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Journal articles on the topic 'Copper monooxygenases'

Author: Grafiati

Published: 25 May 2024

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1

Fukatsu, Arisa, Yuma Morimoto, Hideki Sugimoto, and Shinobu Itoh. "Modelling a ‘histidine brace’ motif in mononuclear copper monooxygenases." Chemical Communications 56, no. 38 (2020): 5123–26. http://dx.doi.org/10.1039/d0cc01392g.

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A mononuclear copper complex bearing a ‘histidine brace’ is synthesised and characterised as an active-site model of mononuclear copper monooxygenases such as lytic polysaccharide monooxygenases (LPMOs) and particulate methane monooxygenase (pMMO).

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2

Musiani, Francesco, Valquiria Broll, Elisa Evangelisti, and Stefano Ciurli. "The model structure of the copper-dependent ammonia monooxygenase." JBIC Journal of Biological Inorganic Chemistry 25, no. 7 (September 14, 2020): 995–1007. http://dx.doi.org/10.1007/s00775-020-01820-0.

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Abstract Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract

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3

Liew, Elissa F., Daochen Tong, Nicholas V. Coleman, and Andrew J. Holmes. "Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper-containing membrane monooxygenase activity." Microbiology 160, no. 6 (June 1, 2014): 1267–77. http://dx.doi.org/10.1099/mic.0.078584-0.

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The hydrocarbon monooxygenase (HMO) of Mycobacterium NBB4 is a member of the copper-containing membrane monooxygenase (CuMMO) superfamily, which also contains particulate methane monooxygenases (pMMOs) and ammonia monooxygenases (AMOs). CuMMOs have broad applications due to their ability to catalyse the oxidation of difficult substrates of environmental and industrial relevance. Most of our understanding of CuMMO biochemistry is based on pMMOs and AMOs as models. All three available structures are from pMMOs. These share two metal sites: a dicopper centre coordinated by histidine residues in subunit-B and a ‘variable-metal’ site coordinated by carboxylate and histidine residues from subunit-C. The exact nature and role of these sites is strongly debated. Significant barriers to progress have been the physiologically specialized nature of methanotrophs and autotrophic ammonia-oxidizers, lack of a recombinant expression system for either enzyme and difficulty in purification of active protein. In this study we use the newly developed HMO model system to perform site-directed mutagenesis on the predicted metal-binding residues in the HmoB and HmoC of NBB4 HMO. All mutations of predicted HmoC metal centre ligands abolished enzyme activity. Mutation of a predicted copper-binding residue of HmoB (B-H155V) reduced activity by 81 %. Mutation of a site that shows conservation within physiologically defined subgroups of CuMMOs was shown to reduce relative HMO activity towards larger alkanes. The study demonstrates that the modelled dicopper site of subunit-B is not sufficient for HMO activity and that a metal centre predicted to be coordinated by residues in subunit-C is essential for activity.

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4

Farhan Ul Haque, Muhammad, Bhagyalakshmi Kalidass, Nathan Bandow, Erick A. Turpin, Alan A. DiSpirito, and Jeremy D. Semrau. "Cerium Regulates Expression of Alternative Methanol Dehydrogenases in Methylosinus trichosporium OB3b." Applied and Environmental Microbiology 81, no. 21 (August 21, 2015): 7546–52. http://dx.doi.org/10.1128/aem.02542-15.

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ABSTRACTMethanotrophs have multiple methane monooxygenases that are well known to be regulated by copper, i.e., a “copper switch.” At low copper/biomass ratios the soluble methane monooxygenase (sMMO) is expressed while expression and activity of the particulate methane monooxygenase (pMMO) increases with increasing availability of copper. In many methanotrophs there are also multiple methanol dehydrogenases (MeDHs), one based on Mxa and another based on Xox. Mxa-MeDH is known to have calcium in its active site, while Xox-MeDHs have been shown to have rare earth elements in their active site. We show here that the expression levels of Mxa-MeDH and Xox-MeDH inMethylosinus trichosporiumOB3b significantly decreased and increased, respectively, when grown in the presence of cerium but the absence of copper compared to the absence of both metals. Expression of sMMO and pMMO was not affected. In the presence of copper, the effect of cerium on gene expression was less significant, i.e., expression of Mxa-MeDH in the presence of copper and cerium was slightly lower than in the presence of copper alone, but Xox-MeDH was again found to increase significantly. As expected, the addition of copper caused sMMO and pMMO expression levels to significantly decrease and increase, respectively, but the simultaneous addition of cerium had no discernible effect on MMO expression. As a result, it appears Mxa-MeDH can be uncoupled from methane oxidation by sMMO inM. trichosporiumOB3b but not from pMMO.

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5

Vu, Van V., and Son Tung Ngo. "Copper active site in polysaccharide monooxygenases." Coordination Chemistry Reviews 368 (August 2018): 134–57. http://dx.doi.org/10.1016/j.ccr.2018.04.005.

