1
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Wang Q, Aleshintsev A, Rai K, Jin E, Gupta R. Proton Transfer via Arginine with Suppressed p Ka Mediates Catalysis by Gentisate and Salicylate Dioxygenase. J Phys Chem B 2024; 128:6797-6805. [PMID: 38978492 PMCID: PMC11264262 DOI: 10.1021/acs.jpcb.4c03164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
Gentisate and salicylate 1,2-dioxygenases (GDO and SDO) facilitate aerobic degradation of aromatic rings by inserting both atoms of dioxygen into their substrates, thereby participating in global carbon cycling. The role of acid-base catalysts in the reaction cycles of these enzymes is debatable. We present evidence of the participation of a proton shuffler during catalysis by GDO and SDO. The pH dependence of Michaelis-Menten parameters demonstrates that a single proton transfer is mandatory for the catalysis. Measurements at variable temperatures and pHs were used to determine the standard enthalpy of ionization (ΔHion°) of 51 kJ/mol for the proton transfer event. Although the observed apparent pKa in the range of 6.0-7.0 for substrates of both enzymes is highly suggestive of a histidine residue, ΔHion° establishes an arginine residue as the likely proton source, providing phylogenetic relevance for this strictly conserved residue in the GDO family. We propose that the atypical 3-histidine ferrous binding scaffold of GDOs contributes to the suppression of arginine pKa and provides support for this argument by employing a 2-histidine-1-carboxylate variant of the enzyme that exhibits elevated pKa. A reaction mechanism considering the role of the proton source in stabilizing key reaction intermediates is proposed.
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Affiliation(s)
- Qian Wang
- Department
of Chemistry, College of Staten Island,
City University of New York, Staten
Island, New York 10314, United States
| | - Aleksey Aleshintsev
- Department
of Chemistry, College of Staten Island,
City University of New York, Staten
Island, New York 10314, United States
- Ph.D.
Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Kamal Rai
- Department
of Chemistry, College of Staten Island,
City University of New York, Staten
Island, New York 10314, United States
| | - Eric Jin
- Staten
Island Technical High School, Staten Island, New York 10306, United States
| | - Rupal Gupta
- Department
of Chemistry, College of Staten Island,
City University of New York, Staten
Island, New York 10314, United States
- Ph.D.
Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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2
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Kato H, Takahashi Y, Suzuki H, Ohashi K, Kawashima R, Nakamura K, Sakai K, Hori C, Takasuka TE, Kato M, Shimizu M. Identification and characterization of methoxy- and dimethoxyhydroquinone 1,2-dioxygenase from Phanerochaete chrysosporium. Appl Environ Microbiol 2024; 90:e0175323. [PMID: 38259078 PMCID: PMC10880611 DOI: 10.1128/aem.01753-23] [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: 10/03/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
White-rot fungi, such as Phanerochaete chrysosporium, are the most efficient degraders of lignin, a major component of plant biomass. Enzymes produced by these fungi, such as lignin peroxidases and manganese peroxidases, break down lignin polymers into various aromatic compounds based on guaiacyl, syringyl, and hydroxyphenyl units. These intermediates are further degraded, and the aromatic ring is cleaved by 1,2,4-trihydroxybenzene dioxygenases. This study aimed to characterize homogentisate dioxygenase (HGD)-like proteins from P. chrysosporium that are strongly induced by the G-unit fragment of vanillin. We overexpressed two homologous recombinant HGDs, PcHGD1 and PcHGD2, in Escherichia coli. Both PcHGD1 and PcHGD2 catalyzed the ring cleavage in methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ). The two enzymes had the highest catalytic efficiency (kcat/Km) for MHQ, and therefore, we named PcHGD1 and PcHGD2 as MHQ dioxygenases 1 and 2 (PcMHQD1 and PcMHQD2), respectively, from P. chrysosporium. This is the first study to identify and characterize MHQ and DMHQ dioxygenase activities in members of the HGD superfamily. These findings highlight the unique and broad substrate spectra of PcHGDs, rendering them attractive candidates for biotechnological applications.IMPORTANCEThis study aimed to elucidate the properties of enzymes responsible for degrading lignin, a dominant natural polymer in terrestrial lignocellulosic biomass. We focused on two homogentisate dioxygenase (HGD) homologs from the white-rot fungus, P. chrysosporium, and investigated their roles in the degradation of lignin-derived aromatic compounds. In the P. chrysosporium genome database, PcMHQD1 and PcMHQD2 were annotated as HGDs that could cleave the aromatic rings of methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ) with a preference for MHQ. These findings suggest that MHQD1 and/or MHQD2 play important roles in the degradation of lignin-derived aromatic compounds by P. chrysosporium. The preference of PcMHQDs for MHQ and DMHQ not only highlights their potential for biotechnological applications but also underscores their critical role in understanding lignin degradation by a representative of white-rot fungus, P. chrysosporium.
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Affiliation(s)
- Hiroyuki Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | | | | | - Keisuke Ohashi
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | | | - Koki Nakamura
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Kiyota Sakai
- Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Chiaki Hori
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | | | - Masashi Kato
- Faculty of Agriculture, Meijo University, Nagoya, Japan
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3
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Bernini A, Spiga O, Santucci A. Structure-Function Relationship of Homogentisate 1,2-dioxygenase: Understanding the Genotype-Phenotype Correlations in the Rare Genetic Disease Alkaptonuria. Curr Protein Pept Sci 2023; 24:380-392. [PMID: 36880186 DOI: 10.2174/1389203724666230307104135] [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: 08/02/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 03/08/2023]
Abstract
Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in organs, which occurs because the homogentisate 1,2-dioxygenase (HGD) enzyme is not functional due to gene variants. Over time, HGA oxidation and accumulation cause the formation of the ochronotic pigment, a deposit that provokes tissue degeneration and organ malfunction. Here, we report a comprehensive review of the variants so far reported, the structural studies on the molecular consequences of protein stability and interaction, and molecular simulations for pharmacological chaperones as protein rescuers. Moreover, evidence accumulated so far in alkaptonuria research will be re-proposed as the bases for a precision medicine approach in a rare disease.
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Affiliation(s)
- Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
- Centro Regionale Medicina di Precisione, Siena, Italy
- ARTES 4.0, Pontedera, Italy
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4
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Styczynski M, Rogowska A, Nyabayo C, Decewicz P, Romaniuk F, Pączkowski C, Szakiel A, Suessmuth R, Dziewit L. Heterologous production and characterization of a pyomelanin of Antarctic Pseudomonas sp. ANT_H4: a metabolite protecting against UV and free radicals, interacting with iron from minerals and exhibiting priming properties toward plant hairy roots. Microb Cell Fact 2022; 21:261. [PMID: 36527127 PMCID: PMC9756463 DOI: 10.1186/s12934-022-01990-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Antarctica has one of the most extreme environments in the world. This region is inhabited by specifically adapted microorganisms that produce various unique secondary metabolites (e.g. pigments) enabling their survival under the harsh environmental conditions. It was already shown that these natural, biologically active molecules may find application in various fields of biotechnology. RESULTS In this study, a cold-active brown-pigment-producing Pseudomonas sp. ANT_H4 strain was characterized. In-depth genomic analysis combined with the application of a fosmid expression system revealed two different pathways of melanin-like compounds biosynthesis by the ANT_H4 strain. The chromatographic behavior and Fourier-transform infrared spectroscopic analyses allowed for the identification of the extracted melanin-like compound as a pyomelanin. Furthermore, optimization of the production and thorough functional analyses of the pyomelanin were performed to test its usability in biotechnology. It was confirmed that ANT_H4-derived pyomelanin increases the sun protection factor, enables scavenging of free radicals, and interacts with the iron from minerals. Moreover, it was shown for the first time that pyomelanin exhibits priming properties toward Calendula officinalis hairy roots in in vitro cultures. CONCLUSIONS Results of the study indicate the significant biotechnological potential of ANT_H4-derived pyomelanin and open opportunities for future applications. Taking into account protective features of analyzed pyomelanin it may be potentially used in medical biotechnology and cosmetology. Especially interesting was showing that pyomelanin exhibits priming properties toward hairy roots, which creates a perspective for its usage for the development of novel and sustainable agrotechnical solutions.
