1
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De Santis E, Alleva S, Minicozzi V, Morante S, Stellato F. Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders. Chempluschem 2024; 89:e202300712. [PMID: 38526934 DOI: 10.1002/cplu.202300712] [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: 12/01/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.
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Affiliation(s)
- Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Stefania Alleva
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Velia Minicozzi
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Silvia Morante
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Francesco Stellato
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
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2
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Munzone A, Pujol M, Tamhankar A, Joseph C, Mazurenko I, Réglier M, Jannuzzi SAV, Royant A, Sicoli G, DeBeer S, Orio M, Simaan AJ, Decroos C. Integrated Experimental and Theoretical Investigation of Copper Active Site Properties of a Lytic Polysaccharide Monooxygenase from Serratia marcescens. Inorg Chem 2024; 63:11063-11078. [PMID: 38814816 DOI: 10.1021/acs.inorgchem.4c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
In this paper, we employed a multidisciplinary approach, combining experimental techniques and density functional theory (DFT) calculations to elucidate key features of the copper coordination environment of the bacterial lytic polysaccharide monooxygenase (LPMO) from Serratia marcescens (SmAA10). The structure of the holo-enzyme was successfully obtained by X-ray crystallography. We then determined the copper(II) binding affinity using competing ligands and observed that the affinity of the histidine brace ligands for copper is significantly higher than previously described. UV-vis, advanced electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy (XAS) techniques, including high-energy resolution fluorescence detected (HERFD) XAS, were further used to gain insight into the copper environment in both the Cu(II) and Cu(I) redox states. The experimental data were successfully rationalized by DFT models, offering valuable information on the electronic structure and coordination geometry of the copper center. Finally, the Cu(II)/Cu(I) redox potential was determined using two different methods at ca. 350 mV vs NHE and rationalized by DFT calculations. This integrated approach not only advances our knowledge of the active site properties of SmAA10 but also establishes a robust framework for future studies of similar enzymatic systems.
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Affiliation(s)
- Alessia Munzone
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Manon Pujol
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Ashish Tamhankar
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Chris Joseph
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | | | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Sergio A V Jannuzzi
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Antoine Royant
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
- European Synchrotron Radiation Facility, Grenoble 38043, France
| | - Giuseppe Sicoli
- LASIRE UMR CNRS 8516, Université de Lille, Villeneuve-d'Arcy 59655, France
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Christophe Decroos
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
- Department of Integrative Structural Biology, Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch 67400, France
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3
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Gerz I, Aunan ES, Finelli V, Abu Rasheed M, Deplano G, Cortez S P R, Schmidtke IL, Wragg DS, Signorile M, Hylland KT, Borfecchia E, Lillerud KP, Bordiga S, Olsbye U, Amedjkouh M. Enabling a bioinspired N, N, N-copper coordination motif through spatial control in UiO-67: synthesis and reactivity. Dalton Trans 2024; 53:8141-8153. [PMID: 38483202 DOI: 10.1039/d3dt03096b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
Metal-organic frameworks (MOFs) featuring zirconium-based clusters are widely used for the development of functionalized materials due to their exceptional stability. In this study, we report the synthesis of a novel N,N,N-ligand compatible with a biphenyl dicarboxylic acid-based MOF. However, the resulting copper(I) complex exhibited unexpected coordination behaviour, lacking the intended trifold coordination motif. Herein, we demonstrate the successful immobilization of a bioinspired ligand within the MOF, which preserved its crystalline and porous nature while generating a well-defined copper site. Comprehensive spectroscopic analyses, including X-ray absorption, UV/Vis, and infrared spectroscopy, were conducted to investigate the copper site and its thermal behaviour. The immobilized ligand exhibited the desired tridentate coordination to copper, providing access to a coordination motif otherwise unattainable. Notably, water molecules were also found to coordinate to copper. Upon heating, the copper centre within the MOF exhibited reversible dehydration, suggesting facile creation of open coordination sites. Furthermore, the copper site displayed reduction at elevated temperatures and subsequent susceptibility to oxidation by molecular oxygen. Lastly, both the molecular complexes and the MOF were evaluated as catalysts for the oxidation of cyclohexane using hydrogen peroxide. This work highlights the successful immobilization of a bioinspired ligand in a zirconium-based MOF, shedding light on the structural features, thermal behaviour, and catalytic potential of the resulting copper sites.
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Affiliation(s)
- Isabelle Gerz
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Erlend S Aunan
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Valeria Finelli
- Department of Chemistry, NIS and INSTM Reference Centre, Università di Torino, Via G. Quarello 15/A, I-10135, and Via P. Giuria 7, I-10125, Turin, Italy
- University School for Advanced Studies, IUSS Pavia, Palazzo del Broletto, Piazza della Vittoria 15, I-27100, Pavia, Italy
| | - Mouhammad Abu Rasheed
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Gabriele Deplano
- Department of Chemistry, NIS and INSTM Reference Centre, Università di Torino, Via G. Quarello 15/A, I-10135, and Via P. Giuria 7, I-10125, Turin, Italy
| | - Rafael Cortez S P
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Inga L Schmidtke
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
| | - David S Wragg
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Matteo Signorile
- Department of Chemistry, NIS and INSTM Reference Centre, Università di Torino, Via G. Quarello 15/A, I-10135, and Via P. Giuria 7, I-10125, Turin, Italy
| | - Knut T Hylland
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Elisa Borfecchia
- Department of Chemistry, NIS and INSTM Reference Centre, Università di Torino, Via G. Quarello 15/A, I-10135, and Via P. Giuria 7, I-10125, Turin, Italy
| | - Karl Petter Lillerud
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Silvia Bordiga
- Department of Chemistry, NIS and INSTM Reference Centre, Università di Torino, Via G. Quarello 15/A, I-10135, and Via P. Giuria 7, I-10125, Turin, Italy
| | - Unni Olsbye
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
| | - Mohamed Amedjkouh
- Department of Chemistry, University of Oslo, P. O. Box 1033 Blindern, N-0315 Oslo, Norway
- Centre for Materials Science and Nanotechnology, University of Oslo, P.O. Box 1126 Blindern, N-0316 Oslo, Norway
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4
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Isaksen I, Jana S, Payne CM, Bissaro B, Røhr ÅK. The rotamer of the second-sphere histidine in AA9 lytic polysaccharide monooxygenase is pH dependent. Biophys J 2024; 123:1139-1151. [PMID: 38571309 PMCID: PMC11079946 DOI: 10.1016/j.bpj.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/10/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH-dependent conformation of a second-sphere histidine (His) that we call the stacking histidine, which is conserved in fungal AA9 LPMOs and is speculated to assist catalysis in several of the LPMO reaction pathways. Using constant-pH and accelerated molecular dynamics simulations, we monitored the dynamics of the stacking His in different protonation states for both the resting Cu(II) and active Cu(I) forms of two fungal LPMOs. Consistent with experimental crystallographic and neutron diffraction data, our calculations suggest that the side chain of the protonated and positively charged form is rotated out of the active site toward the solvent. Importantly, only one of the possible neutral states of histidine (HIE state) is observed in the stacking orientation at neutral pH or when bound to cellulose. Our data predict that, in solution, the stacking His may act as a stabilizer (via hydrogen bonding) of the Cu(II)-superoxo complex after the LPMO-Cu(I) has reacted with O2 in solution, which, in fine, leads to H2O2 formation. Also, our data indicate that the HIE-stacking His is a poor acid/base catalyst when bound to the substrate and, in agreement with the literature, may play an important stabilizing role (via hydrogen bonding) during the peroxygenase catalysis. Our study reveals the pH titration midpoint values of the pH-dependent orientation of the stacking His should be considered when modeling and interpreting LPMO reactions, whether it be for classical LPMO kinetics or in industry-oriented enzymatic cocktails, and for understanding LPMO behavior in slightly acidic natural processes such as fungal wood decay.