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6

Blackburn, Ninian J., Brian Reedy, Eilleen Zhou, Robert Carr, and Steven J. Benkovic. "Chemistry and spectroscopy of copper monooxygenases." Journal of Inorganic Biochemistry 47, no. 3-4 (July 1992): 8. http://dx.doi.org/10.1016/0162-0134(92)84079-3.

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7

Choi, Dong-W., Ryan C. Kunz, Eric S. Boyd, Jeremy D. Semrau, William E. Antholine, J. I. Han, James A. Zahn, Jeffrey M. Boyd, Arlene M. de la Mora, and Alan A. DiSpirito. "The Membrane-Associated Methane Monooxygenase (pMMO) and pMMO-NADH:Quinone Oxidoreductase Complex from Methylococcus capsulatus Bath." Journal of Bacteriology 185, no. 19 (October 1, 2003): 5755–64. http://dx.doi.org/10.1128/jb.185.19.5755-5764.2003.

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ABSTRACT Improvements in purification of membrane-associated methane monooxygenase (pMMO) have resulted in preparations of pMMO with activities more representative of physiological rates: i.e., >130 nmol · min−1 · mg of protein−1. Altered culture and assay conditions, optimization of the detergent/protein ratio, and simplification of the purification procedure were responsible for the higher-activity preparations. Changes in the culture conditions focused on the rate of copper addition. To document the physiological events that occur during copper addition, cultures were initiated in medium with cells expressing soluble methane monooxygenase (sMMO) and then monitored for morphological changes, copper acquisition, fatty acid concentration, and pMMO and sMMO expression as the amended copper concentration was increased from 0 (approximately 0.3 μM) to 95 μM. The results demonstrate that copper not only regulates the metabolic switch between the two methane monooxygenases but also regulates the level of expression of the pMMO and the development of internal membranes. With respect to stabilization of cell-free pMMO activity, the highest cell-free pMMO activity was observed when copper addition exceeded maximal pMMO expression. Optimization of detergent/protein ratios and simplification of the purification procedure also contributed to the higher activity levels in purified pMMO preparations. Finally, the addition of the type 2 NADH:quinone oxidoreductase complex (NADH dehydrogenase [NDH]) from M. capsulatus Bath, along with NADH and duroquinol, to enzyme assays increased the activity of purified preparations. The NDH and NADH were added to maintain a high duroquinol/duroquinone ratio.

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8

Hedegård, Erik Donovan, and Ulf Ryde. "Molecular mechanism of lytic polysaccharide monooxygenases." Chemical Science 9, no. 15 (2018): 3866–80. http://dx.doi.org/10.1039/c8sc00426a.

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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.

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9

Itoh, Shinobu, and Shunichi Fukuzumi. "Dioxygen Activation by Copper Complexes. Mechanistic Insights into Copper Monooxygenases and Copper Oxidases." Bulletin of the Chemical Society of Japan 75, no. 10 (October 2002): 2081–95. http://dx.doi.org/10.1246/bcsj.75.2081.

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10

Maiti, Debabrata, Amy A. Narducci Sarjeant, and Kenneth D. Karlin. "Copper−Hydroperoxo-Mediated N-Debenzylation Chemistry Mimicking Aspects of Copper Monooxygenases." Inorganic Chemistry 47, no. 19 (October 6, 2008): 8736–47. http://dx.doi.org/10.1021/ic800617m.

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11

Fujisawa, K., T. Katayama, N. Kitajima, and Y. Moro-oka. "Reaction aspects of peroxo copper complexes relevant to copper containing monooxygenases." Journal of Inorganic Biochemistry 43, no. 2-3 (August 1991): 216. http://dx.doi.org/10.1016/0162-0134(91)84208-q.

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12

Migliore, Agostino, and David N. Beratan. "Cu-To-Cu Electron Tunneling in Copper Monooxygenases." Biophysical Journal 106, no. 2 (January 2014): 588a. http://dx.doi.org/10.1016/j.bpj.2013.11.3259.

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13

Ciano, Luisa, Alessandro Paradisi, Glyn R. Hemsworth, Morten Tovborg, Gideon J. Davies, and Paul H. Walton. "Insights from semi-oriented EPR spectroscopy studies into the interaction of lytic polysaccharide monooxygenases with cellulose." Dalton Transactions 49, no. 11 (2020): 3413–22. http://dx.doi.org/10.1039/c9dt04065j.

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Semi-orientated EPR spectroscopy reveals that lytic polysaccharide monooxygenases interact with their natural cellulose substrate in a specific way, where the copper active site is positioned adjacent to the edge of a crystalline cellulose fibril.

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14

ITO, M., K. FUJISAWA, N. KITAJIMA, and Y. MORO-OKA. "ChemInform Abstract: Model Studies on Nonheme Monooxygenases. Chemical Models for Nonheme Iron and Copper Monooxygenases." ChemInform 28, no. 28 (August 3, 2010): no. http://dx.doi.org/10.1002/chin.199728284.

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15

Bissaro, Bastien, and Vincent G. H. Eijsink. "Lytic polysaccharide monooxygenases: enzymes for controlled and site-specific Fenton-like chemistry." Essays in Biochemistry 67, no. 3 (March 2023): 575–84. http://dx.doi.org/10.1042/ebc20220250.