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Affiliation(s)
- Michal Styczynski
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agata Rogowska
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Christine Nyabayo
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Przemyslaw Decewicz
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Filip Romaniuk
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Cezary Pączkowski
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Szakiel
- grid.12847.380000 0004 1937 1290Department of Plant Biochemistry, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Roderich Suessmuth
- grid.6734.60000 0001 2292 8254Institute of Chemistry, Technical University of Berlin, Berlin, Germany
| | - Lukasz Dziewit
- grid.12847.380000 0004 1937 1290Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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5
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Pleiotropic Effects of Hfq on the Cytochrome c Content and Pyomelanin Production in Shewanella oneidensis. Appl Environ Microbiol 2022; 88:e0128922. [PMID: 36073941 PMCID: PMC9499022 DOI: 10.1128/aem.01289-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis is the best understood model microorganism for the study of diverse cytochromes (cytos) c that support its unparallel respiratory versatility. Although RNA chaperone Hfq has been implicated in regulation of cyto c production, little is known about the biological pathways that it affects in this bacterium. In this study, from a spontaneous mutant that secretes pyomelanin and has a lowered cyto c content, we identified Hfq to be the regulator that critically associates with both phenotypes in S. oneidensis. We found that expression of the key genes in biosynthesis and degradation of heme is differentially affected by Hfq at under- and overproduced levels, and through modulating heme levels, Hfq influences the cyto c content. Although Hfq in excess results in overproduction of the enzymes responsible for both generation and removal of homogentisic acid (HGA), the precursor of pyomelanin, it is compromised activity of HmgA that leads to excretion and polymerization of HGA to form pyomelanin. We further show that Hfq mediates HmgA activity by lowering intracellular iron content because HmgA is an iron-dependent enzyme. Overall, our work highlights the significance of Hfq-mediated posttranscriptional regulation in the physiology of S. oneidensis, unraveling unexpected mechanisms by which Hfq affects cyto c biosynthesis and pyomelanin production. IMPORTANCE In bacteria, Hfq has been implicated in regulation of diverse biological processes posttranslationally. In S. oneidensis, Hfq affects the content of cytos c that serve as the basis of its respiratory versatility and potential application in bioenergy and bioremediation. In this study, we found that Hfq differentially regulates heme biosynthesis and degradation, leading to altered cyto c contents. Hfq in excess causes a synthetic effect on HmgA, an enzyme responsible for pyomelanin formation. Overall, the data presented manifest that the biological processes in a given bacterium regulated by Hfq are highly complex, amounting to required coordination among multiple physiological aspects to allow cells to respond to environmental changes promptly.
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6
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Abstract
Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.
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Affiliation(s)
- Ephrahime S. Traore
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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7
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Karmakar M, Cicaloni V, Rodrigues CH, Spiga O, Santucci A, Ascher DB. HGDiscovery: An online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase. Curr Res Struct Biol 2022; 4:271-277. [PMID: 36118553 PMCID: PMC9471331 DOI: 10.1016/j.crstbi.2022.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/28/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in the body. Affected individuals lack functional levels of an enzyme required to breakdown HGA. Mutations in the homogentisate 1,2-dioxygenase (HGD) gene cause AKU and they are responsible for deficient levels of functional HGD, which, in turn, leads to excess levels of HGA. Although HGA is rapidly cleared from the body by the kidneys, in the long term it starts accumulating in various tissues, especially cartilage. Over time (rarely before adulthood), it eventually changes the color of affected tissue to slate blue or black. Here we report a comprehensive mutation analysis of 111 pathogenic and 190 non-pathogenic HGD missense mutations using protein structural information. Using our comprehensive suite of graph-based signature methods, mCSM complemented with sequence-based tools, we studied the functional and molecular consequences of each mutation on protein stability, interaction and evolutionary conservation. The scores generated from the structure and sequence-based tools were used to train a supervised machine learning algorithm with 89% accuracy. The empirical classifier was used to generate the variant phenotype for novel HGD missense mutations. All this information is deployed as a user friendly freely available web server called HGDiscovery (https://biosig.lab.uq.edu.au/hgdiscovery/). Functional and phenotypic consequences of HGD non-synonymous variations. Biophysical, structural and evolutionary analysis of novel and known clinical variants. Pathogenic mutations affected protein stability and conformational flexibility. Pathogenic mutations associated with deleterious scores for sequence-based features. HGDiscovery (http://biosig.unimelb.edu.au/hgdiscovery/) – webserver.
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Affiliation(s)
- Malancha Karmakar
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Vittoria Cicaloni
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Carlos H.M. Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biology, University of Queensland, Brisbane, Queensland, Australia
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - David B. Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biology, University of Queensland, Brisbane, Queensland, Australia
- Corresponding author. Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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8
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Pan HR, Chen HJ, Wu ZH, Ge P, Ye S, Lee GH, Hsu HF. Structural and Spectroscopic Evidence for a Side-on Fe(III)-Superoxo Complex Featuring Discrete O-O Bond Distances. JACS AU 2021; 1:1389-1398. [PMID: 34604849 PMCID: PMC8479760 DOI: 10.1021/jacsau.1c00184] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Indexed: 05/26/2023]
Abstract
The O-O bond length is often used as a structural indicator to determine the valence states of bound O2 ligands in biological metal-dioxygen intermediates and related biomimetic complexes. Here, we report very distinct O-O bond lengths found for three crystallographic forms (1.229(4), 1.330(4), 1.387(2) Å at 100 K) of a side-on iron-dioxygen species. Despite their different O-O bond distances, all forms possess the same electronic structure of Fe(III)-O2 •-, as evidenced by their indistinguishable spectroscopic features. Density functional theory and ab initio calculations, which successfully reproduce spectroscopic parameters, predict a flat potential energy surface of an η2-O2 motif binding to the iron center regarding the O-O distance. Therefore, the discrete O-O bond lengths observed likely arise from differential intermolecular interactions in the second coordination sphere. The work suggests that the O-O distance is not a reliable benchmark to unequivocally identify the valence state of O2 ligands for metal-dioxygen species in O2-utilizing metalloproteins and synthetic complexes.
