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Liu Y, Harnden KA, Van Stappen C, Dikanov SA, Lu Y. A designed Copper Histidine-brace enzyme for oxidative depolymerization of polysaccharides as a model of lytic polysaccharide monooxygenase. Proc Natl Acad Sci U S A 2023; 120:e2308286120. [PMID: 37844252 PMCID: PMC10614608 DOI: 10.1073/pnas.2308286120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/03/2023] [Indexed: 10/18/2023] Open
Abstract
The "Histidine-brace" (His-brace) copper-binding site, composed of Cu(His)2 with a backbone amine, is found in metalloproteins with diverse functions. A primary example is lytic polysaccharide monooxygenase (LPMO), a class of enzymes that catalyze the oxidative depolymerization of polysaccharides, providing not only an energy source for native microorganisms but also a route to more effective industrial biomass conversion. Despite its importance, how the Cu His-brace site performs this unique and challenging oxidative depolymerization reaction remains to be understood. To answer this question, we have designed a biosynthetic model of LPMO by incorporating the Cu His-brace motif into azurin, an electron transfer protein. Spectroscopic studies, including ultraviolet-visible (UV-Vis) absorption and electron paramagnetic resonance, confirm copper binding at the designed His-brace site. Moreover, the designed protein is catalytically active towards both cellulose and starch, the native substrates of LPMO, generating degraded oligosaccharides with multiturnovers by C1 oxidation. It also performs oxidative cleavage of the model substrate 4-nitrophenyl-D-glucopyranoside, achieving a turnover number ~9% of that of a native LPMO assayed under identical conditions. This work presents a rationally designed artificial metalloenzyme that acts as a structural and functional mimic of LPMO, which provides a promising system for understanding the role of the Cu His-brace site in LPMO activity and potential application in polysaccharide degradation.
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Affiliation(s)
- Yiwei Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Kevin A. Harnden
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
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2
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Yu X, Zhao Y, Yu J, Wang L. Recent advances in the efficient degradation of lignocellulosic metabolic networks by lytic polysaccharide monooxygenase. Acta Biochim Biophys Sin (Shanghai) 2023; 55:529-539. [PMID: 37036250 DOI: 10.3724/abbs.2023059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
Along with long-term evolution, the plant cell wall generates lignocellulose and other anti-degradation barriers to confront hydrolysis by fungi. Lytic polysaccharide monooxygenase (LPMO) is a newly defined oxidase in lignocellulosic degradation systems that significantly fuels hydrolysis. LPMO accepts electrons from wide sources, such as cellobiose dehydrogenase (CDH), glucose-methanol-choline (GMC) oxidoreductases, and small phenols. In addition, the extracellular cometabolic network formed by cosubstrates improves the degradation efficiency, forming a stable and efficient lignocellulose degradation system. In recent years, using structural proteomics to explore the internal structure and the complex redox system of LPMOs has become a research hotspot. In this review, the diversity of LPMOs, catalytic domains, carbohydrate binding modules, direct electron transfer with CDH, cosubstrates, and degradation networks of LPMOs are explored, which can provide a systematic reference for the application of lignocellulosic degradation systems in industrial approaches.
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Affiliation(s)
- Xinran Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Junhong Yu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao 266035, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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3
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Torbjörnsson M, Hagemann MM, Ryde U, Hedegård ED. Histidine oxidation in lytic polysaccharide monooxygenase. J Biol Inorg Chem 2023; 28:317-328. [PMID: 36828975 PMCID: PMC10036459 DOI: 10.1007/s00775-023-01993-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/26/2023]
Abstract
The lytic polysaccharide monooxygenases (LPMOs) comprise a super-family of copper enzymes that boost the depolymerisation of polysaccharides by oxidatively disrupting the glycosidic bonds connecting the sugar units. Industrial use of LPMOs for cellulose depolymerisation has already begun but is still far from reaching its full potential. One issue is that the LPMOs self-oxidise and thereby deactivate. The mechanism of this self-oxidation is unknown, but histidine residues coordinating to the copper atom are the most susceptible. An unusual methyl modification of the NE2 atom in one of the coordinating histidine residues has been proposed to have a protective role. Furthermore, substrate binding is also known to reduce oxidative damage. We here for the first time investigate the mechanism of histidine oxidation with combined quantum and molecular mechanical (QM/MM) calculations, with outset in intermediates previously shown to form from a reaction with peroxide and a reduced LPMO. We show that an intermediate with a [Cu-O]+ moiety is sufficiently potent to oxidise the nearest C-H bond on both histidine residues, but methylation of the NE2 atom of His-1 increases the reaction barrier of this reaction. The substrate further increases the activation barrier. We also investigate a [Cu-OH]2+ intermediate with a deprotonated tyrosine radical. This intermediate was previously proposed to have a protective role, and we also find it to have higher barriers than the corresponding a [Cu-O]+ intermediate.
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Affiliation(s)
- Magne Torbjörnsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Marlisa M Hagemann
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
| | - Erik Donovan Hedegård
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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4
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Sun XB, Gao DY, Cao JW, Liu Y, Rong ZT, Wang JK, Wang Q. BsLPMO10A from Bacillus subtilis boosts the depolymerization of diverse polysaccharides linked via β-1,4-glycosidic bonds. Int J Biol Macromol 2023; 230:123133. [PMID: 36621733 DOI: 10.1016/j.ijbiomac.2023.123133] [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: 09/13/2022] [Revised: 11/24/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023]
Abstract
Lytic polysaccharide monooxygenase (LPMO) is known as an oxidatively cleaving enzyme in recalcitrant polysaccharide deconstruction. Herein, we report a novel AA10 LPMO derived from Bacillus subtilis (BsLPMO10A). A substrate specificity study revealed that the enzyme exhibited an extensive active-substrate spectrum, particularly for polysaccharides linked via β-1,4 glycosidic bonds, such as β-(Man1 → 4Man), β-(Glc1 → 4Glc) and β-(Xyl1 → 4Xyl). HPAEC-PAD and MALDI-TOF-MS analyses indicated that BsLPMO10A dominantly liberated native oligosaccharides with a degree of polymerization (DP) of 3-6 and C1-oxidized oligosaccharides ranging from DP3ox to DP6ox from mixed linkage glucans and beechwood xylan. Due to its synergistic action with a variety of glycoside hydrolases, including glucanase IDSGLUC5-38, xylanase TfXYN11-1, cellulase IDSGLUC5-11 and chitinase BtCHI18-1, BsLPMO10A dramatically accelerated glucan, xylan, cellulose and chitin saccharification. After co-reaction for 72 h, the reducing sugars in Icelandic moss lichenan, beechwood xylan, phosphoric acid swollen cellulose and chitin yielded 3176 ± 97, 7436 ± 165, 649 ± 44, and 2604 ± 130 μmol/L, which were 1.47-, 1.56-, 1.44- and 1.25-fold higher than those in the GHs alone groups, respectively (P < 0.001). In addition, the synergy of BsLPMO10A and GHs was further validated by the degradation of natural feedstuffs, the co-operation of BsLPMO10A and GHs released 3266 ± 182 and 1725 ± 107 μmol/L of reducing sugars from Oryza sativa L. and Arachis hypogaea L. straws, respectively, which were significantly higher than those produced by GHs alone (P < 0.001). Furthermore, BsLPMO10A also accelerated the liberation of reducing sugars from Celluclast® 1.5 L, a commercial cellulase cocktail, on filter paper, A. hypogaea L. and O. sativa L. straws by 49.58 % (P < 0.05), 72.19 % (P < 0.001) and 54.36 % (P < 0.05), respectively. This work has characterized BsLPMO10A with a broad active-substrate scope, providing a promising candidate for lignocellulosic biomass biorefinery.
