H2O2 in LPMO reaction set-ups is of a great interest. The horseradish peroxidase (HRP)/Amplex Red (AR) assay is one of the most popular and accessible tools for measuring hydrogen peroxide. This assay has been used in various types of biological and biochemical studies, including LPMO research, but suffers from pitfalls that need to be accounted for. In this Chapter, we discuss this method and its use for assessing the often rate-limiting in situ formation of H2O2 in LPMO reactions. We show that, after accounting for multiple potential side reactions, quantitative data on H2O2 production obtained with the HRP/Amplex Red assay provide useful clues for understanding the catalytic activity of LPMOs, including the impact of reductants and transition metal ions.
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Affiliation(s)
- Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
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8
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Schröder GC, O'Dell WB, Webb SP, Agarwal PK, Meilleur F. Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Chem Sci 2022; 13:13303-13320. [PMID: 36507176 PMCID: PMC9683017 DOI: 10.1039/d2sc05031e] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022] Open
Abstract
Metalloproteins perform a diverse array of redox-related reactions facilitated by the increased chemical functionality afforded by their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that are responsible for the breakdown of recalcitrant polysaccharides via oxidative cleavage at the glycosidic bond. The activated copper-oxygen intermediates and their mechanism of formation remains to be established. Neutron protein crystallography which permits direct visualization of protonation states was used to investigate the initial steps of oxygen activation directly following active site copper reduction in Neurospora crassa LPMO9D. Herein, we cryo-trap an activated dioxygen intermediate in a mixture of superoxo and hydroperoxo states, and we identify the conserved second coordination shell residue His157 as the proton donor. Density functional theory calculations indicate that both superoxo and hydroperoxo active site states are stable. The hydroperoxo formed is potentially an early LPMO catalytic reaction intermediate or the first step in the mechanism of hydrogen peroxide formation in the absence of substrate. We observe that the N-terminal amino group of the copper coordinating His1 remains doubly protonated directly following molecular oxygen reduction by copper. Aided by molecular dynamics and mining minima free energy calculations we establish that the conserved second-shell His161 in MtPMO3* displays conformational flexibility in solution and that this flexibility is also observed, though to a lesser extent, in His157 of NcLPMO9D. The imidazolate form of His157 observed in our structure following oxygen intermediate protonation can be attributed to abolished His157 flexibility due steric hindrance in the crystal as well as the solvent-occluded active site environment due to crystal packing. A neutron crystal structure of NcLPMO9D at low pH further supports occlusion of the active site since His157 remains singly protonated even at acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - William B. O'Dell
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
| | - Simon P. Webb
- VeraChem LLC12850 Middlebrook Rd. Ste 205GermantownMD 20874-5244USA
| | - Pratul K. Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterOK 74078USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State UniversityRaleighNC 27695USA,Neutron Scattering Division, Oak Ridge National LaboratoryOak RidgeTN 37831USA
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9
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Bouchey C, Shopov DY, Gruen AD, Tolman WB. Mimicking the Cu Active Site of Lytic Polysaccharide Monooxygenase Using Monoanionic Tridentate N-Donor Ligands. ACS OMEGA 2022; 7:35217-35232. [PMID: 36211076 PMCID: PMC9535706 DOI: 10.1021/acsomega.2c04432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
In an effort to prepare small molecule mimics of the active site of lytic polysaccharide monooxygenase (LPMO), three monoanionic tridentate N donor ligands comprising a central deprotonated amide group flanked by two neutral donors were prepared, and their coordination chemistry with Cu(I) and Cu(II) was evaluated. With Cu(I), a dimer formed, which was characterized by X-ray crystallography and NMR spectroscopy. A variety of mononuclear and dinuclear Cu(II) species with a range of auxiliary ligands (MeCN, Cl-, OH-, OAc-, OBz-, CO3 2-) were prepared and characterized by X-ray diffraction and various spectroscopies (UV-vis, EPR). The complexes exhibit structural similarities to the LPMO active site.
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Affiliation(s)
- Caitlin
J. Bouchey
- Department
of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Dimitar Y. Shopov
- Department
of Chemistry, Washington University in St.
Louis, One Brookings Drive, Campus Box 1134, St.
Louis, Missouri 63130, United States
| | - Aaron D. Gruen
- Department
of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - William B. Tolman
- Department
of Chemistry, Washington University in St.
Louis, One Brookings Drive, Campus Box 1134, St.
Louis, Missouri 63130, United States
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10
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Long L, Hu Y, Sun F, Gao W, Hao Z, Yin H. Advances in lytic polysaccharide monooxygenases with the cellulose-degrading auxiliary activity family 9 to facilitate cellulose degradation for biorefinery. Int J Biol Macromol 2022; 219:68-83. [PMID: 35931294 DOI: 10.1016/j.ijbiomac.2022.07.240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/18/2022]
Abstract
One crucial step in processing the recalcitrant lignocellulosic biomass is the fast hydrolysis of natural cellulose to fermentable sugars that can be subsequently converted to biofuels and bio-based chemicals. Recent studies have shown that lytic polysaccharide monooxygenase (LPMOs) with auxiliary activity family 9 (AA9) are capable of efficiently depolymerizing the crystalline cellulose via regioselective oxidation reaction. Intriguingly, the catalysis by AA9 LPMOs requires reductant to provide electrons, and lignin and its phenolic derivatives can be oxidized, releasing reductant to activate the reaction. The activity of AA9 LPMOs can be enhanced by in-situ generation of H2O2 in the presence of O2. Although scientific understanding of these enzymes remains somewhat unknown or controversial, structure modifications on AA9 LPMOs through protein engineering have emerged in recent years, which are prerequisite for their extensive applications in the development of cellulase-mediated lignocellulosic biorefinery processes. In this review, we critically comment on advances in studies for AA9 LPMOs, i.e., characteristic of AA9 LPMOs catalysis, external electron donors to AA9 LPMOs, especially the role of the oxidization of lignin and its derivatives, and AA9 LPMOs protein engineering as well as their extensive applications in the bioprocessing of lignocellulosic biomass. Perspectives are also highlighted for addressing the challenges.