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Affiliation(s)
- Hung-Ruei Pan
- Department
of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsin-Jou Chen
- Department
of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Zong-Han Wu
- Department
of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Pu Ge
- School
of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China
| | - Shengfa Ye
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Max-Planck-Institut
für Kohlenforschung, Mülheim
an der Ruhr D-45470, Germany
| | - Gene-Hsiang Lee
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hua-Fen Hsu
- Department
of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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9
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Leisinger F, Miarzlou DA, Seebeck FP. Non-Coordinative Binding of O 2 at the Active Center of a Copper-Dependent Enzyme. Angew Chem Int Ed Engl 2021; 60:6154-6159. [PMID: 33245183 DOI: 10.1002/anie.202014981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 12/28/2022]
Abstract
Molecular oxygen (O2 ) is a sustainable oxidation reagent. O2 is strongly oxidizing but kinetically stable and its final reaction product is water. For these reasons learning how to activate O2 and how to steer its reactivity along desired reaction pathways is a longstanding challenge in chemical research.[1] Activation of ground-state diradical O2 can occur either via conversion to singlet oxygen or by one-electron reduction to superoxide. Many enzymes facilitate activation of O2 by direct fomation of a metal-oxygen coordination complex concomitant with inner sphere electron transfer. The formylglycine generating enzyme (FGE) is an unusual mononuclear copper enzyme that appears to follow a different strategy. Atomic-resolution crystal structures of the precatalytic complex of FGE demonstrate that this enzyme binds O2 juxtaposed, but not coordinated to the catalytic CuI . Isostructural complexes that contain AgI instead of CuI or nitric oxide instead of O2 confirm that formation of the initial oxygenated complex of FGE does not depend on redox activity. A stepwise mechanism that decouples binding and activation of O2 is unprecedented for metal-dependent oxidases, but is reminiscent of flavin-dependent enzymes.
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Affiliation(s)
- Florian Leisinger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Dzmitry A Miarzlou
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
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10
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Leisinger F, Miarzlou DA, Seebeck FP. Non‐Coordinative Binding of O
2
at the Active Center of a Copper‐Dependent Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Florian Leisinger
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Dzmitry A. Miarzlou
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
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11
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Structure-guided insights into heterocyclic ring-cleavage catalysis of the non-heme Fe (II) dioxygenase NicX. Nat Commun 2021; 12:1301. [PMID: 33637718 PMCID: PMC7910607 DOI: 10.1038/s41467-021-21567-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Biodegradation of aromatic and heterocyclic compounds requires an oxidative ring cleavage enzymatic step. Extensive biochemical research has yielded mechanistic insights about catabolism of aromatic substrates; yet much less is known about the reaction mechanisms underlying the cleavage of heterocyclic compounds such as pyridine-ring-containing ones like 2,5-hydroxy-pyridine (DHP). 2,5-Dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 uses a mononuclear nonheme Fe(II) to catalyze the oxidative pyridine ring cleavage reaction by transforming DHP into N-formylmaleamic acid (NFM). Herein, we report a crystal structure for the resting form of NicX, as well as a complex structure wherein DHP and NFM are trapped in different subunits. The resting state structure displays an octahedral coordination for Fe(II) with two histidine residues (His265 and His318), a serine residue (Ser302), a carboxylate ligand (Asp320), and two water molecules. DHP does not bind as a ligand to Fe(II), yet its interactions with Leu104 and His105 function to guide and stabilize the substrate to the appropriate position to initiate the reaction. Additionally, combined structural and computational analyses lend support to an apical dioxygen catalytic mechanism. Our study thus deepens understanding of non-heme Fe(II) dioxygenases.
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12
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Yu J, Lai W. Mechanistic insights into dioxygen activation by a manganese corrole complex: a broken-symmetry DFT study. RSC Adv 2021; 11:24852-24861. [PMID: 35481047 PMCID: PMC9036905 DOI: 10.1039/d1ra02722k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022] Open
Abstract
The Mn–oxygen species have been implicated as key intermediates in various Mn-mediated oxidation reactions. However, artificial oxidants were often used for the synthesis of the Mn–oxygen intermediates. Remarkably, the Mn(v)–oxo and Mn(iv)–peroxo species have been observed in the activation of O2 by Mn(iii) corroles in the presence of base (OH−) and hydrogen donors. In this work, density functional theory methods were used to get insight into the mechanism of dioxygen activation and formation of Mn(v)–oxo. The results demonstrated that the dioxygen cannot bind to Mn without the axial OH− ligand. Upon the addition of the axial OH− ligand, the dioxygen can bind to Mn in an end-on fashion to give the Mn(iv)–superoxo species. The hydrogen atom transfer from the hydrogen donor (substrate) to the Mn(iv)–superoxo species is the rate-limiting step, having a high reaction barrier and a large endothermicity. Subsequently, the O–C bond formation is concerted with an electron transfer from the substrate radical to the Mn and a proton transfer from the hydroperoxo moiety to the nearby N atom of the corrole ring, generating an alkylperoxo Mn(iii) complex. The alkylperoxo O–O bond cleavage affords a Mn(v)–oxo complex and a hydroxylated substrate. This novel mechanism for the Mn(v)–oxo formation via an alkylperoxo Mn(iii) intermediate gives insight into the O–O bond activation by manganese complexes. DFT calculations revealed a novel mechanism for the formation of Mn(v)–oxo in the dioxygen activation by a Mn(iii) corrole complex involving a Mn(iii)–alkylperoxo intermediate.![]()
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Affiliation(s)
- Jiangfeng Yu
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Wenzhen Lai
- Department of Chemistry
- Renmin University of China
- Beijing
- China
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13
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Wang Y, Liu KF, Yang Y, Davis I, Liu A. Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc Natl Acad Sci U S A 2020; 117:19720-19730. [PMID: 32732435 PMCID: PMC7443976 DOI: 10.1073/pnas.2005327117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yu Yang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249;
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Transient pockets as mediators of gas molecules routes inside proteins: The case study of dioxygen pathway in homogentisate 1,2-dioxygenase and its implication in Alkaptonuria development. Comput Biol Chem 2020; 88:107356. [PMID: 32823072 DOI: 10.1016/j.compbiolchem.2020.107356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/10/2020] [Accepted: 08/03/2020] [Indexed: 11/20/2022]
Abstract
Alkaptonuria (AKU) is an ultra-rare disease caused by mutations in homogentisate 1,2-dioxygenase (HGD) enzyme, characterized by the loss of enzymatic activity and the accumulation of its substrate, homogentisic acid (HGA) in different tissues, leading to ochronosis and organ degeneration. Although the pathological effects of HGD mutations are largely studied, less is known about the structure of the enzyme, in particular the pathways for dioxygen diffusion to the active site, required for the enzymatic reaction, are still uninvestigated. In the present project, the combination of two in silico techniques, Molecular Dynamics (MD) simulation and Implicit Ligand Sampling (ILS), was used to delineate gas diffusion routes in HGD enzyme. A route from the central opening of the hexameric structure of the enzyme to the back of the active site trough the protein moiety was identified as the path for dioxygen diffusion, also overlapping with a transient pocket, which then assumes an important role in dioxygen diffusion. Along the route the sequence location of the missense variant E401Q, responsible for AKU development, was also found, suggesting such mutation to be conducive of enzymatic activity loss by altering the flow dynamics of dioxygen. Our in silico approach allowed also to delineate the route of HGA substrate to the active site, until now only supposed.