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Affiliation(s)
- Xiao-Bao Sun
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - De-Ying Gao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jia-Wen Cao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhou-Ting Rong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Jia-Kun Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qian Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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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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6
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Zhang H, Zhou H, Zhao Y, Li T, Yin H. Comparative studies of two AA10 family lytic polysaccharide monooxygenases from Bacillus thuringiensis. PeerJ 2023; 11:e14670. [PMID: 36684673 PMCID: PMC9851047 DOI: 10.7717/peerj.14670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/09/2022] [Indexed: 01/19/2023] Open
Abstract
Bacillus thuringiensis, known to be one of the most important biocontrol microorganisms, contains three AA10 family lytic polysaccharide monooxygenases (LPMOs) in its genome. In previous reports, two of them, BtLPMO10A and BtLPMO10B, have been preliminarily characterized. However, some important biochemical features and substrate preference, as well as their potential applications in chitin degradation, still deserve further investigation. Results from present study showed that both BtLPMO10A and BtLPMO10B exhibit similar catalytic domains as well as highly conserved substrate-binding planes. However, unlike BtLPMO10A, which has comparable binding ability to both crystalline and amorphous form of chitins, BtLPMO10B exhibited much stronger binding ability to colloidal chitin, which mainly attribute to its carbohydrate-binding module-5 (CBM5). Interestingly, the relative high binding ability of BtLPMO10B to colloidal chitin does not lead to high catalytic activity of the enzyme. In contrast, the enzyme exhibited higher activity on β-chitin. Further experiments showed that the binding of BtLPMO10B to colloidal chitin was mainly non-productive, indicating a complicated role for CBM5 in LPMO activity. Furthermore, synergistic experiments demonstrated that both LPMOs boosted the activity of the chitinase, and the higher efficiency of BtLPMO10A can be overridden by BtLPMO10B.
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Affiliation(s)
- Huiyan Zhang
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Haichuan Zhou
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yong Zhao
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Tang Li
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Heng Yin
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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7
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Hou J, Lei X, Liu B, Wang Z, Fang G, Liu J, Wang S. A study on the catalytic activity of polypeptides toward the hydrolysis of glucoside compounds gastrodin, polydatin and esculin. J Mater Chem B 2022; 10:9878-9886. [PMID: 36437799 DOI: 10.1039/d2tb01758j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The self-assembly of a series of catalytically active polypeptides toward hydrolysis of glucoside compounds, namely, gastrodin, polydatin and esculin was investigated. These active peptides are composed of two functional fragments: one is the hydrophobic sequence LHLHLRL, which forms assembling segments in the presence of Zn ions (Zn2+); another functional sequence of active peptides are catalytic sites such as Glu (E), Asp (D) and His (H), where carboxylic acids (-COOH) or imidazole groups act like scissors to cleave glucoside bonds of the compounds (according to the acid-base coupling mechanism). The effects of the amino acid sequence of the peptide, Zn2+ concentration, pH and the size or steric hindrance of glucoside compounds on the hydrolytic activity were studied. It was found that the crystalline structure of assembled peptides was crucial to provide the peptide with catalytic hydrolytic activity. Noncovalent interaction index was used to analyse the noncovalent interaction of PEs with glucoside compounds, including hydrogen bonds, van der Waals, and steric effect in the complexes. The binding energy of complexes, the direction and site of nucleophilic attack during deglycosylation processes were also investigated by molecular docking and the electron density Laplace function. This revealed that the differences in the hydrolytic activity of peptides toward glucoside compounds with different sizes originated from different hydrogen bond interactions between the peptides and substrates. These active peptides may find application in the preparation of drugs by de-glycosylation of natural compounds.
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Affiliation(s)
- Juan Hou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Xiangmin Lei
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Borui Liu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Zejiang Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Guozhen Fang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Jifeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.
| | - Shuo Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Quality and Healthy of Tianjin, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China. .,Research Center of Food Science and Human Health, School of Medicine, Nankai University, Tianjin, 300071, P. R. China
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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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Dade CM, Douzi B, Cambillau C, Ball G, Voulhoux R, Forest KT. The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases. Acta Crystallogr D Struct Biol 2022; 78:1064-1078. [PMID: 35916229 PMCID: PMC9344471 DOI: 10.1107/s2059798322007033] [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: 04/16/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
The 3 Å resolution crystal structure of the Pseudomonas aeruginosa virulence factor CbpD both supports and challenges the current model of how lytic polysaccharide monooxygenases bind chitin and raises interesting possibilities about how type 2 secretion-system substrates may interact with the secretion machinery. This structure also demonstrates the utility of new, AI-powered, protein structure-prediction algorithms in making challenging structural targets tractable. Pseudomonas aeruginosa secretes diverse proteins via its type 2 secretion system, including a 39 kDa chitin-binding protein, CbpD. CbpD has recently been shown to be a lytic polysaccharide monooxygenase active on chitin and to contribute substantially to virulence. To date, no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the CBM73 domain of Cellvibrio japonicusCjLPMO10A. Here, the 3.0 Å resolution crystal structure of CbpD solved by molecular replacement is reported, which required ab initio models of each CbpD domain generated by the artificial intelligence deep-learning structure-prediction algorithm RoseTTAFold. The structure of CbpD confirms some previously reported substrate-specificity motifs among LPMOAA10s, while challenging the predictive power of others. Additionally, the structure of CbpD shows that post-translational modifications occur on the chitin-binding surface. Moreover, the structure raises interesting possibilities about how type 2 secretion-system substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure-prediction algorithms in making challenging structural targets tractable.
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Saikia J, Bhat VT, Potnuru LR, Redkar AS, Agarwal V, Ramakrishnan V. Minimalist De Novo Design of an Artificial Enzyme. ACS OMEGA 2022; 7:19131-19140. [PMID: 35721939 PMCID: PMC9202009 DOI: 10.1021/acsomega.1c07075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
We employed a reductionist approach in designing the first heterochiral tripeptide that forms a robust heterogeneous short peptide catalyst similar to the "histidine brace" active site of lytic polysaccharide monooxygenases. The histidine brace is a conserved divalent copper ion-binding motif that comprises two histidine side chains and an amino group to create the T-shaped 3N geometry at the reaction center. The geometry parameters, including a large twist angle (73°) between the two imidazole rings of the model complex, are identical to those of native lytic polysaccharide monooxygenases (72.61°). The complex was synthesized and characterized as a structural and functional mimic of the histidine brace. UV-vis, vis-circular dichroism, Raman, and electron paramagnetic resonance spectroscopic analyses suggest a distorted square-pyramidal geometry with a 3N coordination at pH 7. Solution- and solid-state NMR results further confirm the 3N coordination in the copper center of the complex. The complex is pH-dependent and could catalyze the oxidation of benzyl alcohol in water to benzaldehyde with yields up to 82% in 3 h at pH 7 and above at 40 °C. The catalyst achieved 100% selectivity for benzaldehyde compared to conventional copper catalysis. The design of such a minimalist building block for functional soft materials with a pH switch can be a stepping stone in addressing needs for a cleaner and sustainable future catalyst.