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Abstract The discovery of oxidative cleavage of glycosidic bonds by enzymes currently known as lytic polysaccharide monooxygenases (LPMOs) has profoundly changed our current understanding of enzymatic processes underlying the conversion of polysaccharides in the biosphere. LPMOs are truly unique enzymes, harboring a single copper atom in a solvent-exposed active site, allowing them to oxidize C-H bonds at the C1 and/or C4 carbon of glycosidic linkages found in recalcitrant, often crystalline polysaccharides such as cellulose and chitin. To catalyze this challenging reaction, LPMOs harness and control a powerful oxidative reaction that involves Fenton-like chemistry. In this essay, we first draw a brief portrait of the LPMO field, notably explaining the shift from the monooxygenase paradigm (i.e., using O2 as cosubstrate) to that of a peroxygenase (i.e., using H2O2). Then, we briefly review current understanding of how LPMOs generate and control a hydroxyl radical (HO•) generated through Cu(I)-catalyzed H2O2 homolysis, and how this radical is used to create the proposed Cu(II)-oxyl species, abstracting hydrogen atom of the C-H bond. We also point at the complexity of analyzing redox reactions involving reactive oxygen species and address potential deficiencies in the interpretation of existing LPMO data. Being the first copper enzymes shown to enable site-specific Fenton-like chemistry, and maybe not the only ones, LPMOs may serve as a blueprint for future research on monocopper peroxygenases.

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16

Murrell, J. Colin, Ian R. McDonald, and Bettina Gilbert. "Regulation of expression of methane monooxygenases by copper ions." Trends in Microbiology 8, no. 5 (May 2000): 221–25. http://dx.doi.org/10.1016/s0966-842x(00)01739-x.

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17

Concia, Alda Lisa, Maria Rosa Beccia, Maylis Orio, Francine Terra Ferre, Marciela Scarpellini, Frédéric Biaso, Bruno Guigliarelli, Marius Réglier, and A. Jalila Simaan. "Copper Complexes as Bioinspired Models for Lytic Polysaccharide Monooxygenases." Inorganic Chemistry 56, no. 3 (January 6, 2017): 1023–26. http://dx.doi.org/10.1021/acs.inorgchem.6b02165.

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18

Beeson, William T., Christopher M. Phillips, Jamie H. D. Cate, and Michael A. Marletta. "Oxidative Cleavage of Cellulose by Fungal Copper-Dependent Polysaccharide Monooxygenases." Journal of the American Chemical Society 134, no. 2 (December 28, 2011): 890–92. http://dx.doi.org/10.1021/ja210657t.

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19

Ngo, Son Tung, Han N. Phan, Chinh N. Le, Nhung C. T. Ngo, Khanh Bao Vu, Nguyen Thanh Tung, Cuong X. Luu, and Van V. Vu. "Fine Tuning of the Copper Active Site in Polysaccharide Monooxygenases." Journal of Physical Chemistry B 124, no. 10 (January 28, 2020): 1859–65. http://dx.doi.org/10.1021/acs.jpcb.9b08114.

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20

Bogush, T. A., F. V. Donenko, S. M. Sitdikova, and N. V. Andronova. "Interaction of the copper complex Cu-2 with liver monooxygenases." Bulletin of Experimental Biology and Medicine 104, no. 4 (October 1987): 1394–96. http://dx.doi.org/10.1007/bf00834954.

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21

Hamamura, Natsuko, Chris M. Yeager, and Daniel J. Arp. "Two Distinct Monooxygenases for Alkane Oxidation inNocardioides sp. Strain CF8." Applied and Environmental Microbiology 67, no. 11 (November 1, 2001): 4992–98. http://dx.doi.org/10.1128/aem.67.11.4992-4998.2001.

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ABSTRACT Alkane monooxygenases in Nocardioides sp. strain CF8 were examined at the physiological and genetic levels. Strain CF8 can utilize alkanes ranging in chain length from C2 to C16. Butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. Growth on butane and hexane was strongly inhibited by 1-hexyne, while 1-hexyne did not affect growth on octane or decane. A specific 30-kDa acetylene-binding polypeptide was observed for butane-, hexane-, octane-, and decane-grown cells but was absent from cells grown with octane or decane in the presence of 1-hexyne. These results suggest the presence of two monooxygenases in strain CF8. Degenerate primers designed for PCR amplification of genes related to the binuclear-iron-containing alkane hydroxylase fromPseudomonas oleovorans were used to clone a related gene from strain CF8. Reverse transcription-PCR and Northern blot analysis showed that this gene encoding a binuclear-iron-containing alkane hydroxylase was expressed in cells grown on alkanes above C6. These results indicate the presence of two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8.

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22

Bissaro, Bastien, Bennett Streit, Ingvild Isaksen, Vincent G. H. Eijsink, Gregg T. Beckham, Jennifer L. DuBois, and Åsmund K. Røhr. "Molecular mechanism of the chitinolytic peroxygenase reaction." Proceedings of the National Academy of Sciences 117, no. 3 (January 6, 2020): 1504–13. http://dx.doi.org/10.1073/pnas.1904889117.