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15
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Fujieda N, Umakoshi K, Ochi Y, Nishikawa Y, Yanagisawa S, Kubo M, Kurisu G, Itoh S. Copper–Oxygen Dynamics in the Tyrosinase Mechanism. Angew Chem Int Ed Engl 2020; 59:13385-13390. [DOI: 10.1002/anie.202004733] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Nobutaka Fujieda
- Department of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University 1-1 Gakuen-cho, Naka-ku, Sakai-shi Osaka 599-8531 Japan
| | - Kyohei Umakoshi
- Department of Material and Life Science Graduate School of Engineering Osaka University 2-1 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Yuta Ochi
- Department of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University 1-1 Gakuen-cho, Naka-ku, Sakai-shi Osaka 599-8531 Japan
| | - Yosuke Nishikawa
- Institute for Protein Research Osaka University 3-2 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science University of Hyogo 3-2-1 Kouto, Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Minoru Kubo
- Graduate School of Life Science University of Hyogo 3-2-1 Kouto, Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Genji Kurisu
- Institute for Protein Research Osaka University 3-2 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Shinobu Itoh
- Department of Material and Life Science Graduate School of Engineering Osaka University 2-1 Yamada-oka, Suita Osaka 565-0871 Japan
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16
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Fujieda N, Umakoshi K, Ochi Y, Nishikawa Y, Yanagisawa S, Kubo M, Kurisu G, Itoh S. Copper–Oxygen Dynamics in the Tyrosinase Mechanism. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004733] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nobutaka Fujieda
- Department of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University 1-1 Gakuen-cho, Naka-ku, Sakai-shi Osaka 599-8531 Japan
| | - Kyohei Umakoshi
- Department of Material and Life Science Graduate School of Engineering Osaka University 2-1 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Yuta Ochi
- Department of Applied Life Sciences Graduate School of Life and Environmental Sciences Osaka Prefecture University 1-1 Gakuen-cho, Naka-ku, Sakai-shi Osaka 599-8531 Japan
| | - Yosuke Nishikawa
- Institute for Protein Research Osaka University 3-2 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science University of Hyogo 3-2-1 Kouto, Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Minoru Kubo
- Graduate School of Life Science University of Hyogo 3-2-1 Kouto, Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Genji Kurisu
- Institute for Protein Research Osaka University 3-2 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Shinobu Itoh
- Department of Material and Life Science Graduate School of Engineering Osaka University 2-1 Yamada-oka, Suita Osaka 565-0871 Japan
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17
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Li J, Liao HJ, Tang Y, Huang JL, Cha L, Lin TS, Lee JL, Kurnikov IV, Kurnikova MG, Chang WC, Chan NL, Guo Y. Epoxidation Catalyzed by the Nonheme Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, AsqJ: Mechanistic Elucidation of Oxygen Atom Transfer by a Ferryl Intermediate. J Am Chem Soc 2020; 142:6268-6284. [PMID: 32131594 PMCID: PMC7343540 DOI: 10.1021/jacs.0c00484] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mechanisms of enzymatic epoxidation via oxygen atom transfer (OAT) to an olefin moiety is mainly derived from the studies on thiolate-heme containing epoxidases, such as cytochrome P450 epoxidases. The molecular basis of epoxidation catalyzed by nonheme-iron enzymes is much less explored. Herein, we present a detailed study on epoxidation catalyzed by the nonheme iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase, AsqJ. The native substrate and analogues with different para substituents ranging from electron-donating groups (e.g., methoxy) to electron-withdrawing groups (e.g., trifluoromethyl) were used to probe the mechanism. The results derived from transient-state enzyme kinetics, Mössbauer spectroscopy, reaction product analysis, X-ray crystallography, density functional theory calculations, and molecular dynamic simulations collectively revealed the following mechanistic insights: (1) The rapid O2 addition to the AsqJ Fe(II) center occurs with the iron-bound 2OG adopting an online-binding mode in which the C1 carboxylate group of 2OG is trans to the proximal histidine (His134) of the 2-His-1-carboxylate facial triad, instead of assuming the offline-binding mode with the C1 carboxylate group trans to the distal histidine (His211); (2) The decay rate constant of the ferryl intermediate is not strongly affected by the nature of the para substituents of the substrate during the OAT step, a reactivity behavior that is drastically different from nonheme Fe(IV)-oxo synthetic model complexes; (3) The OAT step most likely proceeds through a stepwise process with the initial formation of a C(benzylic)-O bond to generate an Fe-alkoxide species, which is observed in the AsqJ crystal structure. The subsequent C3-O bond formation completes the epoxide installation.
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Affiliation(s)
- Jikun Li
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Hsuan-Jen Liao
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yijie Tang
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jhih-Liang Huang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Lide Cha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Te-Sheng Lin
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Justin L. Lee
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Igor V. Kurnikov
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Maria G. Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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18
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Zhang S, Liu Y. Mechanism of fatty acid decarboxylation catalyzed by a non-heme iron oxidase (UndA): a QM/MM study. Org Biomol Chem 2019; 17:9808-9818. [PMID: 31710061 DOI: 10.1039/c9ob02116g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UndA is a non-heme iron enzyme that was recognized to catalyze the decarboxylation of medium chain (C10-C14) fatty acids to produce trace amounts of 1-alkenes. Owing to the electron imbalance during the oxidative decarboxylation of the substrate and the reduction of O2, only single turnover reactions were obtained in UndA in vitro assays. Unlike the general non-heme iron enzymes, the catalytic efficiency of UndA is quite low. According to the previous proposal, both FeIII-OO˙- and FeIV[double bond, length as m-dash]O complexes may abstract the β-H of fatty acids to trigger the oxidative decarboxylation reaction. Herein, on the basis of the crystal structures of UndA in complex with the substrate analogues, we constructed a series of computational models and performed quantum mechanics/molecular mechanics (QM/MM) calculations to explore the UndA-catalyzed decarboxylation using lauric acid as the substrate. Our calculation results reveal that only the FeIII-OO˙- complex can initiate the decarboxylation, and the substrate (lauric acid) should monodentately coordinate to the Fe center to facilitate the β-H abstraction. In addition, the monodentate coordination corresponds to higher relative energy than the bidentate mode, which may explain the low efficiency of UndA. It is also revealed that as long as the β-H is extracted by the FeIII-OO˙-, the decarboxylation of the substrate radical is quite easy, and an electron transfer from the substrate to the iron center is the prerequisite. For the FeIV[double bond, length as m-dash]O complex, since the β-H is far from the OFe atom and the angle of ∠Fe-O-H is 53.1°, the H-abstraction is calculated to be difficult.