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Affiliation(s)
- Ingvild Isaksen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway; INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, Marseille, France.
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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5
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de Oliveira Silva YR, Zheng D, Peters SC, Fisher OS. Stabilization of a Cu-binding site by a highly conserved tryptophan residue. J Inorg Biochem 2024; 253:112501. [PMID: 38342077 DOI: 10.1016/j.jinorgbio.2024.112501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Copper serves as an essential cofactor for nearly all living organisms. There are still many gaps remaining in our knowledge of how Gram-positive bacteria import copper and maintain homeostasis. To obtain a better understanding of how these processes work, here we focus on the ycnKJI operon responsible for regulating copper levels in the Gram-positive bacterium Bacillus subtilis. This operon encodes three Cu-related proteins: a copper-dependent transcriptional repressor (YcnK), a putative copper importer (YcnJ), and a copper-binding protein of unknown function (YcnI). We previously found that YcnI's extracellular Domain of Unknown Function 1775 (DUF1775) houses a monohistidine brace motif that coordinates a single Cu(II) ion. The Cu(II) binding site includes a highly conserved tryptophan residue. Here, we investigate the role of that tryptophan and the ability of the protein to interact with other oxidation states of Cu. We find that YcnI exhibits strong preference for binding Cu in the oxidized Cu(II) state, and that the conserved tryptophan residue is not essential for the interaction. We determine the structure of a tryptophan variant to 1.95 Å resolution that indicates that the tryptophan is needed to stabilize the metal binding interaction, and find that this variant has weaker affinity for Cu(II) than the wild-type protein. Together, these data provide further insights into the DUF1775 domain family and reveal the role of the conserved tryptophan residue.
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Affiliation(s)
| | - Dia Zheng
- Department of Chemistry, Lehigh University, 6 E Packer Ave, Bethlehem, PA 18015, USA
| | - Stephen C Peters
- Department of Earth and Environmental Sciences, Lehigh University, 1 W Packer Ave, Bethlehem, PA 18015, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, 6 E Packer Ave, Bethlehem, PA 18015, USA.
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6
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Wieduwilt EK, Lo Leggio L, Hedegård ED. A frontier-orbital view of the initial steps of lytic polysaccharide monooxygenase reactions. Dalton Trans 2024; 53:5796-5807. [PMID: 38445349 DOI: 10.1039/d3dt04275h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that oxidatively cleave the strong C-H bonds in recalcitrant polysaccharide substrates, thereby playing a crucial role in biomass degradation. Recently, LPMOs have also been shown to be important for several pathogens. It is well established that the Cu(II) resting state of LPMOs is inactive, and the electronic structure of the active site needs to be altered to transform the enzyme into an active form. Whether this transformation occurs due to substrate binding or due to a unique priming reduction has remained speculative. Starting from four different crystal structures of the LPMO LsAA9A with well-defined oxidation states, we use a frontier molecular orbital approach to elucidate the initial steps of the LPMO reaction. We give an explanation for the requirement of the unique priming reduction and analyse electronic structure changes upon substrate binding. We further investigate how the presence of the substrate could facilitate an electron transfer from the copper active site to an H2O2 co-substrate. Our findings could help to control experimental LPMO reactions.
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Affiliation(s)
- Erna Katharina Wieduwilt
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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7
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Kumar A, Singh A, Sharma VK, Goel A, Kumar A. The upsurge of lytic polysaccharide monooxygenases in biomass deconstruction: characteristic functions and sustainable applications. FEBS J 2024. [PMID: 38291603 DOI: 10.1111/febs.17063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are one of the emerging classes of copper metalloenzymes that have received considerable attention due to their ability to boost the enzymatic conversion of intractable polysaccharides such as plant cell walls and chitin polymers. LPMOs catalyze the oxidative cleavage of β-1,4-glycosidic bonds using molecular O2 or H2 O2 in the presence of an external electron donor. LPMOs have been classified as an auxiliary active (AA) class of enzymes and, further based on substrate specificity, divided into eight families. Until now, multiple LPMOs from AA9 and AA10 families, mostly from microbial sources, have been investigated; the exact mechanism and structure-function are elusive to date, and recently discovered AA families of LPMOs are just scratched. This review highlights the origin and discovery of the enzyme, nomenclature, three-dimensional protein structure, substrate specificity, copper-dependent reaction mechanism, and different techniques used to determine the product formation through analytical and biochemical methods. Moreover, the diverse functions of proteins in various biological activities such as plant-pathogen/pest interactions, cell wall remodeling, antibiotic sensitivity of biofilms, and production of nanocellulose along with certain obstacles in deconstructing the complex polysaccharides have also been summarized, while highlighting the innovative and creative ways to overcome the limitations of LPMOs in hydrolyzing the biomass.
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Affiliation(s)
- Asheesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Aishwarya Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vijay Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Akshita Goel
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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8
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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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9
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Hall K, Joseph C, Ayuso-Fernández I, Tamhankar A, Rieder L, Skaali R, Golten O, Neese F, Røhr ÅK, Jannuzzi SAV, DeBeer S, Eijsink VGH, Sørlie M. A Conserved Second Sphere Residue Tunes Copper Site Reactivity in Lytic Polysaccharide Monooxygenases. J Am Chem Soc 2023; 145:18888-18903. [PMID: 37584157 PMCID: PMC10472438 DOI: 10.1021/jacs.3c05342] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Indexed: 08/17/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are powerful monocopper enzymes that can activate strong C-H bonds through a mechanism that remains largely unknown. Herein, we investigated the role of a conserved glutamine/glutamate in the second coordination sphere. Mutation of the Gln in NcAA9C to Glu, Asp, or Asn showed that the nature and distance of the headgroup to the copper fine-tune LPMO functionality and copper reactivity. The presence of Glu or Asp close to the copper lowered the reduction potential and decreased the ratio between the reduction and reoxidation rates by up to 500-fold. All mutants showed increased enzyme inactivation, likely due to changes in the confinement of radical intermediates, and displayed changes in a protective hole-hopping pathway. Electron paramagnetic resonance (EPR) and X-ray absorption spectroscopic (XAS) studies gave virtually identical results for all NcAA9C variants, showing that the mutations do not directly perturb the Cu(II) ligand field. DFT calculations indicated that the higher experimental reoxidation rate observed for the Glu mutant could be reconciled if this residue is protonated. Further, for the glutamic acid form, we identified a Cu(III)-hydroxide species formed in a single step on the H2O2 splitting path. This is in contrast to the Cu(II)-hydroxide and hydroxyl intermediates, which are predicted for the WT and the unprotonated glutamate variant. These results show that this second sphere residue is a crucial determinant of the catalytic functioning of the copper-binding histidine brace and provide insights that may help in understanding LPMOs and LPMO-inspired synthetic catalysts.