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Affiliation(s)
- Lingfeng Long
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Wa Gao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
| | - Zhikui Hao
- Institute of Applied Biotechnology, School of Medicine and Pharmaceutical Engineering, Taizhou Vocational and Technical College, Taizhou 318000, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS(, Dalian 116023, China
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11
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Theoretical perspective on mononuclear copper-oxygen mediated C–H and O–H activations: A comparison between biological and synthetic systems. CHINESE JOURNAL OF CATALYSIS 2022. [DOI: 10.1016/s1872-2067(21)63974-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Rieder L, Stepnov AA, Sørlie M, Eijsink VG. Fast and Specific Peroxygenase Reactions Catalyzed by Fungal Mono-Copper Enzymes. Biochemistry 2021; 60:3633-3643. [PMID: 34738811 PMCID: PMC8638258 DOI: 10.1021/acs.biochem.1c00407] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/27/2021] [Indexed: 11/28/2022]
Abstract
The copper-dependent lytic polysaccharide monooxygenases (LPMOs) are receiving attention because of their role in the degradation of recalcitrant biomass and their intriguing catalytic properties. The fundamentals of LPMO catalysis remain somewhat enigmatic as the LPMO reaction is affected by a multitude of LPMO- and co-substrate-mediated (side) reactions that result in a complex reaction network. We have performed kinetic studies with two LPMOs that are active on soluble substrates, NcAA9C and LsAA9A, using various reductants typically employed for LPMO activation. Studies with NcAA9C under "monooxygenase" conditions showed that the impact of the reductant on catalytic activity is correlated with the hydrogen peroxide-generating ability of the LPMO-reductant combination, supporting the idea that a peroxygenase reaction is taking place. Indeed, the apparent monooxygenase reaction could be inhibited by a competing H2O2-consuming enzyme. Interestingly, these fungal AA9-type LPMOs were found to have higher oxidase activity than bacterial AA10-type LPMOs. Kinetic analysis of the peroxygenase activity of NcAA9C on cellopentaose revealed a fast stoichiometric conversion of high amounts of H2O2 to oxidized carbohydrate products. A kcat value of 124 ± 27 s-1 at 4 °C is 20 times higher than a previously described kcat for peroxygenase activity on an insoluble substrate (at 25 °C) and some 4 orders of magnitude higher than typical "monooxygenase" rates. Similar studies with LsAA9A revealed differences between the two enzymes but confirmed fast and specific peroxygenase activity. These results show that the catalytic site arrangement of LPMOs provides a unique scaffold for highly efficient copper redox catalysis.
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Affiliation(s)
- Lukas Rieder
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
| | - Anton A. Stepnov
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
| | - Vincent G.H. Eijsink
- Faculty of Chemistry, Biotechnology,
and Food Sciences, Norwegian University
of Life Sciences (NMBU), P.O. Box 5003,
NO, 1432 Ås, Norway
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13
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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14
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Bergmann J, Oksanen E, Ryde U. Combining crystallography with quantum mechanics. Curr Opin Struct Biol 2021; 72:18-26. [PMID: 34392061 DOI: 10.1016/j.sbi.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 11/19/2022]
Abstract
In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, P. O. Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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15
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C-type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases. Biochem J 2021; 478:2927-2944. [PMID: 34240737 PMCID: PMC8981238 DOI: 10.1042/bcj20210376] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
The release of glucose from lignocellulosic waste for subsequent fermentation into biofuels holds promise for securing humankind's future energy needs. The discovery of a set of copper-dependent enzymes known as lytic polysaccharide monooxygenases (LPMOs) has galvanised new research in this area. LPMOs act by oxidatively introducing chain breaks into cellulose and other polysaccharides, boosting the ability of cellulases to act on the substrate. Although several proteins have been implicated as electron sources in fungal LPMO biochemistry, no equivalent bacterial LPMO electron donors have been previously identified, although the proteins Cbp2D and E from Cellvibrio japonicus have been implicated as potential candidates. Here we analyse a small c-type cytochrome (CjX183) present in Cellvibrio japonicus Cbp2D, and show that it can initiate bacterial CuII/I LPMO reduction and also activate LPMO-catalyzed cellulose-degradation. In the absence of cellulose, CjX183-driven reduction of the LPMO results in less H2O2 production from O2, and correspondingly less oxidative damage to the enzyme than when ascorbate is used as the reducing agent. Significantly, using CjX183 as the activator maintained similar cellulase boosting levels relative to the use of an equivalent amount of ascorbate. Our results therefore add further evidence to the impact that the choice of electron source can have on LPMO action. Furthermore, the study of Cbp2D and other similar proteins may yet reveal new insight into the redox processes governing polysaccharide degradation in bacteria.
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16
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Yan Z, Li X, Chung LW. Multiscale Quantum Refinement Approaches for Metalloproteins. J Chem Theory Comput 2021; 17:3783-3796. [PMID: 34032440 DOI: 10.1021/acs.jctc.1c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.