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Affiliation(s)
- Shiqing Zhang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
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19
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Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. Eur J Hum Genet 2019; 27:888-902. [PMID: 30737480 DOI: 10.1038/s41431-019-0354-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 01/12/2019] [Accepted: 01/24/2019] [Indexed: 11/08/2022] Open
Abstract
Alkaptonuria (AKU) is a rare metabolic disorder caused by a deficient enzyme in the tyrosine degradation pathway, homogentisate 1,2-dioxygenase (HGD). In 172 AKU patients from 39 countries, we identified 28 novel variants of the HGD gene, which include three larger genomic deletions within this gene discovered via self-designed multiplex ligation-dependent probe amplification (MLPA) probes. In addition, using a reporter minigene assay, we provide evidence that three of eight tested variants potentially affecting splicing cause exon skipping or cryptic splice-site activation. Extensive bioinformatics analysis of novel missense variants, and of the entire HGD monomer, confirmed mCSM as an effective computational tool for evaluating possible enzyme inactivation mechanisms. For the first time for AKU, a genotype-phenotype correlation study was performed for the three most frequent HGD variants identified in the Suitability Of Nitisinone in Alkaptonuria 2 (SONIA2) study. We found a small but statistically significant difference in urinary homogentisic acid (HGA) excretion, corrected for dietary protein intake, between variants leading to 1% or >30% residual HGD activity. There was, interestingly, no difference in serum levels or absolute urinary excretion of HGA, or clinical symptoms, indicating that protein intake is more important than differences in HGD variants for the amounts of HGA that accumulate in the body of AKU patients.
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20
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Li S, Lu J, Lai W. Mechanistic insights into ring cleavage of hydroquinone by PnpCD from quantum mechanical/molecular mechanical calculations. Org Biomol Chem 2019; 17:8194-8205. [DOI: 10.1039/c9ob01084j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM calculations for ring cleavage of hydroquinone by PnpCD show that Asn258 loses coordination to the iron when the reaction begins. The first-sphere Glu262 can act as an acid–base catalyst to lower the rate-limiting barrier.
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Affiliation(s)
- Senzhi Li
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Jiarui Lu
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Wenzhen Lai
- Department of Chemistry
- Renmin University of China
- Beijing
- China
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21
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Catechol 1,2-Dioxygenase is an Analogue of Homogentisate 1,2-Dioxygenase in Pseudomonas chlororaphis Strain UFB2. Int J Mol Sci 2018; 20:ijms20010061. [PMID: 30586858 PMCID: PMC6337169 DOI: 10.3390/ijms20010061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 11/16/2022] Open
Abstract
Catechol dioxygenases in microorganisms cleave catechol into cis-cis-muconic acid or 2-hydroxymuconic semialdehyde via the ortho- or meta-pathways, respectively. The aim of this study was to purify, characterize, and predict the template-based three-dimensional structure of catechol 1,2-dioxygenase (C12O) from indigenous Pseudomonas chlororaphis strain UFB2 (PcUFB2). Preliminary studies showed that PcUFB2 could degrade 40 ppm of 2,4-dichlorophenol (2,4-DCP). The crude cell extract showed 10.34 U/mL of C12O activity with a specific activity of 2.23 U/mg of protein. A 35 kDa protein was purified to 1.5-fold with total yield of 13.02% by applying anion exchange and gel filtration chromatography. The enzyme was optimally active at pH 7.5 and a temperature of 30 °C. The Lineweaver⁻Burk plot showed the vmax and Km values of 16.67 µM/min and 35.76 µM, respectively. ES-MS spectra of tryptic digested SDS-PAGE band and bioinformatics studies revealed that C12O shared 81% homology with homogentisate 1,2-dioxygenase reported in other Pseudomonas chlororaphis strains. The characterization and optimization of C12O activity can assist in understanding the 2,4-DCP metabolic pathway in PcUFB2 and its possible application in bioremediation strategies.
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22
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X-Ray Crystallography of Carbon Monoxide Dehydrogenases. Methods Mol Biol 2018. [PMID: 30317481 DOI: 10.1007/978-1-4939-8864-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Carbon monoxide dehydrogenases (CODHs) are central players in the biogeochemical carbon monoxide (CO) cycle and have been extensively studied from the ecological level to the structural/molecular level. Of the two types of CODHs, the oxygen-tolerant CODHs use a bimetallic [CuSMo(=O)OH] center connected to the protein via a pyranopterin cofactor, whereas the oxygen-sensitive CODHs contain a [NiFe4S4-OHx]-cluster. Despite the fact that we have a basic understanding of how both types of CODHs use distinct active sites to catalyze the oxidation of CO with water to CO2, two protons, and two electrons (a reversible reaction in the cases of the oxygen-sensitive CODHs), many questions remain unanswered, especially concerning the electronic structures of the intermediate states. Since these states will likely be only revealed by the interplay of experimental and theoretical methods, there is a need to obtain accurate descriptions of the active site architectures in various states and, consequently, a need to generate crystals with good diffraction quality and collect data at element-specific wavelengths in order to determine the identity of elements in the case of mixed states. This chapter provides a description of the general working protocols for the crystallization and structural analysis of Cu,Mo-CODH and Ni,Fe-CODH that facilitates the mechanistic investigations of these important metalloenzymes.
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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: 316] [Impact Index Per Article: 52.7] [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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24
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Bernini A, Galderisi S, Spiga O, Bernardini G, Niccolai N, Manetti F, Santucci A. Toward a generalized computational workflow for exploiting transient pockets as new targets for small molecule stabilizers: Application to the homogentisate 1,2-dioxygenase mutants at the base of rare disease Alkaptonuria. Comput Biol Chem 2017; 70:133-141. [PMID: 28869836 DOI: 10.1016/j.compbiolchem.2017.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 10/19/2022]
Abstract
Alkaptonuria (AKU) is an inborn error of metabolism where mutation of homogentisate 1,2-dioxygenase (HGD) gene leads to a deleterious or misfolded product with subsequent loss of enzymatic degradation of homogentisic acid (HGA) whose accumulation in tissues causes ochronosis and degeneration. There is no licensed therapy for AKU. Many missense mutations have been individuated as responsible for quaternary structure disruption of the native hexameric HGD. A new approach to the treatment of AKU is here proposed aiming to totally or partially rescue enzyme activity by targeting of HGD with pharmacological chaperones, i.e. small molecules helping structural stability. Co-factor pockets from oligomeric proteins have already been successfully exploited as targets for such a strategy, but no similar sites are present at HGD surface; hence, transient pockets are here proposed as a target for pharmacological chaperones. Transient pockets are detected along the molecular dynamics trajectory of the protein and filtered down to a set of suitable sites for structural stabilization by mean of biochemical and pharmacological criteria. The result is a computational workflow relevant to other inborn errors of metabolism requiring rescue of oligomeric, misfolded enzymes.
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Affiliation(s)
- Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Silvia Galderisi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Giulia Bernardini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
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25
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Reply to Kiser: Dioxygen binding in NOV1 crystal structures. Proc Natl Acad Sci U S A 2017; 114:E6029-E6030. [PMID: 28679635 DOI: 10.1073/pnas.1708124114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Deshpande AR, Pochapsky TC, Ringe D. The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. Chem Rev 2017; 117:10474-10501. [PMID: 28731690 DOI: 10.1021/acs.chemrev.7b00117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe2+ or Ni2+) in the active site. The Fe2+-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni2+-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.