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Affiliation(s)
- Jahnu Saikia
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
| | - Venugopal T. Bhat
- Organic
Synthesis and Catalysis Laboratory SRM Research Institute and Department
of Chemistry SRM Institute of Science and Technology, Kattankulathur 603203, Tamilnadu, India
| | - Lokeswara Rao Potnuru
- TIFR
Centre for Interdisciplinary Sciences, Tata
Institute of Fundamental Research Hyderabad, Hyderabad 500107, India
| | - Amay S. Redkar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
| | - Vipin Agarwal
- TIFR
Centre for Interdisciplinary Sciences, Tata
Institute of Fundamental Research Hyderabad, Hyderabad 500107, India
| | - Vibin Ramakrishnan
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
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11
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Karnaouri A, Chorozian K, Zouraris D, Karantonis A, Topakas E, Rova U, Christakopoulos P. Lytic polysaccharide monooxygenases as powerful tools in enzymatically assisted preparation of nano-scaled cellulose from lignocellulose: A review. BIORESOURCE TECHNOLOGY 2022; 345:126491. [PMID: 34871721 DOI: 10.1016/j.biortech.2021.126491] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Nanocellulose, either in the form of fibers or crystals, constitutes a renewable, biobased, biocompatible material with advantageous mechanical properties that can be isolated from lignocellulosic biomass. Enzyme-assisted isolation of nanocellulose is an attractive, environmentally friendly approach that leads to products of higher quality compared to their chemically prepared counterparts. Lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively cleave the β-1,4-glycosidic bond of polysaccharides upon activation of O2 or H2O2 and presence of an electron donor. Their use for treatment of cellulose fibers towards the preparation of nano-scaled cellulose is related to the ability of LPMOs to create nicking points on the fiber surface, thus facilitating fiber disruption and separation. The aim of this review is to describe the mode of action of LPMOs on cellulose fibers towards the isolation of nanostructures, thus highlighting their great potential for the production of nanocellulose as a novel value added product from lignocellulose.
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Affiliation(s)
- Anthi Karnaouri
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Lab, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece; Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
| | - Koar Chorozian
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Lab, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Dimitrios Zouraris
- Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, Zografou, 15780 Athens, Greece
| | - Antonis Karantonis
- Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, Zografou, 15780 Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Lab, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Ulrika Rova
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
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12
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Wahart AJC, Staniland J, Miller GJ, Cosgrove SC. Oxidase enzymes as sustainable oxidation catalysts. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211572. [PMID: 35242351 PMCID: PMC8753158 DOI: 10.1098/rsos.211572] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/03/2021] [Indexed: 05/03/2023]
Abstract
Oxidation is one of the most important processes used by the chemical industry. However, many of the methods that are used pose significant sustainability and environmental issues. Biocatalytic oxidation offers an alternative to these methods, with a now significant enzymatic oxidation toolbox on offer to chemists. Oxidases are one of these options, and as they only depend on molecular oxygen as a terminal oxidant offer perfect atom economy alongside the selectivity benefits afforded by enzymes. This review will focus on examples of oxidase biocatalysts that have been used for the sustainable production of important molecules and highlight some important processes that have been significantly improved through the use of oxidases. It will also consider emerging classes of oxidases, and how they might fit in a future biorefinery approach for the sustainable production of important chemicals.
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Affiliation(s)
- Alice J. C. Wahart
- Lennard-Jones Laboratories, School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | | | - Gavin J. Miller
- Lennard-Jones Laboratories, School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5BG, UK
- The Keele Centre for Glycoscience Research and Training, Keele University, Staffordshire, ST5 5BG, UK
| | - Sebastian C. Cosgrove
- Lennard-Jones Laboratories, School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5BG, UK
- The Keele Centre for Glycoscience Research and Training, Keele University, Staffordshire, ST5 5BG, UK
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13
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Long L, Sun L, Ding D, Chen K, Lin Q, Ding S. Two C1-oxidizing lytic polysaccharide monooxygenases from Ceriporiopsis subvermispora enhance the saccharification of wheat straw by a commercial cellulase cocktail. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Zouraris D, Karnaouri A, Pandis P, Argirusis C, Topakas E, Karantonis A. On the interaction of lytic polysaccharide monooxygenases (LPMOs) with phosphoric acid-swollen cellulose (PASC). J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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15
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Exploitation of Enzymes for the Production of Biofuels: Electrochemical Determination of Kinetic Parameters of LPMOs. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11114715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) consist of a class of enzymes that boost the release of oxidised products from plant biomass, in an approach that is more eco-friendly than the traditional ones, employing harsh chemicals. Since LPMOs are redox enzymes, they could possibly be exploited by immobilisation on electrode surfaces. Such an approach requires knowledge of kinetic and thermodynamic information for the interaction of the enzyme with the electrode surface. In this work, a novel methodology is applied for the determination of such parameters for an LPMO from the filamentous fungus Thermothelomyces thermophila, MtLPMO9H.
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16
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Schröder GC, O’Dell WB, Swartz PD, Meilleur F. Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions. Acta Crystallogr F Struct Biol Commun 2021; 77:128-133. [PMID: 33830078 PMCID: PMC8034432 DOI: 10.1107/s2053230x21002399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/02/2021] [Indexed: 11/10/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper-oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.
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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
| | - William B. O’Dell
- 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
| | - Paul D. Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, 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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17
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Theibich YA, Sauer SP, Leggio LL, Hedegård ED. Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase. Comput Struct Biotechnol J 2020; 19:555-567. [PMID: 33510861 PMCID: PMC7807142 DOI: 10.1016/j.csbj.2020.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 11/07/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
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Affiliation(s)
- Yusuf A. Theibich
- Department of Chemistry, University of University, Copenhagen, Denmark
| | | | - Leila Lo Leggio
- Department of Chemistry, University of University, Copenhagen, Denmark
| | - Erik D. Hedegård
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
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18
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Zhou X, Xu Z, He J, Li Y, Pan C, Wang C, Deng MR, Zhu H. A myxobacterial LPMO10 has oxidizing cellulose activity for promoting biomass enzymatic saccharification of agricultural crop straws. BIORESOURCE TECHNOLOGY 2020; 318:124217. [PMID: 33096440 DOI: 10.1016/j.biortech.2020.124217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Myxobacteria are soil microorganisms with the ability to break down biological macromolecules due to the secretion of a large number of extracellular enzymes, but there has been no research report on myxobacterial lytic polysaccharide monooxygenases (LPMOs). In this study, two LPMO10s, ViLPMO10A and ViLPMO10B, from myxobacterium Vitiosangium sp. GDMCC 1.1324 were characterized. Of which, ViLPMO10B is a C1-oxidizing cellulose-active LPMO. Moreover, ViLPMO10B could decrease the degree of polymerization of crop straws cellulose and synergize with commercial cellulase to promote the saccharification. When the weight ratio of commercial cellulase to ViLPMO10B was 9:1, the conversion efficiency of corn stalk, sugarcane bagasse, and rice straw into reducing sugar was improved by 17%, 16%, and 22%, respectively, compared with commercial cellulase without ViLPMO10B. These results indicate that ViLPMO10B has the potential to be a component of a high-efficient cellulase cocktail and has application value in the saccharification of agricultural residual biomasses.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhiqiang Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jia He
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yueqiu Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Chengxiang Pan
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Chunling Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ming-Rong Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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19