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Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of monocopper enzymes broadly distributed across the tree of life. Recent reports indicate that LPMOs can use H2O2 as an oxidant and thus carry out a novel type of peroxygenase reaction involving unprecedented copper chemistry. Here, we present a combined computational and experimental analysis of the H2O2-mediated reaction mechanism. In silico studies, based on a model of the enzyme in complex with a crystalline substrate, suggest that a network of hydrogen bonds, involving both the enzyme and the substrate, brings H2O2 into a strained reactive conformation and guides a derived hydroxyl radical toward formation of a copper–oxyl intermediate. The initial cleavage of H2O2 and subsequent hydrogen atom abstraction from chitin by the copper–oxyl intermediate are the main energy barriers. Stopped-flow fluorimetry experiments demonstrated that the priming reduction of LPMO–Cu(II) to LPMO–Cu(I) is a fast process compared to the reoxidation reactions. Using conditions resulting in single oxidative events, we found that reoxidation of LPMO–Cu(I) is 2,000-fold faster with H2O2 than with O2, the latter being several orders of magnitude slower than rates reported for other monooxygenases. The presence of substrate accelerated reoxidation by H2O2, whereas reoxidation by O2 became slower, supporting the peroxygenase paradigm. These insights into the peroxygenase nature of LPMOs will aid in the development and application of enzymatic and synthetic copper catalysts and contribute to a further understanding of the roles of LPMOs in nature, varying from biomass conversion to chitinolytic pathogenesis-defense mechanisms.

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23

Merkler, David J., Raviraj Kulathila, Wilson A. Francisco, David E. Ash, and Joseph Bell. "The irreversible inactivation of two copper-dependent monooxygenases by sulfite: peptidylglycine α-amidating enzyme and dopamine β-monooxygenase." FEBS Letters 366, no. 2-3 (June 12, 1995): 165–69. http://dx.doi.org/10.1016/0014-5793(95)00516-c.

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24

Cowley, Ryan E., Li Tian, and Edward I. Solomon. "Mechanism of O2 activation and substrate hydroxylation in noncoupled binuclear copper monooxygenases." Proceedings of the National Academy of Sciences 113, no. 43 (October 10, 2016): 12035–40. http://dx.doi.org/10.1073/pnas.1614807113.

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Peptidylglycine α-hydroxylating monooxygenase (PHM) and dopamine β-monooxygenase (DβM) are copper-dependent enzymes that are vital for neurotransmitter regulation and hormone biosynthesis. These enzymes feature a unique active site consisting of two spatially separated (by 11 Å in PHM) and magnetically noncoupled copper centers that enables 1e– activation of O2 for hydrogen atom abstraction (HAA) of substrate C–H bonds and subsequent hydroxylation. Although the structures of the resting enzymes are known, details of the hydroxylation mechanism and timing of long-range electron transfer (ET) are not clear. This study presents density-functional calculations of the full reaction coordinate, which demonstrate: (i) the importance of the end-on coordination of superoxide to Cu for HAA along the triplet spin surface; (ii) substrate radical rebound to a CuII hydroperoxide favors the proximal, nonprotonated oxygen; and (iii) long-range ET can only occur at a late step with a large driving force, which serves to inhibit deleterious Fenton chemistry. The large inner-sphere reorganization energy at the ET site is used as a control mechanism to arrest premature ET and dictate the correct timing of ET.

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25

Tandrup, Tobias, Kristian E. H. Frandsen, Katja S. Johansen, Jean-Guy Berrin, and Leila Lo Leggio. "Recent insights into lytic polysaccharide monooxygenases (LPMOs)." Biochemical Society Transactions 46, no. 6 (October 31, 2018): 1431–47. http://dx.doi.org/10.1042/bst20170549.

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Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes discovered within the last 10 years. By degrading recalcitrant substrates oxidatively, these enzymes are major contributors to the recycling of carbon in nature and are being used in the biorefinery industry. Recently, two new families of LPMOs have been defined and structurally characterized, AA14 and AA15, sharing many of previously found structural features. However, unlike most LPMOs to date, AA14 degrades xylan in the context of complex substrates, while AA15 is particularly interesting because they expand the presence of LPMOs from the predominantly microbial to the animal kingdom. The first two neutron crystallography structures have been determined, which, together with high-resolution room temperature X-ray structures, have putatively identified oxygen species at or near the active site of LPMOs. Many recent computational and experimental studies have also investigated the mechanism of action and substrate-binding mode of LPMOs. Perhaps, the most significant recent advance is the increasing structural and biochemical evidence, suggesting that LPMOs follow different mechanistic pathways with different substrates, co-substrates and reductants, by behaving as monooxygenases or peroxygenases with molecular oxygen or hydrogen peroxide as a co-substrate, respectively.