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Affiliation(s)
- Aditi R Deshpande
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Thomas C Pochapsky
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Dagmar Ringe
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
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27
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Reappraisal of dioxygen binding in NOV1 crystal structures. Proc Natl Acad Sci U S A 2017; 114:E6027-E6028. [PMID: 28679636 DOI: 10.1073/pnas.1706550114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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28
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Roy S, Kästner J. Catalytic Mechanism of Salicylate Dioxygenase: QM/MM Simulations Reveal the Origin of Unexpected Regioselectivity of the Ring Cleavage. Chemistry 2017; 23:8949-8962. [DOI: 10.1002/chem.201701286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Subhendu Roy
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
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29
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Ferraroni M, Da Vela S, Kolvenbach BA, Corvini PFX, Scozzafava A. The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:520-530. [PMID: 28232026 DOI: 10.1016/j.bbapap.2017.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/24/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
The crystal structure of hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, which oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes, has been solved by Molecular Replacement, using the coordinates of PnpCD from Pseudomonas sp. strain WBC-3. The enzyme is a heterotetramer, constituted of two subunits α and two β of 19 and 38kDa, respectively. Both the two subunits fold as a cupin, but that of the small α subunit lacks a competent metal binding pocket. Two tetramers are present in the asymmetric unit. Each of the four β subunits in the asymmetric unit binds one Fe(II) ion. The iron ion in each β subunit is coordinated to three protein residues, His258, Glu264, and His305 and a water molecule. The crystal structures of the complexes with the substrate methylhydroquinone, obtained under anaerobic conditions, and with the inhibitors 4-hydroxybenzoate and 4-nitrophenol were also solved. The structures of the native enzyme and of the complexes present significant differences in the active site region compared to PnpCD, the other hydroquinone 1,2-dioxygenase of known structure, and in particular they show a different coordination at the metal center.
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Affiliation(s)
- Marta Ferraroni
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy.
| | - Stefano Da Vela
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy.
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland.
| | - Philippe F X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland.
| | - Andrea Scozzafava
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy.
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30
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Wang Y, Li J, Liu A. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J Biol Inorg Chem 2017; 22:395-405. [PMID: 28084551 DOI: 10.1007/s00775-017-1436-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/03/2017] [Indexed: 11/25/2022]
Abstract
Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O2 so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O2 as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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31
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Dong G, Ryde U. O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162. Inorg Chem 2016; 55:11727-11735. [DOI: 10.1021/acs.inorgchem.6b01732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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32
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Wang CC, Chang HC, Lai YC, Fang H, Li CC, Hsu HK, Li ZY, Lin TS, Kuo TS, Neese F, Ye S, Chiang YW, Tsai ML, Liaw WF, Lee WZ. A Structurally Characterized Nonheme Cobalt–Hydroperoxo Complex Derived from Its Superoxo Intermediate via Hydrogen Atom Abstraction. J Am Chem Soc 2016; 138:14186-14189. [DOI: 10.1021/jacs.6b08642] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chun-Chieh Wang
- Department
of Chemistry and Instrumentation Center, National Taiwan Normal University, Taipei 11677, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hao-Ching Chang
- Department
of Chemistry and Instrumentation Center, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yei-Chen Lai
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Huayi Fang
- Max-Planck Institut für Chemische Energiekonversion, Mülheim an der Ruhr D-45470, Germany
| | - Chieh-Chin Li
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hung-Kai Hsu
- Department
of Chemistry and Instrumentation Center, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Zong-Yan Li
- Department
of Chemistry and Instrumentation Center, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Tien-Sung Lin
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Ting-Shen Kuo
- Department
of Chemistry and Instrumentation Center, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion, Mülheim an der Ruhr D-45470, Germany
| | - Shengfa Ye
- Max-Planck Institut für Chemische Energiekonversion, Mülheim an der Ruhr D-45470, Germany
| | - Yun-Wei Chiang
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ming-Li Tsai
- Department
of Chemistry, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Wen-Feng Liaw
- Department
of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Way-Zen Lee
- Department
of Chemistry and Instrumentation Center, National Taiwan Normal University, Taipei 11677, Taiwan
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33
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Meier KK, Rogers MS, Kovaleva EG, Lipscomb JD, Bominaar EL, Münck E. Enzyme Substrate Complex of the H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Mössbauer and Computational Studies. Inorg Chem 2016; 55:5862-70. [PMID: 27275865 PMCID: PMC4924929 DOI: 10.1021/acs.inorgchem.6b00148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The extradiol, aromatic ring-cleaving enzyme homoprotocatechuate 2,3-dioxygenase (HPCD) catalyzes a complex chain of reactions that involve second sphere residues of the active site. The importance of the second-sphere residue His200 was demonstrated in studies of HPCD variants, such as His200Cys (H200C), which revealed significant retardations of certain steps in the catalytic process as a result of the substitution, allowing novel reaction cycle intermediates to be trapped for spectroscopic characterization. As the H200C variant largely retains the wild-type active site structure and produces the correct ring-cleaved product, this variant presents a valuable target for mechanistic HPCD studies. Here, the high-spin Fe(II) states of resting H200C and the H200C-homoprotocatechuate enzyme-substrate (ES) complex have been characterized with Mössbauer spectroscopy to assess the electronic structures of the active site in these states. The analysis reveals a high-spin Fe(II) center in a low symmetry environment that is reflected in the values of the zero-field splitting (ZFS) (D ≈ - 8 cm(-1), E/D ≈ 1/3 in ES), as well as the relative orientations of the principal axes of the (57)Fe magnetic hyperfine (A) and electric field gradient (EFG) tensors relative to the ZFS tensor axes. A spin Hamiltonian analysis of the spectra for the ES complex indicates that the magnetization axis of the integer-spin S = 2 Fe(II) system is nearly parallel to the symmetry axis, z, of the doubly occupied dxy ground orbital deduced from the EFG and A-values, an observation, which cannot be rationalized by DFT assisted crystal-field theory. In contrast, ORCA/CASSCF calculations for the ZFS tensor in combination with DFT calculations for the EFG- and A-tensors describe the experimental data remarkably well.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Elena G. Kovaleva
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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Qi Y, Lu J, Lai W. Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study. J Phys Chem B 2016; 120:4579-90. [PMID: 27119315 DOI: 10.1021/acs.jpcb.6b03006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O-O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C2 hydroxyl group is not ionized (the nonionized pathway), the O-O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C2 hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C2 hydroxyl group is more likely to be nonionized.
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Affiliation(s)
- Yue Qi
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
| | - Jiarui Lu
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
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35
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Christian GJ, Neese F, Ye S. Unravelling the Molecular Origin of the Regiospecificity in Extradiol Catechol Dioxygenases. Inorg Chem 2016; 55:3853-64. [PMID: 27050565 DOI: 10.1021/acs.inorgchem.5b02978] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many factors have been suggested to control the selectivity for extradiol or intradiol cleavage in catechol dioxygenases. The varied selectivity of model complexes and the ability to force an extradiol enzyme to do intradiol cleavage indicate that the problem may be complex. In this paper we focus on the regiospecificity of the proximal extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase (HPCD), for which considerable advances have been made in our understanding of the mechanism from an experimental and computational standpoint. Two key steps in the reaction mechanism were investigated: (1) attack of the substrate by the superoxide moiety and (2) attack of the substrate by the oxyl radical generated by O-O bond cleavage. The selectivity at both steps was investigated through a systematic study of the role of the substrate and the first and second coordination spheres. For the isolated native substrate, intradiol cleavage is calculated to be both kinetically and thermodynamically favored, therefore nature must use the enzyme environment to reverse this preference. Two second sphere residues were found to play key roles in controlling the regiospecificity of the reaction: Tyr257 and His200. Tyr257 controls the selectivity by modulating the electronic structure of the substrate, while His200 controls selectivity through steric effects and by preventing alternative pathways to intradiol cleavage.