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Affiliation(s)
- Kelsi
R. Hall
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Chris Joseph
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Iván Ayuso-Fernández
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ashish Tamhankar
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Lukas Rieder
- Institute
for Molecular Biotechnology, Graz University
of Technology, 8010, Graz, Austria
| | - Rannei Skaali
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ole Golten
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Åsmund K. Røhr
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Sergio A. V. Jannuzzi
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Vincent G. H. Eijsink
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Morten Sørlie
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
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10
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Abstract
Proteins guide the flows of information, energy, and matter that make life possible by accelerating transport and chemical reactions, by allosterically modulating these reactions, and by forming dynamic supramolecular assemblies. In these roles, conformational change underlies functional transitions. Time-resolved X-ray diffraction methods characterize these transitions either by directly triggering sequences of functionally important motions or, more broadly, by capturing the motions of which proteins are capable. To date, most successful have been experiments in which conformational change is triggered in light-dependent proteins. In this review, I emphasize emerging techniques that probe the dynamic basis of function in proteins lacking natively light-dependent transitions and speculate about extensions and further possibilities. In addition, I review how the weaker and more distributed signals in these data push the limits of the capabilities of analytical methods. Taken together, these new methods are beginning to establish a powerful paradigm for the study of the physics of protein function.
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Affiliation(s)
- Doeke R Hekstra
- Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA;
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11
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Votvik AK, Røhr ÅK, Bissaro B, Stepnov AA, Sørlie M, Eijsink VGH, Forsberg Z. Structural and functional characterization of the catalytic domain of a cell-wall anchored bacterial lytic polysaccharide monooxygenase from Streptomyces coelicolor. Sci Rep 2023; 13:5345. [PMID: 37005446 PMCID: PMC10067821 DOI: 10.1038/s41598-023-32263-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/24/2023] [Indexed: 04/04/2023] Open
Abstract
Bacterial lytic polysaccharide monooxygenases (LPMOs) are known to oxidize the most abundant and recalcitrant polymers in Nature, namely cellulose and chitin. The genome of the model actinomycete Streptomyces coelicolor A3(2) encodes seven putative LPMOs, of which, upon phylogenetic analysis, four group with typical chitin-oxidizing LPMOs, two with typical cellulose-active LPMOs, and one which stands out by being part of a subclade of non-characterized enzymes. The latter enzyme, called ScLPMO10D, and most of the enzymes found in this subclade are unique, not only because of variation in the catalytic domain, but also as their C-terminus contains a cell wall sorting signal (CWSS), which flags the LPMO for covalent anchoring to the cell wall. Here, we have produced a truncated version of ScLPMO10D without the CWSS and determined its crystal structure, EPR spectrum, and various functional properties. While showing several structural and functional features typical for bacterial cellulose active LPMOs, ScLPMO10D is only active on chitin. Comparison with two known chitin-oxidizing LPMOs of different taxa revealed interesting functional differences related to copper reactivity. This study contributes to our understanding of the biological roles of LPMOs and provides a foundation for structural and functional comparison of phylogenetically distant LPMOs with similar substrate specificities.
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Affiliation(s)
- Amanda K Votvik
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
- INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway.
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12
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Revisiting the role of electron donors in lytic polysaccharide monooxygenase biochemistry. Essays Biochem 2023; 67:585-595. [PMID: 36748351 PMCID: PMC10154616 DOI: 10.1042/ebc20220164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
The plant cell wall is rich in carbohydrates and many fungi and bacteria have evolved to take advantage of this carbon source. These carbohydrates are largely locked away in polysaccharides and so these organisms deploy a range of enzymes that can liberate individual sugars from these challenging substrates. Glycoside hydrolases (GHs) are the enzymes that are largely responsible for bringing about this sugar release; however, 12 years ago, a family of enzymes known as lytic polysaccharide monooxygenases (LPMOs) were also shown to be of key importance in this process. LPMOs are copper-dependent oxidative enzymes that can introduce chain breaks within polysaccharide chains. Initial work demonstrated that they could activate O2 to attack the substrate through a reaction that most likely required multiple electrons to be delivered to the enzyme. More recently, it has emerged that LPMO kinetics are significantly improved if H2O2 is supplied to the enzyme as a cosubstrate instead of O2. Only a single electron is required to activate an LPMO and H2O2 cosubstrate and the enzyme has been shown to catalyse multiple turnovers following the initial one-electron reduction of the copper, which is not possible if O2 is used. This has led to further studies of the roles of the electron donor in LPMO biochemistry, and this review aims to highlight recent findings in this area and consider how ongoing research could impact our understanding of the interplay between redox processes in nature.
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13
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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: 4] [Impact Index Per Article: 4.0] [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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14
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Soni T, Zhuang M, Kumar M, Balan V, Ubanwa B, Vivekanand V, Pareek N. Multifaceted production strategies and applications of glucosamine: a comprehensive review. Crit Rev Biotechnol 2023; 43:100-120. [PMID: 34923890 DOI: 10.1080/07388551.2021.2003750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glucosamine (GlcN) and its derivatives are in high demand and used in various applications such as food, a precursor for the biochemical synthesis of fuels and chemicals, drug delivery, cosmetics, and supplements. The vast number of applications attributed to GlcN has raised its demand, and there is a growing emphasis on developing production methods that are sustainable and economical. Several: physical, chemical, enzymatic, microbial fermentation, recombinant processing methods, and their combinations have been reported to produce GlcN from chitin and chitosan available from different sources, such as animals, plants, and fungi. In addition, genetic manipulation of certain organisms has significantly improved the quality and yield of GlcN compared to conventional processing methods. This review will summarize the chitin and chitosan-degrading enzymes found in various organisms and the expression systems that are widely used to produce GlcN. Furthermore, new developments and methods, including genetic and metabolic engineering of Escherichia coli and Bacillus subtilis to produce high titers of GlcN and GlcNAc will be reviewed. Moreover, other sources of glucosamine production viz. starch and inorganic ammonia will also be discussed. Finally, the conversion of GlcN to fuels and chemicals using catalytic and biochemical conversion will be discussed.