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Affiliation(s)
- Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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17
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Manavalan T, Stepnov AA, Hegnar OA, Eijsink VGH. Sugar oxidoreductases and LPMOs - two sides of the same polysaccharide degradation story? Carbohydr Res 2021; 505:108350. [PMID: 34049079 DOI: 10.1016/j.carres.2021.108350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides such as chitin and cellulose and their discovery has revolutionized our understanding of enzymatic biomass conversion. The discovery of LPMOs raises interesting new questions regarding the roles of other oxidoreductases and abiotic redox processes in biomass conversion. LPMOs need reducing power and an oxygen co-substrate and biomass degrading ecosystems contain a multitude of redox enzymes that affect the availability of both. For example, biomass degrading fungi produce multiple sugar oxidoreductases whose biological functions so far have remained somewhat enigmatic. It is now conceivable that these redox enzymes, in particular H2O2-producing sugar oxidases, could play a role in fueling and controlling LPMO reactions. Here, we shortly review contemporary issues in the LPMO field, paying particular attention to the possible roles of sugar oxidoreductases.
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Affiliation(s)
- Tamilvendan Manavalan
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway.
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18
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Wang D, Li Y, Zheng Y, Hsieh YSY. Recent Advances in Screening Methods for the Functional Investigation of Lytic Polysaccharide Monooxygenases. Front Chem 2021; 9:653754. [PMID: 33912540 PMCID: PMC8072006 DOI: 10.3389/fchem.2021.653754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/12/2021] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) is a newly discovered and widely studied enzyme in recent years. These enzymes play a key role in the depolymerization of sugar-based biopolymers (including cellulose, hemicellulose, chitin and starch), and have a positive significance for biomass conversion. LPMO is a copper-dependent enzyme that can oxidize and cleave glycosidic bonds in cellulose and other polysaccharides. Their mechanism of action depends on the correct coordination of copper ions in the active site. There are still difficulties in the analysis of LPMO activity, which often requires multiple methods to be used in concert. In this review, we discussed various LPMO activity analysis methods reported so far, including mature mass spectrometry, chromatography, labeling, and indirect measurements, and summarized the advantages, disadvantages and applicability of different methods.
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Affiliation(s)
- Damao Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Yanping Li
- College of Food Science, Southwest University, Chongqing, China
| | - Yuting Zheng
- College of Food Science, Southwest University, Chongqing, China
| | - Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden.,School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
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19
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Wang Z, Feng S, Rovira C, Wang B. How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Shishi Feng
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 08020 Barcelona Spain
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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20
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Lytic polysaccharide monooxygenases and other histidine-brace copper proteins: structure, oxygen activation and biotechnological applications. Biochem Soc Trans 2021; 49:531-540. [PMID: 33449071 PMCID: PMC7924993 DOI: 10.1042/bst20201031] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mononuclear copper enzymes that catalyse the oxidative cleavage of glycosidic bonds. They are characterised by two histidine residues that coordinate copper in a configuration termed the Cu-histidine brace. Although first identified in bacteria and fungi, LPMOs have since been found in all biological kingdoms. LPMOs are now included in commercial enzyme cocktails used in industrial biorefineries. This has led to increased process yield due to the synergistic action of LPMOs with glycoside hydrolases. However, the introduction of LPMOs makes control of the enzymatic step in industrial stirred-tank reactors more challenging, and the operational stability of the enzymes is reduced. It is clear that much is still to be learned about the interaction between LPMOs and their complex natural and industrial environments, and fundamental scientific studies are required towards this end. Several atomic-resolution structures have been solved providing detailed information on the Cu-coordination sphere and the interaction with the polysaccharide substrate. However, the molecular mechanisms of LPMOs are still the subject of intense investigation; the key question being how the proteinaceous environment controls the copper cofactor towards the activation of the O-O bond in O2 and cleavage of the glycosidic bonds in polysaccharides. The need for biochemical characterisation of each putative LPMO is discussed based on recent reports showing that not all proteins with a Cu-histidine brace are enzymes.
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21
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Cheng C, Haider J, Liu P, Yang J, Tan Z, Huang T, Lin J, Jiang M, Liu H, Zhu L. Engineered LPMO Significantly Boosting Cellulase-Catalyzed Depolymerization of Cellulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:15257-15266. [PMID: 33290065 DOI: 10.1021/acs.jafc.0c05979] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) play a crucial role in the enzymatic depolymerization of cellulose through oxidative cleavage of the glycosidic bond in the highly recalcitrant crystalline cellulose region. Improving the activity of LPMOs is of considerable importance for second-generation biorefinery. In this study, we identified a beneficial amino acid substitution (N526S) located in the cellulose binding module (CBM) of HcLPMO10 (LPMO of Hahella chejuensis) using directed evolution. The improved variant HcLPMO10 M1 (N526S) exhibits 2.1-fold higher activity for the H2O2 production, 2.7-fold higher oxidation activity, and 1.9-fold higher binding capacity toward cellulose compared with those of the wild type (WT). Furthermore, M1 shows 2.1-fold higher activity for degradation of crystalline cellulose in synergy with cellulase, compared to the WT. Structural analysis through molecular modeling and molecular dynamics (MD) simulation revealed that the substitution N526S located in the CBM likely stabilizes the cellulose binding surface and enhances the binding capacity of HcLPMO10 to cellulose, thereby enhancing enzyme activity. These findings demonstrate the important role of the CBM in the catalytic function of LPMO.