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Affiliation(s)
- Gemma J Christian
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.,Avondale College of Higher Education , Cooranbong, New South Wales 2265, Australia
| | - Frank Neese
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Shengfa Ye
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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36
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Scouting new sigma receptor ligands: Synthesis, pharmacological evaluation and molecular modeling of 1,3-dioxolane-based structures and derivatives. Eur J Med Chem 2016; 112:1-19. [DOI: 10.1016/j.ejmech.2016.01.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/13/2016] [Accepted: 01/30/2016] [Indexed: 11/23/2022]
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37
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Catalytic strategies of the non-heme iron dependent oxygenases and their roles in plant biology. Curr Opin Chem Biol 2016; 31:126-35. [PMID: 27015291 PMCID: PMC4879150 DOI: 10.1016/j.cbpa.2016.02.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 12/18/2022]
Abstract
Current evidence for iron-oxo reactive intermediates is reviewed. In crystallo intermediates detected in a native extradiol dioxygenase reaction. Carotenoid cleavage dioxygenases catalyse strigolactone biosynthesis. Identification of plant cysteine oxidases involved in the plant hypoxic response. Applications of enzyme manipulation to plant biology and agriculture are discussed.
Non-heme iron-dependent oxygenases catalyse the incorporation of O2 into a wide range of biological molecules and use diverse strategies to activate their substrates. Recent kinetic studies, including in crystallo, have provided experimental support for some of the intermediates used by different subclasses of this enzyme family. Plant non-heme iron-dependent oxygenases have diverse and important biological roles, including in growth signalling, stress responses and secondary metabolism. Recently identified roles include in strigolactone biosynthesis, O-demethylation in morphine biosynthesis and regulating the stability of hypoxia-responsive transcription factors. We discuss current structural and mechanistic understanding of plant non-heme iron oxygenases, and how their chemical/genetic manipulation could have agricultural benefit, for example, for improved yield, stress tolerance or herbicide development.
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38
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Jeoung JH, Nianios D, Fetzner S, Dobbek H. Quercetin 2,4-Dioxygenase Activates Dioxygen in a Side-On O2-Ni Complex. Angew Chem Int Ed Engl 2016; 55:3281-4. [PMID: 26846734 DOI: 10.1002/anie.201510741] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 02/04/2023]
Abstract
Quercetin 2,4-dioxygenase (quercetinase) from Streptomyces uses nickel as the active-site cofactor to catalyze oxidative cleavage of the flavonol quercetin. How this unusual active-site metal supports catalysis and O2 activation is under debate. We present crystal structures of Ni-quercetinase in three different states, thus providing direct insight into how quercetin and O2 are activated at the Ni(2+) ion. The Ni(2+) ion is coordinated by three histidine residues and a glutamate residue (E(76)) in all three states. Upon binding, quercetin replaces one water ligand at Ni and is stabilized by a short hydrogen bond through E(76) , the carboxylate group of which rotates by 90°. This conformational change weakens the interaction between Ni and the remaining water ligand, thereby preparing a coordination site at Ni to bind O2. O2 binds side-on to the Ni(2+) ion and is perpendicular to the C2-C3 and C3-C4 bonds of quercetin, which are cleaved in the following reaction steps.
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Affiliation(s)
- Jae-Hun Jeoung
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Dimitrios Nianios
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Susanne Fetzner
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.
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39
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Jeoung JH, Nianios D, Fetzner S, Dobbek H. Quercetin-2,4-Dioxygenase aktiviert Sauerstoff in einem “side-on” gebundenen O2
-Ni-Komplex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jae-Hun Jeoung
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Unter den Linden 6 10099 Berlin Deutschland
| | - Dimitrios Nianios
- Institut für Molekulare Mikrobiologie und Biotechnologie; Westfälische Wilhelms-Universität Münster; 48149 Münster Deutschland
| | - Susanne Fetzner
- Institut für Molekulare Mikrobiologie und Biotechnologie; Westfälische Wilhelms-Universität Münster; 48149 Münster Deutschland
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Unter den Linden 6 10099 Berlin Deutschland
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40
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Anneser MR, Haslinger S, Pöthig A, Cokoja M, D'Elia V, Högerl MP, Basset JM, Kühn FE. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe–tetracarbene superoxo complex. Dalton Trans 2016; 45:6449-55. [DOI: 10.1039/c6dt00538a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactivity of a heme-like organometallic Fe–NHC complex with O2 is studied. The formation of a superoxo Fe(iii) intermediate is observed. The reactivity of the intermediate in acetone and acetonitrile is described and the products are identified.
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Affiliation(s)
- Markus R. Anneser
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Stefan Haslinger
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Alexander Pöthig
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Mirza Cokoja
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Valerio D'Elia
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Thuwal
- Kingdom of Saudi Arabia
- Department of Materials Science and Engineering
| | - Manuel P. Högerl
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Thuwal
- Kingdom of Saudi Arabia
| | - Jean-Marie Basset
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Thuwal
- Kingdom of Saudi Arabia
| | - Fritz E. Kühn
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
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41
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Roy S, Kästner J. QM/MM-Simulationen ergeben synergetische Substrat- und Sauerstoffaktivierung in Salicylat-Dioxygenase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Subhendu Roy
- Institut für Theoretische Chemie; Universität Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Deutschland
| | - Johannes Kästner
- Institut für Theoretische Chemie; Universität Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Deutschland
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42
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Roy S, Kästner J. Synergistic Substrate and Oxygen Activation in Salicylate Dioxygenase Revealed by QM/MM Simulations. Angew Chem Int Ed Engl 2015; 55:1168-72. [DOI: 10.1002/anie.201506363] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/18/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Subhendu Roy
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
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43
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Kishima T, Matsumoto T, Nakai H, Hayami S, Ohta T, Ogo S. A High-Valent Iron(IV) Peroxo Core Derived from O2. Angew Chem Int Ed Engl 2015; 55:724-7. [PMID: 26509430 DOI: 10.1002/anie.201507022] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/28/2015] [Indexed: 11/07/2022]
Abstract
Dioxygen-tolerant [NiFe] hydrogenases catalyze not only the conversion of H2 into 2 H(+) and 2 e(-) but also the reduction of O2 to H2O. Chemists have sought to mimic such bifunctional catalysts with structurally simpler compounds to facilitate analysis and improvement. Herein, we report a new [NiFe]-based catalyst for O2 reduction via an O2 adduct. Structural investigations reveal the first example of a side-on iron(IV) peroxo complex.