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Affiliation(s)
- Twinkle Soni
- Microbial Catalysis and Process Engineering Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Mengchuan Zhuang
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, USA
| | - Manish Kumar
- Microbial Catalysis and Process Engineering Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Venkatesh Balan
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, USA
| | - Bryan Ubanwa
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, USA
| | - Vivekanand Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology, Jaipur, India
| | - Nidhi Pareek
- Microbial Catalysis and Process Engineering Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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15
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Cordas CM, Valério GN, Stepnov A, Kommedal E, Kjendseth ÅR, Forsberg Z, Eijsink VGH, Moura JJG. Electrochemical characterization of a family AA10 LPMO and the impact of residues shaping the copper site on reactivity. J Inorg Biochem 2023; 238:112056. [PMID: 36332410 DOI: 10.1016/j.jinorgbio.2022.112056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/09/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
Research on enzymes for lignocellulose biomass degradation has progressively increased in recent years due to the interest in taking advantage of this natural resource. Among these enzymes are the lytic polysaccharide monooxygenases (LPMOs) that oxidatively depolymerize crystalline cellulose using a reactive oxygen species generated in a reduced mono‑copper active site. The copper site comprises of a highly conserved histidine-brace, providing three equatorial nitrogen ligands, whereas less conserved residues close to the copper contribute to shaping and confining the site. The catalytic copper site is exposed to the solvent and to the crystalline substrates, and as so, the influence of the copper environment on LPMO properties, including the redox potential, is of great interest. In the current work, a direct electrochemical study of an LPMO (ScLPMO10C) was conducted allowing to retrieve kinetic and thermodynamic data associated with the redox transition in the catalytic centre. Moreover, two residues that do not bind to the copper but shape the copper sites were mutated, and the properties of the mutants were compared with those of the wild-type enzyme. The direct electrochemical studies, using cyclic voltammetry, yielded redox potentials in the +200 mV range, well in line with LPMO redox potentials determined by other methods. Interestingly, while the mutations hardly affected the formal redox potential of the enzyme, they drastically affected the reactivity of the copper site and enzyme functionality.
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Affiliation(s)
- Cristina M Cordas
- LAQV, REQUIMTE, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
| | - Gabriel N Valério
- LAQV, REQUIMTE, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Anton Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Eirik Kommedal
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Åsmund R Kjendseth
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
| | - José J G Moura
- LAQV, REQUIMTE, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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16
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Tandrup T, Lo Leggio L, Meilleur F. Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature. Acta Crystallogr F Struct Biol Commun 2023; 79:1-7. [PMID: 36598350 PMCID: PMC9813973 DOI: 10.1107/s2053230x22011335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes which cleave polysaccharides oxidatively and are important in pathogen biology, carbon cycling and biotechnology. The Lentinus similis family AA9 isoform A (LsAA9_A) has been extensively studied as a model system because its activity towards smaller soluble saccharide substrates has allowed detailed structural characterization of its interaction with a variety of substrates by X-ray crystallography at high resolution. Here, the joint X-ray/neutron room-temperature crystallographic structure of carbohydrate-free LsAA9_A in the copper(II) resting state refined against X-ray and neutron data at 2.1 and 2.8 Å resolution, respectively, is presented. The results provide an experimental determination of the protonation states of the copper(II)-coordinating residues and second-shell residues in LsAA9_A, paving the way for future neutron crystallographic studies of LPMO-carbohydrate complexes.
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Affiliation(s)
- Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
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17
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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: 16] [Impact Index Per Article: 8.0] [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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18
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Tandrup T, Muderspach SJ, Banerjee S, Santoni G, Ipsen JØ, Hernández-Rollán C, Nørholm MHH, Johansen KS, Meilleur F, Lo Leggio L. Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding. IUCRJ 2022; 9:666-681. [PMID: 36071795 PMCID: PMC9438499 DOI: 10.1107/s2052252522007175] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
The recently discovered lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes capable of degrading polysaccharide substrates oxidatively. The generally accepted first step in the LPMO reaction is the reduction of the active-site metal ion from Cu2+ to Cu+. Here we have used a systematic diffraction data collection method to monitor structural changes in two AA9 LPMOs, one from Lentinus similis (LsAA9_A) and one from Thermoascus auranti-acus (TaAA9_A), as the active-site Cu is photoreduced in the X-ray beam. For LsAA9_A, the protein produced in two different recombinant systems was crystallized to probe the effect of post-translational modifications and different crystallization conditions on the active site and metal photoreduction. We can recommend that crystallographic studies of AA9 LPMOs wishing to address the Cu2+ form use a total X-ray dose below 3 × 104 Gy, while the Cu+ form can be attained using 1 × 106 Gy. In all cases, we observe the transition from a hexa-coordinated Cu site with two solvent-facing ligands to a T-shaped geometry with no exogenous ligands, and a clear increase of the θ2 parameter and a decrease of the θ3 parameter by averages of 9.2° and 8.4°, respectively, but also a slight increase in θT. Thus, the θ2 and θ3 parameters are helpful diagnostics for the oxidation state of the metal in a His-brace protein. On binding of cello-oligosaccharides to LsAA9_A, regardless of the production source, the θT parameter increases, making the Cu site less planar, while the active-site Tyr-Cu distance decreases reproducibly for the Cu2+ form. Thus, the θT increase found on copper reduction may bring LsAA9_A closer to an oligosaccharide-bound state and contribute to the observed higher affinity of reduced LsAA9_A for cellulosic substrates.
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Affiliation(s)
- Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Sebastian J. Muderspach
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Sanchari Banerjee
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Gianluca Santoni
- ESRF, Structural Biology Group, 71 avenue des Martyrs, 38027 Grenoble cedex, France
| | - Johan Ø. Ipsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958-DK, Frederiksberg, Denmark
| | - Cristina Hernández-Rollán
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800-DK, Kgs. Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800-DK, Kgs. Lyngby, Denmark
| | - Katja S. Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958-DK, Frederiksberg, Denmark
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
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19
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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20
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Skåne A, Edvardsen PK, Cordara G, Loose JSM, Leitl KD, Krengel U, Sørum H, Askarian F, Vaaje-Kolstad G. Chitinolytic enzymes contribute to the pathogenicity of Aliivibrio salmonicida LFI1238 in the invasive phase of cold-water vibriosis. BMC Microbiol 2022; 22:194. [PMID: 35941540 PMCID: PMC9361615 DOI: 10.1186/s12866-022-02590-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background Aliivibrio salmonicida is the causative agent of cold-water vibriosis in salmonids (Oncorhynchus mykiss and Salmo salar L.) and gadidae (Gadus morhua L.). Virulence-associated factors that are essential for the full spectrum of A. salmonicida pathogenicity are largely unknown. Chitin-active lytic polysaccharide monooxygenases (LPMOs) have been indicated to play roles in both chitin degradation and virulence in a variety of pathogenic bacteria but are largely unexplored in this context. Results In the present study we investigated the role of LPMOs in the pathogenicity of A. salmonicida LFI238 in Atlantic salmon (Salmo salar L.). In vivo challenge experiments using isogenic deletion mutants of the two LPMOs encoding genes AsLPMO10A and AsLPMO10B, showed that both LPMOs, and in particular AsLPMO10B, were important in the invasive phase of cold-water vibriosis. Crystallographic analysis of the AsLPMO10B AA10 LPMO domain (to 1.4 Å resolution) revealed high structural similarity to viral fusolin, an LPMO known to enhance the virulence of insecticidal agents. Finally, exposure to Atlantic salmon serum resulted in substantial proteome re-organization of the A. salmonicida LPMO deletion variants compared to the wild type strain, indicating the struggle of the bacterium to adapt to the host immune components in the absence of the LPMOs. Conclusion The present study consolidates the role of LPMOs in virulence and demonstrates that such enzymes may have more than one function.
Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02590-2.
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Affiliation(s)
- Anna Skåne
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Per Kristian Edvardsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gabriele Cordara
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Jennifer Sarah Maria Loose
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Kira Daryl Leitl
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Ute Krengel
- Department of Chemistry, University of Oslo, Blindern, P.O. Box 1033, NO-0315, Oslo, Norway
| | - Henning Sørum
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Fatemeh Askarian
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, San Diego, CA, USA.
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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21
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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] [Key Words] [MESH Headings] [Grants] [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
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 japonicus CjLPMO10A. 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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Affiliation(s)
- Christopher M. Dade
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Badreddine Douzi
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
- Aix-Marseille University, CNRS, AFMB, Marseille, France
| | | | - Genevieve Ball
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
| | - Romé Voulhoux
- Aix-Marseille University, CNRS, IMM, LCB, Marseille, France
| | - Katrina T. Forest
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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22
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Lee JL, Ross DL, Barman SK, Ziller JW, Borovik AS. C-H Bond Cleavage by Bioinspired Nonheme Metal Complexes. Inorg Chem 2021; 60:13759-13783. [PMID: 34491738 DOI: 10.1021/acs.inorgchem.1c01754] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The functionalization of C-H bonds is one of the most challenging transformations in synthetic chemistry. In biology, these processes are well-known and are achieved with a variety of metalloenzymes, many of which contain a single metal center within their active sites. The most well studied are those with Fe centers, and the emerging experimental data show that high-valent iron oxido species are the intermediates responsible for cleaving the C-H bond. This Forum Article describes the state of this field with an emphasis on nonheme Fe enzymes and current experimental results that provide insights into the properties that make these species capable of C-H bond cleavage. These parameters are also briefly considered in regard to manganese oxido complexes and Cu-containing metalloenzymes. Synthetic iron oxido complexes are discussed to highlight their utility as spectroscopic and mechanistic probes and reagents for C-H bond functionalization. Avenues for future research are also examined.
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Affiliation(s)
- Justin L Lee
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Dolores L Ross
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Suman K Barman
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Joseph W Ziller
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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23
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C-type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases. Biochem J 2021; 478:2927-2944. [PMID: 34240737 PMCID: PMC8981238 DOI: 10.1042/bcj20210376] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
The release of glucose from lignocellulosic waste for subsequent fermentation into biofuels holds promise for securing humankind's future energy needs. The discovery of a set of copper-dependent enzymes known as lytic polysaccharide monooxygenases (LPMOs) has galvanised new research in this area. LPMOs act by oxidatively introducing chain breaks into cellulose and other polysaccharides, boosting the ability of cellulases to act on the substrate. Although several proteins have been implicated as electron sources in fungal LPMO biochemistry, no equivalent bacterial LPMO electron donors have been previously identified, although the proteins Cbp2D and E from Cellvibrio japonicus have been implicated as potential candidates. Here we analyse a small c-type cytochrome (CjX183) present in Cellvibrio japonicus Cbp2D, and show that it can initiate bacterial CuII/I LPMO reduction and also activate LPMO-catalyzed cellulose-degradation. In the absence of cellulose, CjX183-driven reduction of the LPMO results in less H2O2 production from O2, and correspondingly less oxidative damage to the enzyme than when ascorbate is used as the reducing agent. Significantly, using CjX183 as the activator maintained similar cellulase boosting levels relative to the use of an equivalent amount of ascorbate. Our results therefore add further evidence to the impact that the choice of electron source can have on LPMO action. Furthermore, the study of Cbp2D and other similar proteins may yet reveal new insight into the redox processes governing polysaccharide degradation in bacteria.
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24
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Wang Z, Feng S, Rovira C, Wang B. How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Shishi Feng
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 08020 Barcelona Spain
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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25
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Wang Z, Feng S, Rovira C, Wang B. How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angew Chem Int Ed Engl 2020; 60:2385-2392. [DOI: 10.1002/anie.202011408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/05/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Shishi Feng
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Passeig Lluís Companys 08020 Barcelona Spain
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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26
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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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27
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Forsberg Z, Stepnov AA, Nærdal GK, Klinkenberg G, Eijsink VGH. Engineering lytic polysaccharide monooxygenases (LPMOs). Methods Enzymol 2020; 644:1-34. [PMID: 32943141 DOI: 10.1016/bs.mie.2020.04.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that catalyze the hydroxylation of glycosidic bonds found in the most abundant and recalcitrant polysaccharides on Earth. Since their discovery in 2010, these enzymes have received extensive attention in both fundamental and applied research due to their remarkable oxidative power and synergistic interplay with hydrolytic enzymes. The harsh and unnatural conditions used in industrial enzymatic saccharification processes and the sensitivity of LPMOs for damage induced by reactive oxygen species call for enzyme engineering to develop LPMOs to become robust industrial biocatalysts. Other engineering targets include improved catalytic activity, adjusted substrate specificity and the introduction of completely new activities. Reaching these targets not only requires appropriate methods for measuring enzyme activity, but also requires in-depth knowledge of the active site and the reaction mechanism, which is yet to be achieved in the LPMO field. Here we describe what has been done in the LPMO engineering field so far. Furthermore, we address the difficulties involved in properly assessing LPMO functionality, which are due to common side reactions taking place in LPMO reactions and which complicate screening methods.
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Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Guro Kruge Nærdal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Geir Klinkenberg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.