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McEvoy A, Creutzberg J, Singh RK, Bjerrum MJ, Hedegård ED. The role of the active site tyrosine in the mechanism of lytic polysaccharide monooxygenase. Chem Sci 2020; 12:352-362. [PMID: 34163601 PMCID: PMC8178957 DOI: 10.1039/d0sc05262k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Catalytic breakdown of polysaccharides can be achieved more efficiently by means of the enzymes lytic polysaccharide monooxygenases (LPMOs). However, the LPMO mechanism has remained controversial, preventing full exploitation of their potential. One of the controversies has centered around an active site tyrosine, present in most LPMO classes. Recent investigations have for the first time obtained direct (spectroscopic) evidence for the possibility of chemical modification of this tyrosine. However, the spectroscopic features obtained in the different investigations are remarkably different, with absorption maximum at 420 and 490 nm, respectively. In this paper we use density functional theory (DFT) in a QM/MM formulation to reconcile these (apparently) conflicting results. By modeling the spectroscopy as well as the underlying reaction mechanism we can show how formation of two isomers (both involving deprotonation of tyrosine) explains the difference in the observed spectroscopic features. Both isomers have a [TyrO–Cu–OH]+ moiety with the OH in either the cis- or trans-position to a deprotonated tyrosine. Although the cis-[TyrO–Cu–OH]+ moiety is well positioned for oxidation of the substrate, preliminary calculations with the substrate reveal that the reactivity is at best moderate, making a protective role of tyrosine more likely. With QM/MM, we investigate the mechanism of tyrosine deprotonation in lytic polysaccharide monooxygenases. Our results support deprotonation and our calculated UV-vis spectra show that two isomers must be formed to match recent experiments.![]()
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Affiliation(s)
- Aina McEvoy
- Division of Theoretical Chemistry, Lund University Box 124 SE-221 00 Lund Sweden
| | - Joel Creutzberg
- Division of Theoretical Chemistry, Lund University Box 124 SE-221 00 Lund Sweden
| | - Raushan K Singh
- Department of Chemistry, University of Copenhagen Copenhagen Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen Copenhagen Denmark
| | - Erik D Hedegård
- Division of Theoretical Chemistry, Lund University Box 124 SE-221 00 Lund Sweden
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20
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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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21
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Gonçalves AP, Heller J, Rico-Ramírez AM, Daskalov A, Rosenfield G, Glass NL. Conflict, Competition, and Cooperation Regulate Social Interactions in Filamentous Fungi. Annu Rev Microbiol 2020; 74:693-712. [PMID: 32689913 DOI: 10.1146/annurev-micro-012420-080905] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Social cooperation impacts the development and survival of species. In higher taxa, kin recognition occurs via visual, chemical, or tactile cues that dictate cooperative versus competitive interactions. In microbes, the outcome of cooperative versus competitive interactions is conferred by identity at allorecognition loci, so-called kind recognition. In syncytial filamentous fungi, the acquisition of multicellularity is associated with somatic cell fusion within and between colonies. However, such intraspecific cooperation entails risks, as fusion can transmit deleterious genotypes or infectious components that reduce fitness, or give rise to cheaters that can exploit communal goods without contributing to their production. Allorecognition mechanisms in syncytial fungi regulate somatic cell fusion by operating precontact during chemotropic interactions, during cell adherence, and postfusion by triggering programmed cell death reactions. Alleles at fungal allorecognition loci are highly polymorphic, fall into distinct haplogroups, and show evolutionary signatures of balancing selection, similar to allorecognition loci across the tree of life.
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Affiliation(s)
- A Pedro Gonçalves
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Institute of Molecular Biology, Academia Sinica, Nangang District, Taipei 115, Taiwan
| | - Jens Heller
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Perfect Day, Inc., Emeryville, California 94608, USA
| | - Adriana M Rico-Ramírez
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Asen Daskalov
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Gabriel Rosenfield
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Current Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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22
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Liu H, Xie M, Nie S. Recent trends and applications of polysaccharides for microencapsulation of probiotics. FOOD FRONTIERS 2020. [DOI: 10.1002/fft2.11] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Huan Liu
- State Key Laboratory of Food Science and Technology China–Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang China
| | - Mingyong Xie
- State Key Laboratory of Food Science and Technology China–Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology China–Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang China
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23
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Zhou X, Zhu H. Current understanding of substrate specificity and regioselectivity of LPMOs. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0300-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractRenewable biomass such as cellulose and chitin are the most abundant sustainable sources of energy and materials. However, due to the low degradation efficiency of these recalcitrant substrates by conventional hydrolases, these biomass resources cannot be utilized efficiently. In 2010, the discovery of lytic polysaccharide monooxygenases (LPMOs) led to a major breakthrough. Currently, LPMOs are distributed in 7 families in CAZy database, including AA9–11 and AA13–16, with different species origins, substrate specificity and oxidative regioselectivity. Effective application of LPMOs in the biotransformation of biomass resources needs the elucidation of the molecular basis of their function. Since the discovery of LPMOs, great advances have been made in the study of their substrate specificity and regioselectivity, as well as their structural basis, which will be reviewed below.
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24
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Zhou X, Qi X, Huang H, Zhu H. Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity. Int J Mol Sci 2019; 20:ijms20184594. [PMID: 31533304 PMCID: PMC6771041 DOI: 10.3390/ijms20184594] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are key enzymes in both the natural carbon cycle and the biorefinery industry. Understanding the molecular basis of LPMOs acting on polysaccharide substrates is helpful for improving industrial cellulase cocktails. Here we analyzed the sequences, structures, and substrate binding modes of LPMOs to uncover the factors that influence substrate specificity and regioselectivity. Our results showed that the different compositions of a motif located on L2 affect the electrostatic potentials of substrate binding surfaces, which in turn affect substrate specificities of AA10 LPMOs. A conserved Asn at a distance of 7 Å from the active center Cu might, together with the conserved Ser immediately before the second catalytic His, determine the localization of LPMOs on substrate, and thus contribute to C4-oxidizing regioselectivity. The findings in this work provide an insight into the molecular basis of substrate specificity and regioselectivity of LPMOs.
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Affiliation(s)
- Xiaoli Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Xiaohua Qi
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Hongxia Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
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25
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Jones DR, McLean R, Hobbs JK, Abbott DW. A surrogate structural platform informed by ancestral reconstruction and resurrection of a putative carbohydrate binding module hybrid illuminates the neofunctionalization of a pectate lyase. J Struct Biol 2019; 207:279-286. [PMID: 31200020 DOI: 10.1016/j.jsb.2019.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
Yersinia enterocolitica is a pectinolytic zoonotic foodborne pathogen, the genome of which contains pectin-binding proteins and several different classes of pectinases, including polysaccharide lyases (PLs) and an exopolygalacturonase. These proteins operate within a coordinated pathway to completely saccharify homogalacturonan (HG). Polysaccharide lyase family 2 (PL2) is divided into two major subfamilies that are broadly-associated with contrasting 'endolytic' (PL2A) or 'exolytic' (PL2B) activities on HG. In the Y. enterocolitica genome, the PL2A gene is adjacent to an independent carbohydrate binding module from family 32 (YeCBM32), which possesses a N-terminal secretion tag and is known to specifically bind HG. Independent CBMs are rare in nature and, most commonly, are fused to enzymes in order to potentiate catalysis. The unconventional gene architecture of YePL2A and YeCBM32, therefore, may represent an ancestral relic of a fission event that decoupled PL2A from its cognate CBM. To provide further insight into the evolution of this pectinolytic locus and the molecular basis of HG depolymerisation within Y. enterocolitica, we have resurrected a YePL2A-YeCBM32 chimera and demonstrated that the extant PL2A digests HG more efficiently. In addition, we have engineered a tryptophan from the active site of the exolytic YePL2B into YePL2A (YePL2A-K291W) and demonstrated, using X-ray crystallography of substrate complexes, that it is a structural determinant of exo-activity within the PL2 family. In this manner, surrogate structural platforms may assist in the study of phylogenetic relationships informed by extant and resurrected sequences, and can be used to overcome challenging structural problems within carbohydrate active enzyme families.