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26

Rochman, Fauziah F., Miye Kwon, Roshan Khadka, Ivica Tamas, Azriel Abraham Lopez-Jauregui, Andriy Sheremet, Angela V. Smirnova, et al. "Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria." ISME Journal 14, no. 3 (December 3, 2019): 714–26. http://dx.doi.org/10.1038/s41396-019-0561-2.

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27

Sabbadin, Federico, Saioa Urresti, Bernard Henrissat, Anna O. Avrova, Lydia R. J. Welsh, Peter J. Lindley, Michael Csukai, et al. "Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes." Science 373, no. 6556 (August 12, 2021): 774–79. http://dx.doi.org/10.1126/science.abj1342.

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The oomycete Phytophthora infestans is a damaging crop pathogen and a model organism to study plant-pathogen interactions. We report the discovery of a family of copper-dependent lytic polysaccharide monooxygenases (LPMOs) in plant pathogenic oomycetes and its role in plant infection by P. infestans. We show that LPMO-encoding genes are up-regulated early during infection and that the secreted enzymes oxidatively cleave the backbone of pectin, a charged polysaccharide in the plant cell wall. The crystal structure of the most abundant of these LPMOs sheds light on its ability to recognize and degrade pectin, and silencing the encoding gene in P. infestans inhibits infection of potato, indicating a role in host penetration. The identification of LPMOs as virulence factors in pathogenic oomycetes opens up opportunities in crop protection and food security.

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28

Liu, Yucui, Wei Ma, and Xu Fang. "The Role of the Residue at Position 2 in the Catalytic Activity of AA9 Lytic Polysaccharide Monooxygenases." International Journal of Molecular Sciences 24, no. 9 (May 5, 2023): 8300. http://dx.doi.org/10.3390/ijms24098300.

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AA9 lytic polysaccharide monooxygenases (LPMOs) are copper-dependent metalloenzymes that play a major role in cellulose degradation and plant infection. Understanding the AA9 LPMO mechanism would facilitate the improvement of plant pathogen control and the industrial application of LPMOs. Herein, via point mutation, we investigated the role of glycine 2 residue in cellulose degradation by Thermoascus aurantiacus AA9 LPMOs (TaAA9). A computational simulation showed that increasing the steric properties of this residue by replacing glycine with threonine or tyrosine altered the H-bonding network of the copper center and copper coordination geometry, decreased the surface charge of the catalytic center, weakened the TaAA9-substrate interaction, and enhanced TaAA9-product binding. Compared with wild-type TaAA9, G2T-TaAA9 and G2Y-TaAA9 variants showed attenuated copper affinity, reduced oxidative product diversity and decreased substrate Avicel binding, as determined using ITC, MALDI-TOF/TOF MS and cellulose binding analyses, respectively. Consistently, the enzymatic activity and synergy with cellulase of the G2T-TaAA9 and G2Y-TaAA9 variants were lower than those of TaAA9. Hence, the investigated residue crucially affects the catalytic activity of AA9 LPMOs, and we propose that the electropositivity of copper may correlate with AA9 LPMO activity. Thus, the relationship among the amino acid at position 2, surface charge and catalytic activity may facilitate an understanding of the proteins in AA9 LPMOs.

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29

Prigge, S. T., R. E. Mains, B. A. Eipper, and L. M. Amzel* **. "New insights into copper monooxygenases and peptide amidation: structure, mechanism and function." Cellular and Molecular Life Sciences 57, no. 8 (August 2000): 1236–59. http://dx.doi.org/10.1007/pl00000763.

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30

Itoh, Shinobu. "Dioxygen activation by copper complexes supported by 2-(2-pyridyl)ethylamine ligands. Mechanistic insights into copper monooxygenases and copper oxidases." Journal of Inorganic Biochemistry 96, no. 1 (July 2003): 20. http://dx.doi.org/10.1016/s0162-0134(03)80437-3.

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31

Ipsen, Johan Ø., Magnus Hallas-Møller, Søren Brander, Leila Lo Leggio, and Katja S. Johansen. "Lytic polysaccharide monooxygenases and other histidine-brace copper proteins: structure, oxygen activation and biotechnological applications." Biochemical Society Transactions 49, no. 1 (January 15, 2021): 531–40. http://dx.doi.org/10.1042/bst20201031.

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Lytic polysaccharide monooxygenases (LPMOs) are mononuclear copper enzymes that catalyse the oxidative cleavage of glycosidic bonds. They are characterised by two histidine residues that coordinate copper in a configuration termed the Cu-histidine brace. Although first identified in bacteria and fungi, LPMOs have since been found in all biological kingdoms. LPMOs are now included in commercial enzyme cocktails used in industrial biorefineries. This has led to increased process yield due to the synergistic action of LPMOs with glycoside hydrolases. However, the introduction of LPMOs makes control of the enzymatic step in industrial stirred-tank reactors more challenging, and the operational stability of the enzymes is reduced. It is clear that much is still to be learned about the interaction between LPMOs and their complex natural and industrial environments, and fundamental scientific studies are required towards this end. Several atomic-resolution structures have been solved providing detailed information on the Cu-coordination sphere and the interaction with the polysaccharide substrate. However, the molecular mechanisms of LPMOs are still the subject of intense investigation; the key question being how the proteinaceous environment controls the copper cofactor towards the activation of the O-O bond in O2 and cleavage of the glycosidic bonds in polysaccharides. The need for biochemical characterisation of each putative LPMO is discussed based on recent reports showing that not all proteins with a Cu-histidine brace are enzymes.