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28
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Courtade G, Ciano L, Paradisi A, Lindley PJ, Forsberg Z, Sørlie M, Wimmer R, Davies GJ, Eijsink VGH, Walton PH, Aachmann FL. Mechanistic basis of substrate-O 2 coupling within a chitin-active lytic polysaccharide monooxygenase: An integrated NMR/EPR study. Proc Natl Acad Sci U S A 2020; 117:19178-19189. [PMID: 32723819 PMCID: PMC7431007 DOI: 10.1073/pnas.2004277117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have a unique ability to activate molecular oxygen for subsequent oxidative cleavage of glycosidic bonds. To provide insight into the mode of action of these industrially important enzymes, we have performed an integrated NMR/electron paramagnetic resonance (EPR) study into the detailed aspects of an AA10 LPMO-substrate interaction. Using NMR spectroscopy, we have elucidated the solution-phase structure of apo-BlLPMO10A from Bacillus licheniformis, along with solution-phase structural characterization of the Cu(I)-LPMO, showing that the presence of the metal has minimal effects on the overall protein structure. We have, moreover, used paramagnetic relaxation enhancement (PRE) to characterize Cu(II)-LPMO by NMR spectroscopy. In addition, a multifrequency continuous-wave (CW)-EPR and 15N-HYSCORE spectroscopy study on the uniformly isotope-labeled 63Cu(II)-bound 15N-BlLPMO10A along with its natural abundance isotopologue determined copper spin-Hamiltonian parameters for LPMOs to markedly improved accuracy. The data demonstrate that large changes in the Cu(II) spin-Hamiltonian parameters are induced upon binding of the substrate. These changes arise from a rearrangement of the copper coordination sphere from a five-coordinate distorted square pyramid to one which is four-coordinate near-square planar. There is also a small reduction in metal-ligand covalency and an attendant increase in the d(x2-y2) character/energy of the singly occupied molecular orbital (SOMO), which we propose from density functional theory (DFT) calculations predisposes the copper active site for the formation of a stable Cu-O2 intermediate. This switch in orbital character upon addition of chitin provides a basis for understanding the coupling of substrate binding with O2 activation in chitin-active AA10 LPMOs.
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Affiliation(s)
- Gaston Courtade
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Luisa Ciano
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
- School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
- Photon Science Institute, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Alessandro Paradisi
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Peter J Lindley
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg Ø, Denmark
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom;
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491 Trondheim, Norway;
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29
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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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30
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Munzone A, El Kerdi B, Fanuel M, Rogniaux H, Ropartz D, Réglier M, Royant A, Simaan AJ, Decroos C. Characterization of a bacterial copper‐dependent lytic polysaccharide monooxygenase with an unusual second coordination sphere. FEBS J 2020; 287:3298-3314. [DOI: 10.1111/febs.15203] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/05/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Alessia Munzone
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
| | - Bilal El Kerdi
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
| | - Mathieu Fanuel
- INRA UR1268 Biopolymers Interactions Assemblies Nantes France
| | - Hélène Rogniaux
- INRA UR1268 Biopolymers Interactions Assemblies Nantes France
| | - David Ropartz
- INRA UR1268 Biopolymers Interactions Assemblies Nantes France
| | - Marius Réglier
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
| | - Antoine Royant
- Univ. Grenoble Alpes CNRS CEA Institut de Biologie Structurale (IBS) Grenoble France
- European Synchrotron Radiation Facility Grenoble France
| | - A. Jalila Simaan
- Aix Marseille Univ CNRS Centrale Marseille iSm2 Marseille France
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31
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Paradisi A, Johnston EM, Tovborg M, Nicoll CR, Ciano L, Dowle A, McMaster J, Hancock Y, Davies GJ, Walton PH. Formation of a Copper(II)-Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by H 2O 2. J Am Chem Soc 2019; 141:18585-18599. [PMID: 31675221 PMCID: PMC7007232 DOI: 10.1021/jacs.9b09833] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 01/14/2023]
Abstract
Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen peroxide is high, but it is accompanied by rapid inactivation of the enzymes, presumably through protein oxidation. Herein, we use UV-vis, CD, XAS, EPR, VT/VH-MCD, and resonance Raman spectroscopies, augmented with mass spectrometry and DFT calculations, to show that the product of reaction of an AA9 LPMO with H2O2 at higher pHs is a singlet Cu(II)-tyrosyl radical species, which is inactive for the oxidation of saccharidic substrates. The Cu(II)-tyrosyl radical center entails the formation of significant Cu(II)-(●OTyr) overlap, which in turn requires that the plane of the d(x2-y2) SOMO of the Cu(II) is orientated toward the tyrosyl radical. We propose from the Marcus cross-relation that the active site tyrosine is part of a "hole-hopping" charge-transfer mechanism formed of a pathway of conserved tyrosine and tryptophan residues, which can protect the protein active site from inactivation during uncoupled turnover.
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Affiliation(s)
- Alessandro Paradisi
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Esther M. Johnston
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | | | - Callum R. Nicoll
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Luisa Ciano
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Adam Dowle
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Jonathan McMaster
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Y. Hancock
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
- York
Cross-Disciplinary Centre for Systems Analysis, University of York, Heslington,
York YO10 5GE, United Kingdom
| | - Gideon J. Davies
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Paul H. Walton
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
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32
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Voshol GP, Punt PJ, Vijgenboom E. Profile Comparer Extended: phylogeny of lytic polysaccharide monooxygenase families using profile hidden Markov model alignments. F1000Res 2019; 8:1834. [PMID: 31956399 PMCID: PMC6950343 DOI: 10.12688/f1000research.21104.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
Insight into the inter- and intra-family relationship of protein families is important, since it can aid understanding of substrate specificity evolution and assign putative functions to proteins with unknown function. To study both these inter- and intra-family relationships, the ability to build phylogenetic trees using the most sensitive sequence similarity search methods (e.g. profile hidden Markov model (pHMM)-pHMM alignments) is required. However, existing solutions require a very long calculation time to obtain the phylogenetic tree. Therefore, a faster protocol is required to make this approach efficient for research. To contribute to this goal, we extended the original Profile Comparer program (PRC) for the construction of large pHMM phylogenetic trees at speeds several orders of magnitude faster compared to pHMM-tree. As an example, PRC Extended (PRCx) was used to study the phylogeny of over 10,000 sequences of lytic polysaccharide monooxygenase (LPMO) from over seven families. Using the newly developed program we were able to reveal previously unknown homologs of LPMOs, namely the PFAM Egh16-like family. Moreover, we show that the substrate specificities have evolved independently several times within the LPMO superfamily. Furthermore, the LPMO phylogenetic tree, does not seem to follow taxonomy-based classification.
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Affiliation(s)
- Gerben P. Voshol
- Department of Microbial Biotechnology and Health, Insitute of Biology Leiden, Leiden, 2333BE, The Netherlands
- Dutch DNA Biotech B.V., Utrecht, 3584CH, The Netherlands
| | - Peter J. Punt
- Department of Microbial Biotechnology and Health, Insitute of Biology Leiden, Leiden, 2333BE, The Netherlands
- Dutch DNA Biotech B.V., Utrecht, 3584CH, The Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology and Health, Insitute of Biology Leiden, Leiden, 2333BE, The Netherlands
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33
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Polyakov KM, Gavryushov S, Fedorova TV, Glazunova OA, Popov AN. The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:804-816. [DOI: 10.1107/s2059798319010684] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X-ray diffraction data sets were collected with increasing doses of absorbed X-ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.