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Affiliation(s)
- Chao Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Junaid Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Zijian Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Tianchen Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Department of Biological Engineering, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, P. R. China
| | - Jianping Lin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, P. R. China
| | - Haifeng Liu
- Institute of Chemistry, NAWI Graz, BioTechMed Graz, University of Graz, Heinrichstrasse 28, Graz 8010, Austria
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
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22
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Wang Z, Feng S, Rovira C, Wang B. How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angew Chem Int Ed Engl 2020; 60:2385-2392. [DOI: 10.1002/anie.202011408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/05/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Shishi Feng
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 08020 Barcelona Spain
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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23
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Kont R, Bissaro B, Eijsink VGH, Väljamäe P. Kinetic insights into the peroxygenase activity of cellulose-active lytic polysaccharide monooxygenases (LPMOs). Nat Commun 2020; 11:5786. [PMID: 33188177 PMCID: PMC7666214 DOI: 10.1038/s41467-020-19561-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/13/2020] [Indexed: 01/06/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are widely distributed in Nature, where they catalyze the hydroxylation of glycosidic bonds in polysaccharides. Despite the importance of LPMOs in the global carbon cycle and in industrial biomass conversion, the catalytic properties of these monocopper enzymes remain enigmatic. Strikingly, there is a remarkable lack of kinetic data, likely due to a multitude of experimental challenges related to the insoluble nature of LPMO substrates, like cellulose and chitin, and to the occurrence of multiple side reactions. Here, we employed competition between well characterized reference enzymes and LPMOs for the H2O2 co-substrate to kinetically characterize LPMO-catalyzed cellulose oxidation. LPMOs of both bacterial and fungal origin showed high peroxygenase efficiencies, with kcat/KmH2O2 values in the order of 105-106 M-1 s-1. Besides providing crucial insight into the cellulolytic peroxygenase reaction, these results show that LPMOs belonging to multiple families and active on multiple substrates are true peroxygenases.
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Affiliation(s)
- Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.,INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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24
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Wang B, Wang Z, Davies GJ, Walton PH, Rovira C. Activation of O2 and H2O2 by Lytic Polysaccharide Monooxygenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02914] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Paul H. Walton
- Department of Chemistry, University of York, Heslington, YO10 5DD, U.K
| | - Carme Rovira
- Departament de Quı́mica Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martı́ i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluı́s Companys, 23, 08020 Barcelona, Spain
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25
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Brander S, Horvath I, Ipsen JØ, Peciulyte A, Olsson L, Hernández-Rollán C, Nørholm MHH, Mossin S, Leggio LL, Probst C, Thiele DJ, Johansen KS. Biochemical evidence of both copper chelation and oxygenase activity at the histidine brace. Sci Rep 2020; 10:16369. [PMID: 33004835 PMCID: PMC7529816 DOI: 10.1038/s41598-020-73266-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/15/2020] [Indexed: 12/22/2022] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) and copper binding protein CopC share a similar mononuclear copper site. This site is defined by an N-terminal histidine and a second internal histidine side chain in a configuration called the histidine brace. To understand better the determinants of reactivity, the biochemical and structural properties of a well-described cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A) is compared with that of CopC from Pseudomonas fluorescens (PfCopC) and with the LPMO-like protein Bim1 from Cryptococcus neoformans. PfCopC is not reduced by ascorbate but is a very strong Cu(II) chelator due to residues that interacts with the N-terminus. This first biochemical characterization of Bim1 shows that it is not redox active, but very sensitive to H2O2, which accelerates the release of Cu ions from the protein. TaAA9A oxidizes ascorbate at a rate similar to free copper but through a mechanism that produce fewer reactive oxygen species. These three biologically relevant examples emphasize the diversity in how the proteinaceous environment control reactivity of Cu with O2.
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Affiliation(s)
- Søren Brander
- Department of Geoscience and Natural Resource Management, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Istvan Horvath
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Johan Ø Ipsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Ausra Peciulyte
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
| | - Cristina Hernández-Rollán
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Susanne Mossin
- Centre for Catalysis and Sustainable Chemistry, Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Corinna Probst
- Department of Biochemistry, Pharmacology and Cancer Biology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dennis J Thiele
- Department of Biochemistry, Pharmacology and Cancer Biology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Katja S Johansen
- Department of Geoscience and Natural Resource Management, University of Copenhagen, 1958, Frederiksberg, Denmark. .,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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26
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Larsson ED, Dong G, Veryazov V, Ryde U, Hedegård ED. Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes? Dalton Trans 2020; 49:1501-1512. [PMID: 31922155 DOI: 10.1039/c9dt04486h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The lytic polysaccharide monooxygenase (LPMO) enzymes boost polysaccharide depolymerization through oxidative chemistry, which has fueled the hope for more energy-efficient production of biofuel. We have recently proposed a mechanism for the oxidation of the polysaccharide substrate (E. D. Hedegård and U. Ryde, Chem. Sci., 2018, 9, 3866-3880). In this mechanism, intermediates with superoxide, oxyl, as well as hydroxyl (i.e. [CuO2]+, [CuO]+ and [CuOH]2+) cores were involved. These complexes can have both singlet and triplet spin states, and both spin-states may be important for how LPMOs function during catalytic turnover. Previous calculations on LPMOs have exclusively been based on density functional theory (DFT). However, different DFT functionals are known to display large differences for spin-state splittings in transition-metal complexes, and this has also been an issue for LPMOs. In this paper, we study the accuracy of DFT for spin-state splittings in superoxide, oxyl, and hydroxyl intermediates involved in LPMO turnover. As reference we employ multiconfigurational perturbation theory (CASPT2).