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Affiliation(s)
- Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Richard McLean
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada.
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26
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Allorecognition upon Fungal Cell-Cell Contact Determines Social Cooperation and Impacts the Acquisition of Multicellularity. Curr Biol 2019; 29:3006-3017.e3. [PMID: 31474536 DOI: 10.1016/j.cub.2019.07.060] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
Somatic cell fusion and conspecific cooperation are crucial social traits for microbial unicellular-to-multicellular transitions, colony expansion, and substrate foraging but are also associated with risks of parasitism. We identified a cell wall remodeling (cwr) checkpoint that acts upon cell contact to assess genetic compatibility and regulate cell wall dissolution during somatic cell fusion in a wild population of the filamentous fungus Neurospora crassa. Non-allelic interactions between two linked loci, cwr-1 and cwr-2, were necessary and sufficient to block cell fusion: cwr-1 encodes a polysaccharide monooxygenase (PMO), a class of enzymes associated with extracellular degradative capacities, and cwr-2 encodes a predicted transmembrane protein. Mutations of sites in CWR-1 essential for PMO catalytic activity abolished the block in cell fusion between formerly incompatible strains. In Neurospora, alleles cwr-1 and cwr-2 were highly polymorphic, fell into distinct haplogroups, and showed trans-species polymorphisms. Distinct haplogroups and trans-species polymorphisms at cwr-1 and cwr-2 were also identified in the distantly related genus Fusarium, suggesting convergent evolution. Proteins involved in chemotropic processes showed extended localization at contact sites, suggesting that cwr regulates the transition between chemotropic growth and cell wall dissolution. Our work revealed an allorecognition surveillance system based on kind discrimination that inhibits cooperative behavior in fungi by blocking cell fusion upon contact, contributing to fungal immunity by preventing formation of chimeras between genetically non-identical colonies.
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27
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Yadav SK, Singh R, Singh PK, Vasudev PG. Insecticidal fern protein Tma12 is possibly a lytic polysaccharide monooxygenase. PLANTA 2019; 249:1987-1996. [PMID: 30903269 DOI: 10.1007/s00425-019-03135-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/09/2019] [Indexed: 05/25/2023]
Abstract
Amino acid sequence and crystal structure analyses of Tma12, an insecticidal protein isolated from the fern Tectaria macrodonta, identify it as a carbohydrate-binding protein belonging to the AA10 family of lytic polysaccharide monooxygenases, and provide the first evidence of AA10 proteins in plants. Tma12, isolated from the fern Tectaria macrodonta, is a next-generation insecticidal protein. Transgenic cotton expressing Tma12 exhibits resistance against whitefly and viral diseases. Beside its insecticidal property, the structure and function of Tma12 are unknown. This limits understanding of the insecticidal mechanism of the protein and targeted improvement in its efficacy. Here we report the amino acid sequence analysis and the crystal structure of Tma12, suggesting that it is possibly a lytic polysaccharide monooxygenase (LPMO) of the AA10 family. Amino acid sequence of Tma12 shows 45% identity with a cellulolytic LPMO of Streptomyces coelicolor. The crystal structure of Tma12, obtained at 2.2 Å resolution, possesses all the major structural characteristics of AA10 LPMOs. A H2O2-based enzymatic assay also supports this finding. It is the first report of the occurrence of LPMO-like protein in a plant. The two facts that Tma12 possesses insecticidal activity and shows structural similarity with LPMOs collectively advocate exploration of microbial LPMOs for insecticidal potential.
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Affiliation(s)
- Sunil K Yadav
- Genetics and Plant Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Rahul Singh
- Genetics and Plant Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Pradhyumna Kumar Singh
- Genetics and Plant Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
| | - Prema G Vasudev
- Metabolic and Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
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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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Chylenski P, Bissaro B, Sørlie M, Røhr ÅK, Várnai A, Horn SJ, Eijsink VG. Lytic Polysaccharide Monooxygenases in Enzymatic Processing of Lignocellulosic Biomass. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00246] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Piotr Chylenski
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Åsmund K. Røhr
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Svein J. Horn
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
| | - Vincent G.H. Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, N-1432 Ås, Norway
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Muthuramalingam S, Maheshwaran D, Velusamy M, Mayilmurugan R. Regioselective oxidative carbon-oxygen bond cleavage catalysed by copper(II) complexes: A relevant model study for lytic polysaccharides monooxygenases activity. J Catal 2019. [DOI: 10.1016/j.jcat.2019.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Caldararu O, Oksanen E, Ryde U, Hedegård ED. Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase. Chem Sci 2019; 10:576-586. [PMID: 30746099 PMCID: PMC6334667 DOI: 10.1039/c8sc03980a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/18/2018] [Indexed: 12/27/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-containing metalloenzymes that can cleave the glycosidic link in polysaccharides. This could become crucial for production of energy-efficient biofuels from recalcitrant polysaccharides. Although LPMOs are considered oxygenases, recent investigations have shown that H2O2 can also act as a co-substrate for LPMOs. Intriguingly, LPMOs generate H2O2 in the absence of a polysaccharide substrate. Here, we elucidate a new mechanism for H2O2 generation starting from an AA10-LPMO crystal structure with an oxygen species bound, using QM/MM calculations. The reduction level and protonation state of this oxygen-bound intermediate has been unclear. However, this information is crucial to the mechanism. We therefore investigate the oxygen-bound intermediate with quantum refinement (crystallographic refinement enhanced with QM calculations), against both X-ray and neutron data. Quantum refinement calculations suggest a Cu(ii)-O-2 system in the active site of the AA10-LPMO and a neutral protonated -NH2 state for the terminal nitrogen atom, the latter in contrast to the original interpretation. Our QM/MM calculations show that H2O2 generation is possible only from a Cu(i) center and that the most favourable reaction pathway is to involve a nearby glutamate residue, adding two electrons and two protons to the Cu(ii)-O-2 system, followed by dissociation of H2O2.
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Affiliation(s)
- Octav Caldararu
- Division 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
- Department of Biochemistry and Structural Biology , Lund University , Chemical Centre , P. O. Box 124 , SE-221 00 Lund , Sweden
| | - Ulf Ryde
- Division of Theoretical Chemistry , Lund University , Chemical Centre , P. O. Box 124 , SE-221 00 Lund , Sweden . ;
| | - Erik D Hedegård
- Division of Theoretical Chemistry , Lund University , Chemical Centre , P. O. Box 124 , SE-221 00 Lund , Sweden . ;
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Arora R, Bharval P, Sarswati S, Sen TZ, Yennamalli RM. Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region. J Mol Graph Model 2018; 88:1-10. [PMID: 30612037 DOI: 10.1016/j.jmgm.2018.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/03/2018] [Accepted: 12/18/2018] [Indexed: 12/17/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), which are found in fungi, bacteria, and viruses, are redox enzymes utilizing copper to break glycosidic bonds in recalcitrant crystalline form of polysaccharides, such as chitin and cellulose. They are classified by the Carbohydrate-Active enZYmes (CAZy) database under various families. LPMOs's structure with a flat substrate binding region has been shown to contribute to its function, however, the role that LPMOs structural dynamics play during polysaccharide degradation and its mechanism of binding towards substrate are relatively unknown. Here, we report an exhaustive implementation of coarse-grained simulations using Elastic Network Models on multiple LPMO structures to shed light on how their structural dynamics contribute to their chemical function. Using Gaussian network models and Anisotropic network models, we show that the substrate binding region is highly flexible with significant and sustained micro-scale level conformational changes. Significantly, the loops on the binding side of the substrate are most mobile, in concert with the dynamic modes influencing the motions during binding. We also observed dynamic differences between four families of LPMO, namely AA9, AA10, AA11, and AA13 that consist of more than one structure. Specifically, the patterns of motion in the loop regions among the AA9 structures are distinct from those in the AA10 structures.