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Affiliation(s)
- Takahiro Kishima
- Center for Small Molecule Energy, Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395 (Japan) ogo.seiji.872m.kyushu-u.ac.jp http://www.cstm.kyushu-u.ac.jp/ogo/
| | - Takahiro Matsumoto
- Center for Small Molecule Energy, Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395 (Japan) ogo.seiji.872m.kyushu-u.ac.jp http://www.cstm.kyushu-u.ac.jp/ogo/
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395 (Japan)
| | - Hidetaka Nakai
- Center for Small Molecule Energy, Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395 (Japan) ogo.seiji.872m.kyushu-u.ac.jp http://www.cstm.kyushu-u.ac.jp/ogo/
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395 (Japan)
| | - Shinya Hayami
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555 (Japan)
| | - Takehiro Ohta
- Institute for Materials Chemistry and Engineering, Kyushu University, Higashi-ku, Fukuoka 812-8581 (Japan)
| | - Seiji Ogo
- Center for Small Molecule Energy, Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395 (Japan) ogo.seiji.872m.kyushu-u.ac.jp http://www.cstm.kyushu-u.ac.jp/ogo/
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395 (Japan)
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44
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Kishima T, Matsumoto T, Nakai H, Hayami S, Ohta T, Ogo S. A High-Valent Iron(IV) Peroxo Core Derived from O2. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Liu S, Su T, Zhang C, Zhang WM, Zhu D, Su J, Wei T, Wang K, Huang Y, Guo L, Xu S, Zhou NY, Gu L. Crystal structure of PnpCD, a two-subunit hydroquinone 1,2-dioxygenase, reveals a novel structural class of Fe2+-dependent dioxygenases. J Biol Chem 2015; 290:24547-60. [PMID: 26304122 DOI: 10.1074/jbc.m115.673558] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 11/06/2022] Open
Abstract
Aerobic microorganisms have evolved a variety of pathways to degrade aromatic and heterocyclic compounds. However, only several classes of oxygenolytic fission reaction have been identified for the critical ring cleavage dioxygenases. Among them, the most well studied dioxygenases proceed via catecholic intermediates, followed by noncatecholic hydroxy-substituted aromatic carboxylic acids. Therefore, the recently reported hydroquinone 1,2-dioxygenases add to the diversity of ring cleavage reactions. Two-subunit hydroquinone 1,2-dioxygenase PnpCD, the key enzyme in the hydroquinone pathway of para-nitrophenol degradation, catalyzes the ring cleavage of hydroquinone to γ-hydroxymuconic semialdehyde. Here, we report three PnpCD structures, named apo-PnpCD, PnpCD-Fe(3+), and PnpCD-Cd(2+)-HBN (substrate analog hydroxyenzonitrile), respectively. Structural analysis showed that both the PnpC and the C-terminal domains of PnpD comprise a conserved cupin fold, whereas PnpC cannot form a competent metal binding pocket as can PnpD cupin. Four residues of PnpD (His-256, Asn-258, Glu-262, and His-303) were observed to coordinate the iron ion. The Asn-258 coordination is particularly interesting because this coordinating residue has never been observed in the homologous cupin structures of PnpCD. Asn-258 is proposed to play a pivotal role in binding the iron prior to the enzymatic reaction, but it might lose coordination to the iron when the reaction begins. PnpD also consists of an intriguing N-terminal domain that might have functions other than nucleic acid binding in its structural homologs. In summary, PnpCD has no apparent evolutionary relationship with other iron-dependent dioxygenases and therefore defines a new structural class. The study of PnpCD might add to the understanding of the ring cleavage of dioxygenases.
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Affiliation(s)
- Shiheng Liu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Tiantian Su
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Cong Zhang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Wen-Mao Zhang
- the Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071
| | - Deyu Zhu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Jing Su
- the College of Food Science and Engineering, Qilu University of Technology, Jinan, Shandong 250353, and
| | - Tiandi Wei
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Kang Wang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Yan Huang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Liming Guo
- the Rizhao Center for Diseases Prevention and Control, Rizhao Health Bureau, Rizhao, Shandong 276826, China
| | - Sujuan Xu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Ning-Yi Zhou
- the Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, the State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240,
| | - Lichuan Gu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100,
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Piégu B, Bire S, Arensburger P, Bigot Y. A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity. Mol Phylogenet Evol 2015; 86:90-109. [PMID: 25797922 DOI: 10.1016/j.ympev.2015.03.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 10/25/2022]
Abstract
The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).
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Affiliation(s)
- Benoît Piégu
- UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France
| | - Solenne Bire
- UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France; Institute of Biotechnology, University of Lausanne, Center for Biotechnology UNIL-EPFL, 1015 Lausanne, Switzerland
| | - Peter Arensburger
- UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France; Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, United States.
| | - Yves Bigot
- UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France.
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Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase. Proc Natl Acad Sci U S A 2014; 112:388-93. [PMID: 25548185 DOI: 10.1073/pnas.1419118112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe(3+) to activate O2 and catecholic substrates for reaction. The inability of Fe(3+) to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe(3+) species, and the anhydride-Fe(3+) intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe(2+)-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe(2+) intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.
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Microbial biosynthesis of medium-chain 1-alkenes by a nonheme iron oxidase. Proc Natl Acad Sci U S A 2014; 111:18237-42. [PMID: 25489112 DOI: 10.1073/pnas.1419701112] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aliphatic medium-chain 1-alkenes (MCAEs, ∼10 carbons) are "drop-in" compatible next-generation fuels and precursors to commodity chemicals. Mass production of MCAEs from renewable resources holds promise for mitigating dependence on fossil hydrocarbons. An MCAE, such as 1-undecene, is naturally produced by Pseudomonas as a semivolatile metabolite through an unknown biosynthetic pathway. We describe here the discovery of a single gene conserved in Pseudomonas responsible for 1-undecene biosynthesis. The encoded enzyme is able to convert medium-chain fatty acids (C10-C14) into their corresponding terminal olefins using an oxygen-activating, nonheme iron-dependent mechanism. Both biochemical and X-ray crystal structural analyses suggest an unusual mechanism of β-hydrogen abstraction during fatty acid substrate activation. Our discovery unveils previously unidentified chemistry in the nonheme Fe(II) enzyme family, provides an opportunity to explore the biology of 1-undecene in Pseudomonas, and paves the way for tailored bioconversion of renewable raw materials to MCAE-based biofuels and chemical commodities.
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Chiang CW, Kleespies ST, Stout HD, Meier KK, Li PY, Bominaar EL, Que L, Münck E, Lee WZ. Characterization of a paramagnetic mononuclear nonheme iron-superoxo complex. J Am Chem Soc 2014; 136:10846-9. [PMID: 25036460 PMCID: PMC4132977 DOI: 10.1021/ja504410s] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
O2 bubbling into a THF solution of Fe(II)(BDPP) (1) at -80 °C generates a reversible bright yellow adduct 2. Characterization by resonance Raman and Mössbauer spectroscopy provides complementary insights into the nature of 2. The former shows a resonance-enhanced vibration at 1125 cm(-1), which can be assigned to the ν(O-O) of a bound superoxide, while the latter reveals the presence of a high-spin iron(III) center that is exchange-coupled to the superoxo ligand, like the Fe(III)-O2(-) pair found for the O2 adduct of 4-nitrocatechol-bound homoprotocatechuate 2,3-dioxygenase. Lastly, 2 oxidizes dihydroanthracene to anthracene, supporting the notion that Fe(III)-O2(-) species can carry out H atom abstraction from a C-H bond to initiate the 4-electron oxidation of substrates proposed for some nonheme iron enzymes.
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Affiliation(s)
- Chien-Wei Chiang
- Department of Chemistry, National Taiwan Normal University , Taipei 11677, Taiwan (ROC)
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Affiliation(s)
- John D Lipscomb
- From the Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
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