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34
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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35
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Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O 2 activation. Proc Natl Acad Sci U S A 2019; 116:5370-5375. [PMID: 30824597 DOI: 10.1073/pnas.1818274116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The formylglycine-generating enzyme (FGE) is required for the posttranslational activation of type I sulfatases by oxidation of an active-site cysteine to Cα-formylglycine. FGE has emerged as an enabling biotechnology tool due to the robust utility of the aldehyde product as a bioconjugation handle in recombinant proteins. Here, we show that Cu(I)-FGE is functional in O2 activation and reveal a high-resolution X-ray crystal structure of FGE in complex with its catalytic copper cofactor. We establish that the copper atom is coordinated by two active-site cysteine residues in a nearly linear geometry, supporting and extending prior biochemical and structural data. The active cuprous FGE complex was interrogated directly by X-ray absorption spectroscopy. These data unambiguously establish the configuration of the resting enzyme metal center and, importantly, reveal the formation of a three-coordinate tris(thiolate) trigonal planar complex upon substrate binding as furthermore supported by density functional theory (DFT) calculations. Critically, inner-sphere substrate coordination turns on O2 activation at the copper center. These collective results provide a detailed mechanistic framework for understanding why nature chose this structurally unique monocopper active site to catalyze oxidase chemistry for sulfatase activation.
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36
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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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Courtade G, Aachmann FL. Chitin-Active Lytic Polysaccharide Monooxygenases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:115-129. [PMID: 31102244 DOI: 10.1007/978-981-13-7318-3_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze the cleavage of 1,4-glycosidic bonds various plant cell wall polysaccharides and chitin. In contrast to glycoside hydrolases, LPMOs are active on the crystalline regions of polysaccharides and thus synergize with hydrolytic enzymes. This synergism leads to an overall increase in the biomass-degradation activity of enzyme mixtures. Chitin-active LPMOs were discovered in 2010 and are currently classified in families AA10, AA11, and AA15 of the Carbohydrate-Active enZYmes database, which include LPMOs from bacteria, fungi, insects, and viruses. LPMOs have become important enzymes both industrially and scientifically and, in this chapter, we provide a brief introduction to chitin-active LPMOs including a summary of the 20+ chitin-active LPMOs that have been characterized so far. Then, we describe their structural features, catalytic mechanism, and appended carbohydrate modules. Finally, we show how chitin-active LPMOs can be used to perform chemo-enzymatic modification of chitin substrates.
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Affiliation(s)
- Gaston Courtade
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NOBIPOL, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491, Trondheim, Norway.
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Fowler CA, Sabbadin F, Ciano L, Hemsworth GR, Elias L, Bruce N, McQueen-Mason S, Davies GJ, Walton PH. Discovery, activity and characterisation of an AA10 lytic polysaccharide oxygenase from the shipworm symbiont Teredinibacter turnerae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:232. [PMID: 31583018 PMCID: PMC6767633 DOI: 10.1186/s13068-019-1573-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/21/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND The quest for novel enzymes for cellulosic biomass-degradation has recently been focussed on lytic polysaccharide monooxygenases (LPMOs/PMOs), Cu-containing proteins that catalyse the oxidative degradation of otherwise recalcitrant polysaccharides using O2 or H2O2 as a co-substrate. RESULTS Although classical saprotrophic fungi and bacteria have been a rich source of lytic polysaccharide monooxygenases (LPMOs), we were interested to see if LPMOs from less evident bio-environments could be discovered and assessed for their cellulolytic activity in a biofuel context. In this regard, the marine shipworm Lyrodus pedicellatus represents an interesting source of new enzymes, since it must digest wood particles ingested during its natural tunnel boring behaviour and plays host to a symbiotic bacterium, Teredinibacter turnerae, the genome of which has revealed a multitude of enzymes dedicated to biomass deconstruction. Here, we show that T. turnerae encodes a cellulose-active AA10 LPMO. The 3D structure, at 1.4 Å resolution, along with its EPR spectrum is distinct from other AA10 polysaccharide monooxygenases insofar as it displays a "histidine-brace" catalytic apparatus with changes to the surrounding coordination sphere of the copper. Furthermore, TtAA10A possesses a second, surface accessible, Cu site 14 Å from the classical catalytic centre. Activity measurements show that the LPMO oxidises cellulose and thereby significantly augments the rate of degradation of cellulosic biomass by classical glycoside hydrolases. CONCLUSION Shipworms are wood-boring marine molluscs that can live on a diet of lignocellulose. Bacterial symbionts of shipworms provide many of the enzymes needed for wood digestion. The shipworm symbiont T. turnerae produces one of the few LPMOs yet described from the marine environment, notably adding to the capability of shipworms to digest recalcitrant polysaccharides.
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Affiliation(s)
| | - Federico Sabbadin
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Luisa Ciano
- Department of Chemistry, University of York, York, YO10 5DD UK
- Present Address: School of Chemistry and Photon Science Institute, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Glyn R. Hemsworth
- Department of Chemistry, University of York, York, YO10 5DD UK
- Present Address: Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT UK
| | - Luisa Elias
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Neil Bruce
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | - Simon McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD UK
| | | | - Paul H. Walton
- Department of Chemistry, University of York, York, YO10 5DD UK
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39
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Muderspach SJ, Tandrup T, Frandsen KEH, Santoni G, Poulsen JCN, Leggio LL. Further structural studies of the lytic polysaccharide monooxygenase AoAA13 belonging to the starch-active AA13 family. ACTA ACUST UNITED AC 2019. [DOI: 10.1515/amylase-2019-0004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are recently discovered copper enzymes that cleave recalcitrant polysaccharides by oxidation. The structure of an Aspergillus oryzae LPMO from the starch degrading family AA13 (AoAA13) has previously been determined from an orthorhombic crystal grown in the presence of copper, which is photoreduced in the structure. Here we describe how crystals reliably grown in presence of Zn can be Cu-loaded post crystallization. A partly photoreduced structure was obtained by severely limiting the X-ray dose, showing that this LPMO is much more prone to photoreduction than others. A serial synchrotron crystallography structure was also obtained, showing that this technique may be promising for further studies, to reduce even further photoreduction. We additionally present a triclinic structure of AoAA13, which has less occluded ligand binding site than the orthorhombic one. The availability of the triclinic crystals prompted new ligand binding studies, which lead us to the conclusion that small starch analogues do not bind to AoAA13 to an appreciable extent. A number of disordered conformations of the metal binding histidine brace have been encountered in this and other studies, and we have previously hypothesized that this disorder may be a consequence of loss of copper. We performed molecular dynamics in the absence of active site metal, and showed that the dynamics in solution differ somewhat from the disorder observed in the crystal, though the extent is equally dramatic.