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Affiliation(s)
- Radhika Arora
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Priya Bharval
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Sheena Sarswati
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India
| | - Taner Z Sen
- U.S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA, 94710, USA; Iowa State University, Department of Genetics, Development, and Cell Biology, Ames, IA, 50011, USA
| | - Ragothaman M Yennamalli
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, 173234, India.
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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Jagadeeswaran G, Gainey L, Mort AJ. An AA9-LPMO containing a CBM1 domain in Aspergillus nidulans is active on cellulose and cleaves cello-oligosaccharides. AMB Express 2018; 8:171. [PMID: 30328527 PMCID: PMC6192940 DOI: 10.1186/s13568-018-0701-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/10/2018] [Indexed: 11/14/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper dependent enzymes that carry out oxidative cleavage of cellulose and other polysaccharides. Aspergillus nidulans, an ascomycete fungus that contains multiple AA9 LPMOs in the genome, offers an excellent model system to study their activity during the oxidative degradation of biomass. AN1602, a dual domain AA9-LPMO in A. nidulans appended with a carbohydrate-binding module, CBM1, was expressed in Pichia pastoris for analyzing oxidative cleavage on cellulosic substrates. The mass spectral and HPAEC analyses showed that the enzyme cleaves phosphoric acid swollen cellulose (PASC) in the presence of a reducing agent, yielding a range of cello-oligosaccharides. In addition to the polymeric substrate cellulose, AN1602 is also active on soluble cellohexaose, a property that is restricted to only a few characterized LPMOs. Product analysis of AN1602 cleaved cellohexaose revealed that C4 was the sole site of oxidation. The sequence and predicted structure of the catalytic domain of AN1602 matched very closely to known C4 cellohexaose active enzymes.
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Kadowaki MAS, Várnai A, Jameson JK, T. Leite AE, Costa-Filho AJ, Kumagai PS, Prade RA, Polikarpov I, Eijsink VGH. Functional characterization of a lytic polysaccharide monooxygenase from the thermophilic fungus Myceliophthora thermophila. PLoS One 2018; 13:e0202148. [PMID: 30125294 PMCID: PMC6101365 DOI: 10.1371/journal.pone.0202148] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/27/2018] [Indexed: 12/29/2022] Open
Abstract
Thermophilic fungi are a promising source of thermostable enzymes able to hydrolytically or oxidatively degrade plant cell wall components. Among these enzymes are lytic polysaccharide monooxygenases (LPMOs), enzymes capable of enhancing biomass hydrolysis through an oxidative mechanism. Myceliophthora thermophila (synonym Sporotrichum thermophile), an Ascomycete fungus, expresses and secretes over a dozen different LPMOs. In this study, we report the overexpression and biochemical study of a previously uncharacterized LPMO (MtLPMO9J) from M. thermophila M77 in Aspergillus nidulans. MtLPMO9J is a single-domain LPMO and has 63% sequence similarity with the catalytic domain of NcLPMO9C from Neurospora crassa. Biochemical characterization of MtLPMO9J revealed that it performs C4-oxidation and is active against cellulose, soluble cello-oligosaccharides and xyloglucan. Moreover, biophysical studies showed that MtLPMO9J is structurally stable at pH above 5 and at temperatures up to 50°C. Importantly, LC-MS analysis of the peptides after tryptic digestion of the recombinantly produced protein revealed not only the correct processing of the signal peptide and methylation of the N-terminal histidine, but also partial autoxidation of the catalytic center. This shows that redox conditions need to be controlled, not only during LPMO reactions but also during protein production, to protect LPMOs from oxidative damage.
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Affiliation(s)
- Marco A. S. Kadowaki
- Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - John-Kristian Jameson
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ana E. T. Leite
- Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Antonio J. Costa-Filho
- Department of Physics, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patricia S. Kumagai
- Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Rolf A. Prade
- Departments of Biochemistry & Molecular Biology and Microbiology & Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Igor Polikarpov
- Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Vincent G. H. Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Urresti S, Cartmell A, Liu F, Walton PH, Davies GJ. Structural studies of the unusual metal-ion site of the GH124 endoglucanase from Ruminiclostridium thermocellum. Acta Crystallogr F Struct Biol Commun 2018; 74:496-505. [PMID: 30084399 PMCID: PMC6096483 DOI: 10.1107/s2053230x18006842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022] Open
Abstract
The recent discovery of `lytic' polysaccharide monooxygenases, copper-dependent enzymes for biomass degradation, has provided new impetus for the analysis of unusual metal-ion sites in carbohydrate-active enzymes. In this context, the CAZY family GH124 endoglucanase from Ruminiclostridium thermocellum contains an unusual metal-ion site, which was originally modelled as a Ca2+ site but features aspartic acid, asparagine and two histidine imidazoles as coordinating residues, which are more consistent with a transition-metal binding environment. It was sought to analyse whether the GH124 metal-ion site might accommodate other metals. It is demonstrated through thermal unfolding experiments that this metal-ion site can accommodate a range of transition metals (Fe2+, Cu2+, Mn2+ and Ni2+), whilst the three-dimensional structure and mass spectrometry show that one of the histidines is partially covalently modified and is present as a 2-oxohistidine residue; a feature that is rarely observed but that is believed to be involved in an `off-switch' to transition-metal binding. Atomic resolution (<1.1 Å) complexes define the metal-ion site and also reveal the binding of an unusual fructosylated oligosaccharide, which was presumably present as a contaminant in the cellohexaose used for crystallization. Although it has not been possible to detect a biological role for the unusual metal-ion site, this work highlights the need to study some of the many metal-ion sites in carbohydrate-active enzymes that have long been overlooked or previously mis-assigned.
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Affiliation(s)
- Saioa Urresti
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, England
| | - Feng Liu
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Paul H. Walton
- Department of Chemistry, University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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Zouraris D, Dimarogona M, Karnaouri A, Topakas E, Karantonis A. Direct electron transfer of lytic polysaccharide monooxygenases (LPMOs) and determination of their formal potentials by large amplitude Fourier transform alternating current cyclic voltammetry. Bioelectrochemistry 2018; 124:149-155. [PMID: 30032096 DOI: 10.1016/j.bioelechem.2018.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 11/17/2022]
Abstract
MtLPMO9 and FoLPMO9 are two lytic polysaccharide monooxygenases (LPMOs), from the filamentous fungi Thermothelomyces thermophila and Fusarium oxysporum, respectively. In the present study an attempt has been made to achieve direct electron transfer between these enzymes and a glassy carbon electrode by immobilization in Nafion polyelectrolyte. The method used to ascertain the feasibility of direct electron transfer was large amplitude Fourier transform alternating current voltammetry (FTacV) and the formal potentials of these enzymes were determined at different temperatures. The findings of this paper indicate that LPMOs can be studied by direct electron transfer, which could be exploited in the near future for their biochemical characterization.
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Affiliation(s)
- D Zouraris
- Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Athens, Greece
| | - M Dimarogona
- Section of Process and Environmental Engineering, Department of Chemical Engineering, University of Patras, 26504 Rio, Patras, Greece
| | - A Karnaouri
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Athens, Greece
| | - E Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Athens, Greece
| | - A Karantonis
- Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Athens, Greece.