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32

N. Le, Chinh, Cuong X. Luu, Son Tung Ngo, and Van V. Vu. "DFT studies of the copper active site in AA13 polysaccharide monooxygenase." Ministry of Science and Technology, Vietnam 64, no. 4 (December 15, 2022): 28–31. http://dx.doi.org/10.31276/vjste.64(4).28-31.

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AA13 polysaccharide monooxygenases (AA13 PMOs) are novel enzymes that break down starch using a copper active site in a substrate binding groove on a solvent-exposed surface. The structure of the copper active site is influenced by the residues in the groove, while the crystal structure of Cu(II)-AA13 was damaged by photoreduction and lacked two exogenous ligands. We utilized density functional theory (DFT) calculations to obtain insights into the structure of Cu(II)-AA13 in the presence and absence of a key residue (G89) of the groove that interferes with the distal coordination site. Results show that the copper active site of AA13 PMOs can exhibit both 6-coordinate and a 5-coordinate structures depending on position of G89. The active site features are intermediate to those in AA9 and AA10 PMOs, which are the most abundant and well characterized PMO families. In addition, the superoxo species of AA13 has structural parameters halfway between those in AA9 and AA10 PMOs. The structural relationship between the active site and intermediates of AA13 with AA9 and AA10 PMOs is also consistent with their evolutionary relationship.

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33

Courtade, Gaston, Reinhard Wimmer, Åsmund K. Røhr, Marita Preims, Alfons K. G. Felice, Maria Dimarogona, Gustav Vaaje-Kolstad, et al. "Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase." Proceedings of the National Academy of Sciences 113, no. 21 (May 5, 2016): 5922–27. http://dx.doi.org/10.1073/pnas.1602566113.

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Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds using molecular oxygen and an external electron donor. We have used NMR and isothermal titration calorimetry (ITC) to study the interactions of a broad-specificity fungal LPMO, NcLPMO9C, with various substrates and with cellobiose dehydrogenase (CDH), a known natural supplier of electrons. The NMR studies revealed interactions with cellohexaose that center around the copper site. NMR studies with xyloglucans, i.e., branched β-glucans, showed an extended binding surface compared with cellohexaose, whereas ITC experiments showed slightly higher affinity and a different thermodynamic signature of binding. The ITC data also showed that although the copper ion alone hardly contributes to affinity, substrate binding is enhanced for metal-loaded enzymes that are supplied with cyanide, a mimic of O2−. Studies with CDH and its isolated heme b cytochrome domain unambiguously showed that the cytochrome domain of CDH interacts with the copper site of the LPMO and that substrate binding precludes interaction with CDH. Apart from providing insights into enzyme–substrate interactions in LPMOs, the present observations shed new light on possible mechanisms for electron supply during LPMO action.

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Blain, Ingrid, Patrick Slama, Michel Giorgi, Thierry Tron, and Marius Réglier. "Copper-containing monooxygenases: enzymatic and biomimetic studies of the O-atom transfer catalysis." Reviews in Molecular Biotechnology 90, no. 2 (April 2002): 95–112. http://dx.doi.org/10.1016/s1389-0352(01)00068-x.

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35

Filandr, Frantisek, Daniel Kavan, Daniel Kracher, Christophe V. F. P. Laurent, Roland Ludwig, Petr Man, and Petr Halada. "Structural Dynamics of Lytic Polysaccharide Monooxygenase during Catalysis." Biomolecules 10, no. 2 (February 5, 2020): 242. http://dx.doi.org/10.3390/biom10020242.

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

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Itoh, Shinobu, Hajime Nakao, and Shunichi Fukuzumi. "Mechanistic studies of aliphatic ligand hydroxylation of a copper complex by dioxygen: A model reaction for copper monooxygenases." Journal of Inorganic Biochemistry 67, no. 1-4 (July 1997): 65. http://dx.doi.org/10.1016/s0162-0134(97)89946-1.

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37

Itoh, Shinobu, Hajime Nakao, Lisa M. Berreau, Toshihiko Kondo, Mitsuo Komatsu, and Shunichi Fukuzumi. "Mechanistic Studies of Aliphatic Ligand Hydroxylation of a Copper Complex by Dioxygen: A Model Reaction for Copper Monooxygenases." Journal of the American Chemical Society 120, no. 12 (April 1998): 2890–99. http://dx.doi.org/10.1021/ja972809q.

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38

Ivanova, Anastasia A., Igor Y. Oshkin, Olga V. Danilova, Dmitriy A. Philippov, Nikolai V. Ravin, and Svetlana N. Dedysh. "Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns." Microorganisms 10, no. 1 (December 22, 2021): 11. http://dx.doi.org/10.3390/microorganisms10010011.

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Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands.