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40
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Singh RK, Blossom BM, Russo DA, van Oort B, Croce R, Jensen PE, Felby C, Bjerrum MJ. Thermal unfolding and refolding of a lytic polysaccharide monooxygenase fromThermoascus aurantiacus. RSC Adv 2019; 9:29734-29742. [PMID: 35531517 PMCID: PMC9072093 DOI: 10.1039/c9ra05920b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/11/2019] [Indexed: 11/21/2022] Open
Abstract
TaLPMO9A regains its catalytic power after a thermal unfolding and refolding cycle.
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Affiliation(s)
- Raushan K. Singh
- Department of Chemistry
- University of Copenhagen
- Copenhagen
- Denmark
| | - Benedikt M. Blossom
- Department of Geosciences and Natural Resource Management
- University of Copenhagen
- Frederiksberg C
- Denmark
| | - D. A. Russo
- Department of Plant and Environmental Sciences
- University of Copenhagen
- Frederiksberg C
- Denmark
| | - B. van Oort
- Biophysics of Photosynthesis
- Vrije Universiteit Amsterdam
- Amsterdam
- Netherlands
| | - R. Croce
- Biophysics of Photosynthesis
- Vrije Universiteit Amsterdam
- Amsterdam
- Netherlands
| | - P. E. Jensen
- Department of Plant and Environmental Sciences
- University of Copenhagen
- Frederiksberg C
- Denmark
| | - C. Felby
- Department of Geosciences and Natural Resource Management
- University of Copenhagen
- Frederiksberg C
- Denmark
| | - M. J. Bjerrum
- Department of Chemistry
- University of Copenhagen
- Copenhagen
- Denmark
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41
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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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42
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Zhang H, Dong S, Lou T, Wang S. Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208. J Basic Microbiol 2018; 59:267-276. [PMID: 30589093 DOI: 10.1002/jobm.201800563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 11/10/2022]
Abstract
Marine Streptomyces sp. CC0208 isolated from the Bohai Bay showed high efficiency of cellulose degradation under optimized fermentation parameters. Also, as one of the bioinformatics-based approaches for the discovery of novel natural product and enzyme effectively, genome mining has been developed and applied widely. Herein, we reported the complete genome sequence of Streptomyces sp. CC0208.Whole-genome sequencing analysis revealed a genome size of 9,325,981 bp with a linear chromosome, GC content of 70.59% and 8487 protein-coding genes. Abundant genes have predicted functions in antibiotic metabolism and enzymes. A 20 enzymes closely associated with cellulose degradation were discovered. A total of 25 biosynthetic gene clusters (BGCs) of secondary metabolites were identified, including diverse classes of natural products. The availability of genome sequence of Streptomyces sp. CC0208 not only will assist in cracking the mechanism of cellulose degradation but also will provide the insights into the significant secondary metabolic potentials for the production of diverse compound classes based on rational strategies.
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Affiliation(s)
- Hongyu Zhang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shirui Dong
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Tingting Lou
- Tianjin Entry and Exit Inspection and Quarantine Bureau, Tianjin, China
| | - Suying Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
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43
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Recent insights into lytic polysaccharide monooxygenases (LPMOs). Biochem Soc Trans 2018; 46:1431-1447. [DOI: 10.1042/bst20170549] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/14/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
Abstract
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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44
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45
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46
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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: 64] [Impact Index Per Article: 10.7] [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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47
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Meier KK, Jones SM, Kaper T, Hansson H, Koetsier MJ, Karkehabadi S, Solomon EI, Sandgren M, Kelemen B. Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. Chem Rev 2018; 118:2593-2635. [PMID: 29155571 PMCID: PMC5982588 DOI: 10.1021/acs.chemrev.7b00421] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M. Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Martijn J. Koetsier
- DuPont Industrial Biosciences, Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Bradley Kelemen
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
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Jasniewski AJ, Que L. Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes. Chem Rev 2018; 118:2554-2592. [PMID: 29400961 PMCID: PMC5920527 DOI: 10.1021/acs.chemrev.7b00457] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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49
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An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion. Nat Commun 2018; 9:756. [PMID: 29472725 PMCID: PMC5823890 DOI: 10.1038/s41467-018-03142-x] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/22/2018] [Indexed: 02/02/2023] Open
Abstract
Thermobia domestica belongs to an ancient group of insects and has a remarkable ability to digest crystalline cellulose without microbial assistance. By investigating the digestive proteome of Thermobia, we have identified over 20 members of an uncharacterized family of lytic polysaccharide monooxygenases (LPMOs). We show that this LPMO family spans across several clades of the Tree of Life, is of ancient origin, and was recruited by early arthropods with possible roles in remodeling endogenous chitin scaffolds during development and metamorphosis. Based on our in-depth characterization of Thermobia's LPMOs, we propose that diversification of these enzymes toward cellulose digestion might have endowed ancestral insects with an effective biochemical apparatus for biomass degradation, allowing the early colonization of land during the Paleozoic Era. The vital role of LPMOs in modern agricultural pests and disease vectors offers new opportunities to help tackle global challenges in food security and the control of infectious diseases.
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50
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Boada R, Cibin G, Coleman F, Diaz-Moreno S, Gianolio D, Hardacre C, Hayama S, Holbrey JD, Ramli R, Seddon KR, Srinivasan G, Swadźba-Kwaśny M. Mercury capture on a supported chlorocuprate(ii) ionic liquid adsorbent studied using operando synchrotron X-ray absorption spectroscopy. Dalton Trans 2018; 45:18946-18953. [PMID: 27844084 DOI: 10.1039/c6dt03014a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mercury scrubbing from gas streams using a supported 1-butyl-3-methylimidazolium chlorocuprate(ii) ionic liquid ([C4mim]2[Cu2Cl6]) has been studied using operando EXAFS. Initial oxidative capture as [HgCl3]- anions was confirmed, this was then followed by the unanticipated generation of mercury(i) chloride through comproportionation with additional mercury from the gas stream. Combining these two mechanisms leads to net one electron oxidative extraction of mercury from the gas with increased potential capacity and efficiency for supported ionic liquid mercury scrubbers.
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Affiliation(s)
- Roberto Boada
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Giannantonio Cibin
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Fergal Coleman
- QUILL, School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, Northern Ireland, UK.
| | - Sofia Diaz-Moreno
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Diego Gianolio
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Christopher Hardacre
- QUILL, School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, Northern Ireland, UK.
| | - Shusaku Hayama
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - John D Holbrey
- QUILL, School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, Northern Ireland, UK.
| | - Rafin Ramli
- QUILL, School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, Northern Ireland, UK.
| | - Kenneth R Seddon
- QUILL, School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, Northern Ireland, UK.
| | - Geetha Srinivasan
- QUILL, School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, Northern Ireland, UK.
| | - Małgorzata Swadźba-Kwaśny
- QUILL, School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, Northern Ireland, UK.
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