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Hangasky JA, Marletta MA. A Random-Sequential Kinetic Mechanism for Polysaccharide Monooxygenases. Biochemistry 2018; 57:3191-3199. [PMID: 29683313 DOI: 10.1021/acs.biochem.8b00129] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polysaccharide monooxygenases (PMOs) are mononuclear copper enzymes that catalyze the hydroxylation of polysaccharides leading to the scission of the glycosidic bond. The mechanism, in which PMOs utilize molecular oxygen to oxidize the polysaccharide substrate, still remains largely unknown. Here, steady-state kinetics assays were used to probe the mechanism of oxygen-dependent cellohexaose oxidation catalyzed by MtPMO9E. Kinetic analysis indicated that both kcat/ KM(O2) and kcat/ KM(Glc6) were dependent on the concentration of the second substrate. Inhibition studies using carbon monoxide were also carried out. In addition, KD values for Glc6 were determined for the Cu(I) and Cu(II) forms of the enzyme. Taken together, PMOs follow a random-sequential kinetic mechanism to form a ternary ES-O2 complex. The optimal pH for MtPMO9E turnover was determined to be between pH 6.00 and pH 7.00. Furthermore, the kinetic parameters kcat, kcat/ KM(O2), and kcat/ KM(Glc6) demonstrate a decrease in PMO activity at a low pH and provide equivalent kinetic p Ka's of 5.10. This points to the protonation of a general base required for turnover. These results provide a basis for the initial chemical steps in the mechanism of PMOs.
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Affiliation(s)
- John A Hangasky
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States
| | - Michael A Marletta
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States.,Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
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40
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Hedegård ED, Ryde U. Molecular mechanism of lytic polysaccharide monooxygenases. Chem Sci 2018; 9:3866-3880. [PMID: 29780519 PMCID: PMC5935029 DOI: 10.1039/c8sc00426a] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/23/2018] [Indexed: 11/23/2022] Open
Abstract
The lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism and hence boost generation of biofuel from e.g. cellulose. By employing density functional theory in a combination of quantum mechanics and molecular mechanics (QM/MM), we report a complete description of the molecular mechanism of LPMOs.
The lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism and hence boost generation of biofuel from e.g. cellulose. By employing density functional theory in a combination of quantum mechanics and molecular mechanics (QM/MM), we report a complete description of the molecular mechanism of LPMOs. The QM/MM scheme allows us to describe all reaction steps with a detailed protein environment and we show that this is necessary. Several active species capable of abstracting a hydrogen from the substrate have been proposed previously and starting from recent crystallographic work on a substrate–LPMO complex, we investigate previously suggested paths as well as new ones. We describe the generation of the reactive intermediates, the abstraction of a hydrogen atom from the polysaccharide substrate, as well as the final recombination step in which OH is transferred back to the substrate. We show that a superoxo [CuO2]+ complex can be protonated by a nearby histidine residue (suggested by recent mutagenesis studies and crystallographic work) and, provided an electron source is available, leads to formation of an oxyl-complex after cleavage of the O–O bond and dissociation of water. The oxyl complex either reacts with the substrate or is further protonated to a hydroxyl complex. Both the oxyl and hydroxyl complexes are also readily generated from a reaction with H2O2, which was recently suggested to be the true co-substrate, rather than O2. The C–H abstraction by the oxyl and hydroxy complexes is overall favorable with activation barriers of 69 and 94 kJ mol–1, compared to the much higher barrier (156 kJ mol–1) obtained for the copper–superoxo species. We obtain good structural agreement for intermediates for which structural data are available and the estimated reaction energies agree with experimental rate constants. Thus, our suggested mechanism is the most complete to date and concur with available experimental evidence.
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Affiliation(s)
- Erik Donovan Hedegård
- Department of Theoretical Chemistry , Lund University , P. O. Box 124 , SE-221 00 , Lund , Sweden .
| | - Ulf Ryde
- Department of Theoretical Chemistry , Lund University , P. O. Box 124 , SE-221 00 , Lund , Sweden .
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Bertini L, Breglia R, Lambrughi M, Fantucci P, De Gioia L, Borsari M, Sola M, Bortolotti CA, Bruschi M. Catalytic Mechanism of Fungal Lytic Polysaccharide Monooxygenases Investigated by First-Principles Calculations. Inorg Chem 2017; 57:86-97. [PMID: 29232119 DOI: 10.1021/acs.inorgchem.7b02005] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes that facilitate the degradation of recalcitrant polysaccharides by the oxidative cleavage of glycosidic bonds. They are gaining rapidly increasing attention as key players in biomass conversion, especially for the production of second-generation biofuels. Elucidation of the detailed mechanism of the LPMO reaction is a major step toward the assessment and optimization of LPMO efficacy in industrial biotechnology, paving the way to utilization of sustainable fuel sources. Here, we used density functional theory calculations to study the reaction pathways suggested to date, exploiting a very large active-site model for a fungal AA9 LPMO and using a celloheptaose unit as a substrate mimic. We identify a copper oxyl intermediate as being responsible for H-atom abstraction from the substrate, followed by a rapid, water-assisted hydroxyl rebound, leading to substrate hydroxylation.
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Affiliation(s)
- Luca Bertini
- Department of Biotechnology and Biosciences, University of Milan-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Raffaella Breglia
- Department of Earth and Environmental Sciences, University of Milan-Bicocca , Piazza della Scienza 1, 20126 Milan, Italy
| | | | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences, University of Milan-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | | | | | | | - Maurizio Bruschi
- Department of Earth and Environmental Sciences, University of Milan-Bicocca , Piazza della Scienza 1, 20126 Milan, Italy
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Hedegård ED, Ryde U. Targeting the reactive intermediate in polysaccharide monooxygenases. J Biol Inorg Chem 2017; 22:1029-1037. [PMID: 28698982 PMCID: PMC5613103 DOI: 10.1007/s00775-017-1480-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/29/2017] [Indexed: 01/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism, making them interesting for the production of biofuel from cellulose. However, the details of this activation are unknown; in particular, the nature of the intermediate that attacks the glycoside C-H bond in the polysaccharide is not known, and a number of different species have been suggested. The homolytic bond-dissociation energy (BDE) has often been used as a descriptor for the bond-activation power, especially for inorganic model complexes. We have employed quantum-chemical cluster calculations to estimate the BDE for a number of possible LPMO intermediates to bridge the gap between model complexes and the actual LPMO active site. The calculated BDEs suggest that the reactive intermediate is either a Cu(II)-oxyl, a Cu(III)-oxyl, or a Cu(III)-hydroxide, which indicate that O-O bond breaking occurs before the C-H activation step.
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Affiliation(s)
- Erik D. Hedegård
- Department of Chemistry, Chemical Centre, Lund University, Sölvegatan 39, Lund, Sweden
| | - Ulf Ryde
- Department of Chemistry, Chemical Centre, Lund University, Sölvegatan 39, Lund, Sweden
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43
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Fungal lytic polysaccharide monooxygenases from family AA9: Recent developments and application in lignocelullose breakdown. Int J Biol Macromol 2017; 102:771-778. [DOI: 10.1016/j.ijbiomac.2017.04.077] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022]
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44
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Tanghe M, Danneels B, Last M, Beerens K, Stals I, Desmet T. Disulfide bridges as essential elements for the thermostability of lytic polysaccharide monooxygenase LPMO10C from Streptomyces coelicolor. Protein Eng Des Sel 2017; 30:401-408. [PMID: 28338903 DOI: 10.1093/protein/gzx014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/20/2017] [Indexed: 12/17/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are crucial components of cellulase mixtures but their stability has not yet been studied in detail, let alone been engineered for industrial applications. In this work, we have evaluated the importance of disulfide bridges for the thermodynamic stability of Streptomyces coelicolor LPMO10C. Interestingly, this enzyme was found to retain 34% of its activity after 2-h incubation at 80°C while its apparent melting temperature (Tm) is only 51°C. When its three disulfide bridges were broken, however, irreversible unfolding occurred and no residual activity could be detected after a similar heat treatment. Based on these findings, additional disulfide bridges were introduced, as predicted by computational tools (MOdelling of DIsulfide bridges in Proteins (MODiP) and Disulfide by Design (DbD)) and using the most flexible positions in the structure as target sites. Four out of 16 variants displayed an improvement in Tm, ranging from 2 to 9°C. Combining the positive mutations yielded additional improvements (up to 19°C) but aberrant unfolding patterns became apparent in some cases, resulting in a diminished capacity for heat resistance. Nonetheless, the best variant, a combination of A143C-P183C and S73C-A115C, displayed a 12°C increase in Tm and was able to retain and was able to retain no less than 60% of its activity after heat treatment.