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Schicke, Olivier, Bruno Faure, Yannick Carissan, Michel Giorgi, Ariane Jalila Simaan, and Marius Réglier. "Synthesis and Characterization of a Dinuclear Copper Complex Bearing a Hydrophobic Cavity as a Model for Copper-Containing Monooxygenases." European Journal of Inorganic Chemistry 2015, no. 21 (June 3, 2015): 3512–18. http://dx.doi.org/10.1002/ejic.201500280.

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40

Ayub, Hina, Min-Ju Kang, Adeel Farooq, and Man-Young Jung. "Ecological Aerobic Ammonia and Methane Oxidation Involved Key Metal Compounds, Fe and Cu." Life 12, no. 11 (November 7, 2022): 1806. http://dx.doi.org/10.3390/life12111806.

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Interactions between metals and microbes are critical in geomicrobiology and vital in microbial ecophysiological processes. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing microorganisms (AOM) are key members in aerobic environments to start the C and N cycles. Ammonia and methane are firstly oxidized by copper-binding metalloproteins, monooxygenases, and diverse iron and copper-containing enzymes that contribute to electron transportation in the energy gain pathway, which is evolutionally connected between MOB and AOM. In this review, we summarized recently updated insight into the diverse physiological pathway of aerobic ammonia and methane oxidation of different MOB and AOM groups and compared the metabolic diversity mediated by different metalloenzymes. The elevation of iron and copper concentrations in ecosystems would be critical in the activity and growth of MOB and AOM, the outcome of which can eventually influence the global C and N cycles. Therefore, we also described the impact of various concentrations of metal compounds on the physiology of MOB and AOM. This review study could give a fundamental strategy to control MOB and AOM in diverse ecosystems because they are significantly related to climate change, eutrophication, and the remediation of contaminated sites for detoxifying pollutants.

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Branch, Jessie, Badri S. Rajagopal, Alessandro Paradisi, Nick Yates, Peter J. Lindley, Jake Smith, Kristian Hollingsworth, et al. "C-type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases." Biochemical Journal 478, no. 14 (July 28, 2021): 2927–44. http://dx.doi.org/10.1042/bcj20210376.

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The release of glucose from lignocellulosic waste for subsequent fermentation into biofuels holds promise for securing humankind's future energy needs. The discovery of a set of copper-dependent enzymes known as lytic polysaccharide monooxygenases (LPMOs) has galvanised new research in this area. LPMOs act by oxidatively introducing chain breaks into cellulose and other polysaccharides, boosting the ability of cellulases to act on the substrate. Although several proteins have been implicated as electron sources in fungal LPMO biochemistry, no equivalent bacterial LPMO electron donors have been previously identified, although the proteins Cbp2D and E from Cellvibrio japonicus have been implicated as potential candidates. Here we analyse a small c-type cytochrome (CjX183) present in Cellvibrio japonicus Cbp2D, and show that it can initiate bacterial CuII/I LPMO reduction and also activate LPMO-catalyzed cellulose-degradation. In the absence of cellulose, CjX183-driven reduction of the LPMO results in less H2O2 production from O2, and correspondingly less oxidative damage to the enzyme than when ascorbate is used as the reducing agent. Significantly, using CjX183 as the activator maintained similar cellulase boosting levels relative to the use of an equivalent amount of ascorbate. Our results therefore add further evidence to the impact that the choice of electron source can have on LPMO action. Furthermore, the study of Cbp2D and other similar proteins may yet reveal new insight into the redox processes governing polysaccharide degradation in bacteria.

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Svenning, Mette M., Anne Grethe Hestnes, Ingvild Wartiainen, Lisa Y. Stein, Martin G. Klotz, Marina G. Kalyuzhnaya, Anja Spang, et al. "Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96." Journal of Bacteriology 193, no. 22 (July 1, 2011): 6418–19. http://dx.doi.org/10.1128/jb.05380-11.

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Methylobacter tundripaludum SV96 T (ATCC BAA-1195) is a psychrotolerant aerobic methane-oxidizing gammaproteobacterium ( Methylococcales , Methylococcaceae ) living in High Arctic wetland soil. The strain was isolated from soil harvested in July 1996 close to the settlement Ny-Ålesund, Svalbard, Norway (78°56′N, 11°53′E), and described as a novel species in 2006. The genome includes pmo and pxm operons encoding copper membrane monooxygenases (Cu-MMOs), genes required for nitrogen fixation, and the nirS gene implicated in dissimilatory nitrite reduction to NO but no identifiable inventory for further processing of nitrogen oxides. These genome data provide the basis to investigate M. tundripaludum SV96, identified as a major player in the biogeochemistry of Arctic environments.

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43

Samanta, Dipayan, Tanvi Govil, Priya Saxena, Lee Krumholz, Venkataramana Gadhamshetty, Kian Mau Goh, and Rajesh K. Sani. "Genetical and Biochemical Basis of Methane Monooxygenases of Methylosinus trichosporium OB3b in Response to Copper." Methane 3, no. 1 (February 20, 2024): 103–21. http://dx.doi.org/10.3390/methane3010007.