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Affiliation(s)
- Ernst D Larsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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27
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Courtade G, Ciano L, Paradisi A, Lindley PJ, Forsberg Z, Sørlie M, Wimmer R, Davies GJ, Eijsink VGH, Walton PH, Aachmann FL. Mechanistic basis of substrate-O 2 coupling within a chitin-active lytic polysaccharide monooxygenase: An integrated NMR/EPR study. Proc Natl Acad Sci U S A 2020; 117:19178-19189. [PMID: 32723819 PMCID: PMC7431007 DOI: 10.1073/pnas.2004277117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have a unique ability to activate molecular oxygen for subsequent oxidative cleavage of glycosidic bonds. To provide insight into the mode of action of these industrially important enzymes, we have performed an integrated NMR/electron paramagnetic resonance (EPR) study into the detailed aspects of an AA10 LPMO-substrate interaction. Using NMR spectroscopy, we have elucidated the solution-phase structure of apo-BlLPMO10A from Bacillus licheniformis, along with solution-phase structural characterization of the Cu(I)-LPMO, showing that the presence of the metal has minimal effects on the overall protein structure. We have, moreover, used paramagnetic relaxation enhancement (PRE) to characterize Cu(II)-LPMO by NMR spectroscopy. In addition, a multifrequency continuous-wave (CW)-EPR and 15N-HYSCORE spectroscopy study on the uniformly isotope-labeled 63Cu(II)-bound 15N-BlLPMO10A along with its natural abundance isotopologue determined copper spin-Hamiltonian parameters for LPMOs to markedly improved accuracy. The data demonstrate that large changes in the Cu(II) spin-Hamiltonian parameters are induced upon binding of the substrate. These changes arise from a rearrangement of the copper coordination sphere from a five-coordinate distorted square pyramid to one which is four-coordinate near-square planar. There is also a small reduction in metal-ligand covalency and an attendant increase in the d(x2-y2) character/energy of the singly occupied molecular orbital (SOMO), which we propose from density functional theory (DFT) calculations predisposes the copper active site for the formation of a stable Cu-O2 intermediate. This switch in orbital character upon addition of chitin provides a basis for understanding the coupling of substrate binding with O2 activation in chitin-active AA10 LPMOs.
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Affiliation(s)
- Gaston Courtade
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Luisa Ciano
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
- School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
- Photon Science Institute, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Alessandro Paradisi
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Peter J Lindley
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg Ø, Denmark
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom;
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491 Trondheim, Norway;
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Zhou H, Zhang Y, Li T, Tan H, Li G, Yin H. Distinct Interaction of Lytic Polysaccharide Monooxygenase with Cellulose Revealed by Computational and Biochemical Studies. J Phys Chem Lett 2020; 11:3987-3992. [PMID: 32352790 DOI: 10.1021/acs.jpclett.0c00918] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A distinct interaction pattern of lytic polysaccharide monooxygenases (LPMOs) with their insoluble substrate, cellulose, was revealed through the combination of computational and biochemical approaches. The results indicated that the enzymes can stably bind on the flat hydrophobic surface of cellulose via the interactions of the key residues located in the axis across the conserved distal tyrosine residue and copper ion with two adjacent cellulose chains. Further studies on the correlation of substrate binding and H2O2 accumulation suggested that LPMOs involved in the productive binding on the insoluble polysaccharides not only fail to accumulate H2O2 but also consume the H2O2 produced by the unbound molecules under the lab condition. This was further substantiated by quantum-mechanical calculations. These findings broadened our knowledge of the interaction between enzymes and insoluble substrates and deepened our understanding of the role that H2O2 plays in LPMO activity.
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Affiliation(s)
- Haichuan Zhou
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuebin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Tang Li
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haidong Tan
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Heng Yin
- Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Kinetic analysis of amino acid radicals formed in H 2O 2-driven Cu I LPMO reoxidation implicates dominant homolytic reactivity. Proc Natl Acad Sci U S A 2020; 117:11916-11922. [PMID: 32414932 PMCID: PMC7275769 DOI: 10.1073/pnas.1922499117] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have been proposed to react with both [Formula: see text] and [Formula: see text] as cosubstrates. In this study, the [Formula: see text] reaction with reduced Hypocrea jecorina LPMO9A (CuI-HjLPMO9A) is demonstrated to be 1,000-fold faster than the [Formula: see text] reaction while producing the same oxidized oligosaccharide products. Analysis of the reactivity in the absence of polysaccharide substrate by stopped-flow absorption and rapid freeze-quench (RFQ) electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) yields two intermediates corresponding to neutral tyrosyl and tryptophanyl radicals that are formed along minor reaction pathways. The dominant reaction pathway is characterized by RFQ EPR and kinetic modeling to directly produce CuII-HjLPMO9A and indicates homolytic O-O cleavage. Both optical intermediates exhibit magnetic exchange coupling with the CuII sites reflecting facile electron transfer (ET) pathways, which may be protective against uncoupled turnover or provide an ET pathway to the active site with substrate bound. The reactivities of nonnative organic peroxide cosubstrates effectively exclude the possibility of a ping-pong mechanism.
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30
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Zhang R. Functional characterization of cellulose-degrading AA9 lytic polysaccharide monooxygenases and their potential exploitation. Appl Microbiol Biotechnol 2020; 104:3229-3243. [PMID: 32076777 DOI: 10.1007/s00253-020-10467-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 12/25/2019] [Accepted: 02/12/2020] [Indexed: 01/05/2023]
Abstract
Cellulose-degrading auxiliary activity family 9 (AA9) lytic polysaccharide monooxygenases (LPMOs) are known to be widely distributed among filamentous fungi and participate in the degradation of lignocellulose via the oxidative cleavage of celluloses, cello-oligosaccharides, or hemicelluloses. AA9 LPMOs have been reported to have extensive interactions with not only cellulases but also oxidases. The addition of AA9 LPMOs can greatly reduce the amount of cellulase needed for saccharification and increase the yield of glucose. The discovery of AA9 LPMOs has greatly changed our understanding of how fungi degrade cellulose. In this review, apart from summarizing the recent discoveries related to their catalytic reaction, functional diversity, and practical applications, the stability, expression system, and protein engineering of AA9 LPMOs are reviewed for the first time. This review may provide a reference value to further broaden the substrate range of AA9 LPMOs, expand the scope of their practical applications, and realize their customization for industrial utilization.Key Points• The stability and expression system of AA9 LPMOs are reviewed for the first time.• The protein engineering of AA9 LPMOs is systematically summarized for the first time.• The latest research results on the catalytic mechanism of AA9 LPMOs are summarized.• The application of AA9 LPMOs and their relationship with other enzymes are reviewed.
