1
|
Hu WY, Li K, Weitz A, Wen A, Kim H, Murray JC, Cheng R, Chen B, Naowarojna N, Grinstaff MW, Elliott SJ, Chen JS, Liu P. Light-Driven Oxidative Demethylation Reaction Catalyzed by a Rieske-Type Non-heme Iron Enzyme Stc2. ACS Catal 2022; 12:14559-14570. [PMID: 37168530 PMCID: PMC10168674 DOI: 10.1021/acscatal.2c04232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rieske-type non-heme iron oxygenases/oxidases catalyze a wide range of transformations. Their applications in bioremediation or biocatalysis face two key barriers: the need of expensive NAD(P)H as a reductant and a proper reductase to mediate the electron transfer from NAD(P)H to the oxygenases. To bypass the need of both the reductase and NAD(P)H, using Rieske-type oxygenase (Stc2) catalyzed oxidative demethylation as the model system, we report Stc2 photocatalysis using eosin Y/sulfite as the photosensitizer/sacrificial reagent pair. In a flow-chemistry setting to separate the photo-reduction half-reaction and oxidation half-reaction, Stc2 photo-biocatalysis outperforms the Stc2-NAD(P)H-reductase (GbcB) system. In addition, in a few other selected Rieske enzymes (NdmA, CntA, and GbcA), and a flavin-dependent enzyme (iodotyrosine deiodinase, IYD), the eosin Y/sodium sulfite photo-reduction pair could also serve as the NAD(P)H-reductase surrogate to support catalysis, which implies the potential applicability of this photo-reduction system to other redox enzymes.
Collapse
Affiliation(s)
- Wei-Yao Hu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, P. R. China
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Kelin Li
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Andrew Weitz
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Aiwen Wen
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Hyomin Kim
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Jessica C. Murray
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Baixiong Chen
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Mark W. Grinstaff
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Jie-Sheng Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, P. R. China
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| |
Collapse
|
2
|
Contribution of dicarboxylic acids to pyrene biodegradation and transcriptomic responses of Enterobacter sp. PRd5. Appl Microbiol Biotechnol 2022; 106:7949-7961. [PMID: 36227340 DOI: 10.1007/s00253-022-12217-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
Abstract
The colonization of degrading endophytic bacteria is an effective means to reduce the residues of polycyclic aromatic hydrocarbons (PAHs) in crops. Dicarboxylic acids, as the main active components in crops, can affect the physiological activities of endophytic bacteria and alter the biodegradation process of PAHs in crops. In this study, malonic acid and succinic acid were selected as the representatives to investigate the contribution of dicarboxylic acids to pyrene biodegradation by endophytic Enterobacter sp. PRd5 in vitro. The results showed that dicarboxylic acids improved the biodegradation of pyrene and altered the expression of the functional gene of strain PRd5. Malonic acid and succinic acid reduced the half-life of pyrene by 20.0% and 27.8%, respectively. The degrading enzyme activities were significantly stimulated by dicarboxylic acids. There were 386 genes up-regulated and 430 genes down-regulated in strain PRd5 with malonic acid, while 293 genes up-regulated and 340 genes down-regulated with succinic acid. Those up-regulated genes were distributed in the functional classification of signal transduction, membrane transport, energy metabolism, carbohydrate metabolism, and amino acid metabolism. Malonic acid mainly enhanced the central carbon metabolism, cell proliferation, and cell activity. Succinic acid mainly improved the expression of degrading gene. Overall, the findings of this study provide new insights into the regulation and control of PAH stress by crops. KEY POINTS: • Dicarboxylic acids improved the biodegradation of pyrene by Enterobacter sp. PRd5. • The degrading enzyme activities were stimulated by dicarboxylic acids. • There are different facilitation mechanisms between malonic acid and succinic acid.
Collapse
|
3
|
Mahto JK, Neetu N, Waghmode B, Kuatsjah E, Sharma M, Sircar D, Sharma AK, Tomar S, Eltis LD, Kumar P. Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. J Biol Chem 2021; 297:101416. [PMID: 34800435 PMCID: PMC8649396 DOI: 10.1016/j.jbc.2021.101416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Phthalate, a plasticizer, endocrine disruptor, and potential carcinogen, is degraded by a variety of bacteria. This degradation is initiated by phthalate dioxygenase (PDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of phthalate to a dihydrodiol. PDO has long served as a model for understanding ROs despite a lack of structural data. Here we purified PDOKF1 from Comamonas testosteroni KF1 and found that it had an apparent kcat/Km for phthalate of 0.58 ± 0.09 μM-1s-1, over 25-fold greater than for terephthalate. The crystal structure of the enzyme at 2.1 Å resolution revealed that it is a hexamer comprising two stacked α3 trimers, a configuration not previously observed in RO crystal structures. We show that within each trimer, the protomers adopt a head-to-tail configuration typical of ROs. The stacking of the trimers is stabilized by two extended helices, which make the catalytic domain of PDOKF1 larger than that of other characterized ROs. Complexes of PDOKF1 with phthalate and terephthalate revealed that Arg207 and Arg244, two residues on one face of the active site, position these substrates for regiospecific hydroxylation. Consistent with their roles as determinants of substrate specificity, substitution of either residue with alanine yielded variants that did not detectably turnover phthalate. Together, these results provide critical insights into a pollutant-degrading enzyme that has served as a paradigm for ROs and facilitate the engineering of this enzyme for bioremediation and biocatalytic applications.