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Affiliation(s)
- Magali Tanghe
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Barbara Danneels
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Matthias Last
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ingeborg Stals
- Industrial Catalysis and Adsorption Technology (INCAT), Faculty of Engineering and Architecture, Ghent University, Valentin Vaerwyckweg 1, B-9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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45
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Physiological and Molecular Understanding of Bacterial Polysaccharide Monooxygenases. Microbiol Mol Biol Rev 2017; 81:81/3/e00015-17. [PMID: 28659491 DOI: 10.1128/mmbr.00015-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria have long been known to secrete enzymes that degrade cellulose and chitin. The degradation of these two polymers predominantly involves two enzyme families that work synergistically with one another: glycoside hydrolases (GHs) and polysaccharide monooxygenases (PMOs). Although bacterial PMOs are a relatively recent addition to the known biopolymer degradation machinery, there is an extensive amount of literature implicating PMO in numerous physiological roles. This review focuses on these diverse and physiological aspects of bacterial PMOs, including facilitating endosymbiosis, conferring a nutritional advantage, and enhancing virulence in pathogenic organisms. We also discuss the correlation between the presence of PMOs and bacterial lifestyle and speculate on the advantages conferred by PMOs under these conditions. In addition, the molecular aspects of bacterial PMOs, as well as the mechanisms regulating PMO expression and the function of additional domains associated with PMOs, are described. We anticipate that increasing research efforts in this field will continue to expand our understanding of the molecular and physiological roles of bacterial PMOs.
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46
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Span EA, Suess DLM, Deller MC, Britt RD, Marletta MA. The Role of the Secondary Coordination Sphere in a Fungal Polysaccharide Monooxygenase. ACS Chem Biol 2017; 12:1095-1103. [PMID: 28257189 DOI: 10.1021/acschembio.7b00016] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polysaccharide monooxygenases (PMOs) are secreted metalloenzymes that catalyze the oxidative degradation of polysaccharides in a copper-, oxygen-, and reductant-dependent manner. Cellulose-active fungal PMOs degrade cellulosic substrates to be utilized as a carbon source for fungal growth. To gain insight into the PMO mechanism, the role of conserved residues in the copper coordination sphere was investigated. Here, we report active-site hydrogen-bonding motifs in the secondary copper coordination sphere of MtPMO3*, a C1-oxidizing PMO from the ascomycete fungus Myceliophthora thermophila. A series of point substitutions that disrupt this conserved network are used to interrogate its function. Activity assays, in conjunction with EPR spectroscopy, demonstrate that residues H161 and Q167 are involved in stabilizing bound oxygen, and H161 appears to play a role in proton transfer. Additionally, Q167 increases the ligand donor strength of Y169 to the copper via a hydrogen-bonding interaction. Altogether, H161 and Q167 are important for oxygen activation, and the results are suggestive of a copper-oxyl active intermediate.
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Affiliation(s)
- Elise A. Span
- Biophysics
Graduate Group, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel L. M. Suess
- Department
of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Marc C. Deller
- The
Joint Center for Structural Genomics, The Scripps Research Institute, La
Jolla, California 92037, United States
| | - R. David Britt
- Department
of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Michael A. Marletta
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
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47
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Quist DA, Diaz DE, Liu JJ, Karlin KD. Activation of dioxygen by copper metalloproteins and insights from model complexes. J Biol Inorg Chem 2017; 22:253-288. [PMID: 27921179 PMCID: PMC5600896 DOI: 10.1007/s00775-016-1415-2] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/11/2016] [Indexed: 02/08/2023]
Abstract
Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof. An emphasis has also been placed on cofactor biogenesis, a fundamentally important process whereby biomolecules are post-translationally modified by the pro-enzyme active site to generate cofactors which are essential for the catalytic enzymatic reaction. Significant questions remaining in copper-ion-mediated O2-activation in copper proteins are addressed.
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Affiliation(s)
- David A Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Daniel E Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeffrey J Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.
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48
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Hedegård ED, Ryde U. Multiscale Modelling of Lytic Polysaccharide Monooxygenases. ACS OMEGA 2017; 2:536-545. [PMID: 31457454 PMCID: PMC6641039 DOI: 10.1021/acsomega.6b00521] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 05/27/2023]
Abstract
Lytic polysaccharide monooxygenase (LPMO) enzymes have attracted considerable attention owing to their ability to enhance polysaccharide depolymerization, making them interesting with respect to production of biofuel from cellulose. LPMOs are metalloenzymes that contain a mononuclear copper active site, capable of activating dioxygen. However, many details of this activation are unclear. Some aspects of the mechanism have previously been investigated from a computational angle. Yet, either these studies have employed only molecular mechanics (MM), which are inaccurate for metal active sites, or they have described only the active site with quantum mechanics (QM) and neglected the effect of the protein. Here, we employ hybrid QM and MM (QM/MM) methods to investigate the first steps of the LPMO mechanism, which is reduction of CuII to CuI and the formation of a CuII-superoxide complex. In the latter complex, the superoxide can bind either in an equatorial or an axial position. For both steps, we obtain structures that are markedly different from previous suggestions, based on small QM-cluster calculations. Our calculations show that the equatorial isomer of the superoxide complex is over 60 kJ/mol more stable than the axial isomer because it is stabilized by interactions with a second-coordination-sphere glutamine residue, suggesting a possible role for this residue. The coordination of superoxide in this manner agrees with recent experimental suggestions.
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49
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Concia AL, Beccia MR, Orio M, Ferre FT, Scarpellini M, Biaso F, Guigliarelli B, Réglier M, Simaan AJ. Copper Complexes as Bioinspired Models for Lytic Polysaccharide Monooxygenases. Inorg Chem 2017; 56:1023-1026. [DOI: 10.1021/acs.inorgchem.6b02165] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alda Lisa Concia
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Francine Terra Ferre
- Instituto de Química, Universidade Federal do Rio de Janerio, Ilha da Cidade Universitária, 219414-909 Rio de Janeiro, Brazil
| | - Marciela Scarpellini
- Instituto de Química, Universidade Federal do Rio de Janerio, Ilha da Cidade Universitária, 219414-909 Rio de Janeiro, Brazil
| | | | | | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - A. Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
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50
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Effect of Glycyrrhiza uralensis Fisch polysaccharide on growth performance and immunologic function in mice in Ural City, Xinjiang. ASIAN PAC J TROP MED 2016; 9:1078-1083. [DOI: 10.1016/j.apjtm.2016.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/07/2016] [Accepted: 08/10/2016] [Indexed: 11/19/2022] Open
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