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Affiliation(s)
- Ruiqin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.
- Department of Bioengineering, Huainan Normal University, No. 278 Xueyuannan Road, Huainan, 232038, China.
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31
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Semenova MV, Gusakov AV, Telitsin VD, Rozhkova AM, Kondratyeva EG, Sinitsyn AP. Purification and characterization of two forms of the homologously expressed lytic polysaccharide monooxygenase (PvLPMO9A) from Penicillium verruculosum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140297. [DOI: 10.1016/j.bbapap.2019.140297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/17/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022]
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32
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum. Acta Crystallogr D Struct Biol 2020; 76:85-86. [PMID: 31909746 PMCID: PMC8573741 DOI: 10.1107/s2059798319016383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
Corrections are published for the article by Caldararu et al. [(2019), Acta Cryst. D75, 368–380].
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33
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Wu P, Fan F, Song J, Peng W, Liu J, Li C, Cao Z, Wang B. Theory Demonstrated a "Coupled" Mechanism for O 2 Activation and Substrate Hydroxylation by Binuclear Copper Monooxygenases. J Am Chem Soc 2019; 141:19776-19789. [PMID: 31746191 DOI: 10.1021/jacs.9b09172] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multiscale simulations have been performed to address the longstanding issue of "dioxygen activation" by the binuclear copper monooxygenases (PHM and DβM), which have been traditionally classified as "noncoupled" binuclear copper enzymes. Our QM/MM calculations rule out that CuM(II)-O2• is an active species for H-abstraction from the substrate. In contrast, CuM(II)-O2• would abstract an H atom from the cosubstrate ascorbate to form a CuM(II)-OOH intermediate in PHM and DβM. Consistent with the recently reported structural features of DβM, the umbrella sampling shows that the "open" conformation of the CuM(II)-OOH intermediate could readily transform into the "closed" conformation in PHM, in which we located a mixed-valent μ-hydroperoxodicopper(I,II) intermediate, (μ-OOH)Cu(I)Cu(II). The subsequent O-O cleavage and OH moiety migration to CuH generate the unexpected species (μ-O•)(μ-OH)Cu(II)Cu(II), which is revealed to be the reactive intermediate responsible for substrate hydroxylation. We also demonstrate that the flexible Met ligand is favorable for O-O cleavage reactions, while the replacement of Met with the strongly bound His ligand would inhibit the O-O cleavage reactivity. As such, the study not only demonstrates a "coupled" mechanism for O2 activation by binuclear copper monooxygenases but also deciphers the full catalytic cycle of PHM and DβM in accord with the available experimental data. These findings of O2 activation and substrate hydroxylation by binuclear copper monooxygenases could expand our understanding of the reactivities of the synthetic monocopper complexes.
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Affiliation(s)
- Peng Wu
- State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences , Fuzhou , Fujian 350002 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , People's Republic of China
| | - Jinshuai Song
- College of Chemistry, and Institute of Green Catalysis , Zhengzhou University , Zhengzhou 450001 , People's Republic of China
| | - Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , People's Republic of China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , People's Republic of China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry , Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences , Fuzhou , Fujian 350002 , People's Republic of China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen , Fujian 361005 , People's Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , People's Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 360015 , People's Republic of China
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34
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Forsberg Z, Sørlie M, Petrović D, Courtade G, Aachmann FL, Vaaje-Kolstad G, Bissaro B, Røhr ÅK, Eijsink VGH. Polysaccharide degradation by lytic polysaccharide monooxygenases. Curr Opin Struct Biol 2019; 59:54-64. [DOI: 10.1016/j.sbi.2019.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/22/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
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35
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Diaz DE, Bhadra M, Karlin KD. Dimethylanilinic N-Oxides and Their Oxygen Surrogacy Role in the Formation of a Putative High-Valent Copper-Oxygen Species. Inorg Chem 2019; 58:13746-13750. [PMID: 31580063 PMCID: PMC6896993 DOI: 10.1021/acs.inorgchem.9b02066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction of p-cyano-N,N-dimethylaniline N-oxide, an O-atom donor, with different copper(I) complexes (at room temperature and in acetone) indicates the formation via O-atom transfer of a high-valent copper oxyl species, CuII-O•, a putative key intermediate in the catalytic cycle of copper-containing monooxygenases. The formation of p-cyano-N-hydroxymethyl-N-methylaniline and p-cyano-N-methylaniline as the main products of the reaction highlight the capability of this species to hydroxylate strong C-H bonds (bond dissociation energy ∼ 90 kcal/mol). A plausible mechanism for the reactivity of this catalytic system is proposed.