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Over the past decade, copper (Cu) has been recognized as a crucial metal in the differential expression of soluble (sMMO) and particulate (pMMO) forms of methane monooxygenase (MMO) through a mechanism referred to as the “Cu switch”. In this study, we used Methylosinus trichosporium OB3b as a model bacterium to investigate the range of Cu concentrations that trigger the expression of sMMO to pMMO and its effect on growth and methane oxidation. The Cu switch was found to be regulated within Cu concentrations from 3 to 5 µM, with a strict increase in the methane consumption rates from 3.09 to 3.85 µM occurring on the 6th day. Our findings indicate that there was a decrease in the fold changes in the expression of methanobactin (Mbn) synthesis gene (mbnA) with a higher Cu concentration, whereas the Ton-B siderophore receptor gene (mbnT) showed upregulation at all Cu concentrations. Furthermore, the upregulation of the di-heme enzyme at concentrations above 5 µM Cu may play a crucial role in the copper switch by increasing oxygen consumption; however, the role has yet not been elucidated. We developed a quantitative assay based on the naphthalene–Molisch principle to distinguish between the sMMO- and pMMO-expressing cells, which coincided with the regulation profile of the sMMO and pMMO genes. At 0 and 3 µM Cu, the naphthol concentration was higher (8.1 and 4.2 µM, respectively) and gradually decreased to 0 µM naphthol when pMMO was expressed and acted as the sole methane oxidizer at concentrations above 5 µM Cu. Using physical protein–protein interaction, we identified seven transporters, three cell wall biosynthesis or degradation proteins, Cu resistance operon proteins, and 18 hypothetical proteins that may be involved in Cu toxicity and homeostasis. These findings shed light on the key regulatory genes of the Cu switch that will have potential implications for bioremediation and biotechnology applications.

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44

Frandsen, Kristian E. H., and Leila Lo Leggio. "Lytic polysaccharide monooxygenases: a crystallographer's view on a new class of biomass-degrading enzymes." IUCrJ 3, no. 6 (October 14, 2016): 448–67. http://dx.doi.org/10.1107/s2052252516014147.

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Lytic polysaccharide monooxygenases (LPMOs) are a new class of microbial copper enzymes involved in the degradation of recalcitrant polysaccharides. They have only been discovered and characterized in the last 5–10 years and have stimulated strong interest both in biotechnology and in bioinorganic chemistry. In biotechnology, the hope is that these enzymes will finally help to make enzymatic biomass conversion, especially of lignocellulosic plant waste, economically attractive. Here, the role of LPMOs is likely to be in attacking bonds that are not accessible to other enzymes. LPMOs have attracted enormous interest since their discovery. The emphasis in this review is on the past and present contribution of crystallographic studies as a guide to functional understanding, with a final look towards the future.

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45

Wu, Peng, Fangfang Fan, Jinshuai Song, Wei Peng, Jia Liu, Chunsen Li, Zexing Cao, and Binju Wang. "Theory Demonstrated a “Coupled” Mechanism for O2 Activation and Substrate Hydroxylation by Binuclear Copper Monooxygenases." Journal of the American Chemical Society 141, no. 50 (November 20, 2019): 19776–89. http://dx.doi.org/10.1021/jacs.9b09172.

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46

Kim, S., J. Stahlberg, M. Sandgren, R. S. Paton, and G. T. Beckham. "Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism." Proceedings of the National Academy of Sciences 111, no. 1 (December 16, 2013): 149–54. http://dx.doi.org/10.1073/pnas.1316609111.

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47

Schröder, Gabriela C., William B. O'Dell, Paul D. Swartz, and Flora Meilleur. "Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions." Acta Crystallographica Section F Structural Biology Communications 77, no. 4 (March 31, 2021): 128–33. http://dx.doi.org/10.1107/s2053230x21002399.

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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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48

Castillo, Ivan, Andrea C. Neira, Ebbe Nordlander, and Erica Zeglio. "Bis(benzimidazolyl)amine copper complexes with a synthetic ‘histidine brace’ structural motif relevant to polysaccharide monooxygenases." Inorganica Chimica Acta 422 (October 2014): 152–57. http://dx.doi.org/10.1016/j.ica.2014.06.027.

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49

Xing, Zhilin, Tiantao Zhao, Lijie Zhang, Yanhui Gao, Shuai Liu, and Xu Yang. "Effects of copper on expression of methane monooxygenases, trichloroethylene degradation, and community structure in methanotrophic consortia." Engineering in Life Sciences 18, no. 4 (February 22, 2018): 236–43. http://dx.doi.org/10.1002/elsc.201700153.

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50

Naik, Anil D., Pattubala A. N. Reddy, Munirathinam Nethaji, and Akhil R. Chakravarty. "Ternary copper(II) complexes of thiosemicarbazones and heterocyclic bases showing N3OS coordination as models for the type-2 centers of copper monooxygenases." Inorganica Chimica Acta 349 (June 2003): 149–58. http://dx.doi.org/10.1016/s0020-1693(03)00091-4.

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