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Affiliation(s)
- Daniel E. Diaz
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mayukh Bhadra
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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36
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Neira A, Martínez-Alanis PR, Aullón G, Flores-Alamo M, Zerón P, Company A, Chen J, Kasper JB, Browne WR, Nordlander E, Castillo I. Oxidative Cleavage of Cellobiose by Lytic Polysaccharide Monooxygenase (LPMO)-Inspired Copper Complexes. ACS OMEGA 2019; 4:10729-10740. [PMID: 31460171 PMCID: PMC6648734 DOI: 10.1021/acsomega.9b00785] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
The potentially tridentate ligand bis[(1-methyl-2-benzimidazolyl)ethyl]amine (2BB) was employed to prepare copper complexes [(2BB)CuI]OTf and [(2BB)CuII(H2O)2](OTf)2 as bioinspired models of lytic polysaccharide copper-dependent monooxygenase (LPMO) enzymes. Solid-state characterization of [(2BB)CuI]OTf revealed a Cu(I) center with a T-shaped coordination environment and metric parameters in the range of those observed in reduced LPMOs. Solution characterization of [(2BB)CuII(H2O)2](OTf)2 indicates that [(2BB)CuII(H2O)2]2+ is the main species from pH 4 to 7.5; above pH 7.5, the hydroxo-bridged species [{(2BB)CuII(H2O) x }2(μ-OH)2]2+ is also present, on the basis of cyclic voltammetry and mass spectrometry. These observations imply that deprotonation of the central amine of Cu(II)-coordinated 2BB is precluded, and by extension, amine deprotonation in the histidine brace of LPMOs appears unlikely at neutral pH. The complexes [(2BB)CuI]OTf and [(2BB)CuII(H2O)2](OTf)2 act as precursors for the oxidative degradation of cellobiose as a cellulose model substrate. Spectroscopic and reactivity studies indicate that a dicopper(II) side-on peroxide complex generated from [(2BB)CuI]OTf/O2 or [(2BB)CuII(H2O)2](OTf)2/H2O2/NEt3 oxidizes cellobiose both in acetonitrile and aqueous phosphate buffer solutions, as evidenced from product analysis by high-performance liquid chromatography-mass spectrometry. The mixture of [(2BB)CuII(H2O)2](OTf)2/H2O2/NEt3 results in more extensive cellobiose degradation. Likewise, the use of both [(2BB)CuI]OTf and [(2BB)CuII(H2O)2](OTf)2 with KO2 afforded cellobiose oxidation products. In all cases, a common Cu(II) complex formulated as [(2BB)CuII(OH)(H2O)]+ was detected by mass spectrometry as the final form of the complex.
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Affiliation(s)
- Andrea.
C. Neira
- Instituto
de Química and Facultad de Química, División
de Estudios de Posgrado, Universidad Nacional
Autónoma de México, Circuito Exterior, CU, 04510 Ciudad de
México, México
| | - Paulina R. Martínez-Alanis
- Departament
de Química Inorgànica i Orgànica and Institut
de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Gabriel Aullón
- Departament
de Química Inorgànica i Orgànica and Institut
de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Marcos Flores-Alamo
- Instituto
de Química and Facultad de Química, División
de Estudios de Posgrado, Universidad Nacional
Autónoma de México, Circuito Exterior, CU, 04510 Ciudad de
México, México
| | - Paulino Zerón
- Instituto
de Química and Facultad de Química, División
de Estudios de Posgrado, Universidad Nacional
Autónoma de México, Circuito Exterior, CU, 04510 Ciudad de
México, México
| | - Anna Company
- Institut
de Química Computacional i Catàlisi (IQCC), Departament
de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Juan Chen
- Molecular
Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of
Science and Health, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Johann B. Kasper
- Molecular
Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of
Science and Health, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Wesley R. Browne
- Molecular
Inorganic Chemistry, Stratingh Institute for Chemistry, Faculty of
Science and Health, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Ebbe Nordlander
- Chemical
Physics, Department of Chemistry, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Ivan Castillo
- Instituto
de Química and Facultad de Química, División
de Estudios de Posgrado, Universidad Nacional
Autónoma de México, Circuito Exterior, CU, 04510 Ciudad de
México, México
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37
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Alwan KB, Welch EF, Arias RJ, Gambill BF, Blackburn NJ. Rational Design of a Histidine-Methionine Site Modeling the M-Center of Copper Monooxygenases in a Small Metallochaperone Scaffold. Biochemistry 2019; 58:3097-3108. [PMID: 31243953 DOI: 10.1021/acs.biochem.9b00312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mononuclear copper monooxygenases peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase (DBM) catalyze the hydroxylation of high energy C-H bonds utilizing a pair of chemically distinct copper sites (CuH and CuM) separated by 11 Å. In earlier work, we constructed single-site PHM variants that were designed to allow the study of the M- and H-centers independently in order to place their reactivity sequentially along the catalytic pathway. More recent crystallographic studies suggest that these single-site variants may not be truly representative of the individual active sites. In this work, we describe an alternative approach that uses a rational design to construct an artificial PHM model in a small metallochaperone scaffold. Using site-directed mutagenesis, we constructed variants that provide a His2Met copper-binding ligand set that mimics the M-center of PHM. The results show that the model accurately reproduces the chemical and spectroscopic properties of the M-center, including details of the methionine coordination, and the properties of Cu(I) and Cu(II) states in the presence of endogenous ligands such as CO and azide. The rate of reduction of the Cu(II) form of the model by the chromophoric reductant N,N'-dimethyl phenylenediamine (DMPD) has been compared with that of the PHM M-center, and the reaction chemistry of the Cu(I) forms with molecular oxygen has also been explored, revealing an unusually low reactivity toward molecular oxygen. This latter finding emphasizes the importance of substrate triggering of oxygen reactivity and implies that the His2Met ligand set, while necessary, is insufficient on its own to activate oxygen in these enzyme systems.
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Affiliation(s)
- Katherine B Alwan
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Evan F Welch
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Renee J Arias
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Ben F Gambill
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
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38
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Wang B, Walton PH, Rovira C. Molecular Mechanisms of Oxygen Activation and Hydrogen Peroxide Formation in Lytic Polysaccharide Monooxygenases. ACS Catal 2019; 9:4958-4969. [PMID: 32051771 PMCID: PMC7007194 DOI: 10.1021/acscatal.9b00778] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/17/2019] [Indexed: 12/26/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes for the degradation of recalcitrant polysaccharides such as chitin and cellulose. Unlike classical hydrolytic enzymes (cellulases), LPMOs catalyze the cleavage of the glycosidic bond via an oxidative mechanism using oxygen and a reductant. The full enzymatic molecular mechanisms, starting from the initial electron transfer from a reductant to oxygen activation and hydrogen peroxide formation, are not yet understood. Using quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, we have uncovered the oxygen activation mechanisms by LPMO in the presence of ascorbic acid, one of the most-used reductants in LPMOs assays. Our simulations capture the sequential formation of Cu(II)-O2 - and Cu(II)-OOH- intermediates via facile H atom abstraction from ascorbate. By investigating all the possible reaction pathways from the Cu(II)-OOH- intermediate, we ruled out Cu(II)-O• - formation via direct O-O cleavage of Cu(II)-OOH-. Meanwhile, we identified a possible pathway in which the proximal O atom of Cu(II)-OOH- abstracts a hydrogen atom from ascorbate, leading to Cu(I) and H2O2. The in-situ-generated H2O2 either converts to LPMO-Cu(II)-O• - via a homolytic reaction, or diffuses into the bulk water in an uncoupled pathway. The competition of these two pathways is strongly dependent on the binding of the carbohydrate substrate, which plays a role in barricading the in-situ-generated H2O2 molecule, preventing its diffusion from the active site into the bulk water. Based on the present results, we propose a catalytic cycle of LPMOs that is consistent with the experimental information available. In particular, it explains the enigmatic substrate dependence of the reactivity of the LPMO with H2O2.
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Affiliation(s)
- Binju Wang
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Paul H. Walton
- Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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Hangasky JA, Detomasi TC, Marletta MA. Glycosidic Bond Hydroxylation by Polysaccharide Monooxygenases. TRENDS IN CHEMISTRY 2019. [DOI: 10.1016/j.trechm.2019.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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40
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Caldararu O, Manzoni F, Oksanen E, Logan DT, Ryde U. Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:368-380. [PMID: 30988254 PMCID: PMC6465982 DOI: 10.1107/s205979831900175x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022]
Abstract
A method has been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. Applications to structures of the galectin-3C–lactose complex and lytic polysaccharide monooxygenase show that it can improve the geometry of hydrogen bonds, particularly those involving water molecules, as well as determine the protonation states of key residues. Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Francesco Manzoni
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
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Bailey WD, Dhar D, Cramblitt AC, Tolman WB. Mechanistic Dichotomy in Proton-Coupled Electron-Transfer Reactions of Phenols with a Copper Superoxide Complex. J Am Chem Soc 2019; 141:5470-5480. [PMID: 30907590 DOI: 10.1021/jacs.9b00466] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The kinetics and mechanism(s) of the reactions of [K(Krypt)][LCuO2] (Krypt = 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane, L = a bis(arylcarboxamido)pyridine ligand) with 2,2,6,6-tetramethylpiperdine- N-hydroxide (TEMPOH) and the para-substituted phenols XArOH (X = para substituent NO2, CF3, Cl, H, Me, tBu, OMe, or NMe2) at low temperatures were studied. The reaction with TEMPOH occurs rapidly ( k = 35.4 ± 0.3 M-1 s-1) by second-order kinetics to yield TEMPO• and [LCuOOH]- on the basis of electron paramagnetic resonance spectroscopy, the production of H2O2 upon treatment with protic acid, and independent preparation from reaction of [NBu4][LCuOH] with H2O2 ( Keq = 0.022 ± 0.007 for the reverse reaction). The reactions with XArOH also follow second-order kinetics, and analysis of the variation of the k values as a function of phenol properties (Hammett σ parameter, O-H bond dissociation free energy, p Ka, E1/2) revealed a change in mechanism across the series, from proton transfer/electron transfer for X = NO2, CF3, Cl to concerted-proton/electron transfer (or hydrogen-atom transfer) for X = OMe, NMe2 (data for X = H, Me, tBu are intermediate between the extremes). Thermodynamic analysis and comparisons to previous results for LCuOH, a different copper-oxygen intermediate with the same supporting ligand, and literature for other [CuO2]+ complexes reveal significant differences in proton-coupled electron-transfer mechanisms that have implications for understanding oxidation catalysis by copper-containing enzymes and abiological catalysts.
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Affiliation(s)
- Wilson D Bailey
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive, Campus Box 1134 , St. Louis , Missouri 63130-4899 , United States
| | - Debanjan Dhar
- Department of Chemistry and Center for Metals in Biocatalysis , University of Minnesota , 207 Pleasant Street SE , Minneapolis , Minnesota 55455 , United States
| | - Anna C Cramblitt
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive, Campus Box 1134 , St. Louis , Missouri 63130-4899 , United States
| | - William B Tolman
- Department of Chemistry , Washington University in St. Louis , One Brookings Drive, Campus Box 1134 , St. Louis , Missouri 63130-4899 , United States.,Department of Chemistry and Center for Metals in Biocatalysis , University of Minnesota , 207 Pleasant Street SE , Minneapolis , Minnesota 55455 , United States
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