Collapse
Affiliation(s)
- Jai Krishna Mahto
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Neetu Neetu
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Eugene Kuatsjah
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Monica Sharma
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Shailly Tomar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India.
| |
Collapse
|
4
|
Massmig M, Reijerse E, Krausze J, Laurich C, Lubitz W, Jahn D, Moser J. Carnitine metabolism in the human gut: characterization of the two-component carnitine monooxygenase CntAB from Acinetobacter baumannii. J Biol Chem 2020; 295:13065-13078. [PMID: 32694223 DOI: 10.1074/jbc.ra120.014266] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/24/2020] [Indexed: 01/29/2023] Open
Abstract
Bacterial formation of trimethylamine (TMA) from carnitine in the gut microbiome has been linked to cardiovascular disease. During this process, the two-component carnitine monooxygenase (CntAB) catalyzes the oxygen-dependent cleavage of carnitine to TMA and malic semialdehyde. Individual redox states of the reductase CntB and the catalytic component CntA were investigated based on mutagenesis and electron paramagnetic resonance (EPR) spectroscopic approaches. Protein ligands of the flavin mononucleotide (FMN) and the plant-type [2Fe-2S] cluster of CntB and also of the Rieske-type [2Fe-2S] cluster and the mononuclear [Fe] center of CntA were identified. EPR spectroscopy of variant CntA proteins suggested a hierarchical metallocenter maturation, Rieske [2Fe-2S] followed by the mononuclear [Fe] center. NADH-dependent electron transfer via the redox components of CntB and within the trimeric CntA complex for the activation of molecular oxygen was investigated. EPR experiments indicated that the two electrons from NADH were allocated to the plant-type [2Fe-2S] cluster and to FMN in the form of a flavin semiquinone radical. Single-turnover experiments of this reduced CntB species indicated the translocation of the first electron onto the [Fe] center and the second electron onto the Rieske-type [2Fe-2S] cluster of CntA to finally allow for oxygen activation as a basis for carnitine cleavage. EPR spectroscopic investigation of CntA variants indicated an unusual intermolecular electron transfer between the subunits of the CntA trimer via the "bridging" residue Glu-205. On the basis of these data, a redox catalytic cycle for carnitine monooxygenase was proposed.
Collapse
Affiliation(s)
- Marco Massmig
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Edward Reijerse
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Joern Krausze
- Institute of Plant Biology, Technical University Braunschweig, Braunschweig, Germany
| | - Christoph Laurich
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Dieter Jahn
- Braunschweig Centre of Integrated Systems Biology, Braunschweig, Germany
| | - Jürgen Moser
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany.
| |
Collapse
|
5
|
Lanfranchi E, Trajković M, Barta K, de Vries JG, Janssen DB. Exploring the Selective Demethylation of Aryl Methyl Ethers with a
Pseudomonas
Rieske Monooxygenase. Chembiochem 2018; 20:118-125. [DOI: 10.1002/cbic.201800594] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Elisa Lanfranchi
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
- Present address: School of Food and Nutritional Science SciencesUniversity College Cork College Road Cork T12 YN60 Republic of Ireland
| | - Miloš Trajković
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
| | - Katalin Barta
- Synthetic Organic ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
| | - Johannes G. de Vries
- Synthetic Organic ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
- Leibniz-Institut für Katalyse e.V. Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Dick B. Janssen
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
| |
Collapse
|
6
|
Guevara G, Heras LFDL, Perera J, Llorens JMN. Functional characterization of 3-ketosteroid 9α-hydroxylases in Rhodococcus ruber strain chol-4. J Steroid Biochem Mol Biol 2017. [PMID: 28642093 DOI: 10.1016/j.jsbmb.2017.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The 3-Ketosteroid-9α-Hydroxylase, also known as KshAB [androsta-1,4-diene-3,17-dione, NADH:oxygen oxidoreductase (9α-hydroxylating); EC 1.14.13.142)], is a key enzyme in the general scheme of the bacterial steroid catabolism in combination with a 3-ketosteroid-Δ1-dehydrogenase activity (KstD), being both responsible of the steroid nucleus (rings A/B) breakage. KshAB initiates the opening of the steroid ring by the 9α-hydroxylation of the C9 carbon of 4-ene-3-oxosteroids (e.g. AD) or 1,4-diene-3-oxosteroids (e.g. ADD), transforming them into 9α-hydroxy-4-androsten-3,17-dione (9OHAD) or 9α-hydroxy-1,4-androstadiene-3,17-dione (9OHADD), respectively. The redundancy of these enzymes in the actinobacterial genomes results in a serious difficulty for metabolic engineering this catabolic pathway to obtain intermediates of industrial interest. In this work, we have identified three homologous kshA genes and one kshB gen in different genomic regions of R. ruber strain Chol-4. We present a set of data that helps to understand their specific roles in this strain, including: i) description of the KshAB enzymes ii) construction and characterization of ΔkshB and single, double and triple ΔkshA mutants in R. ruber iii) growth studies of the above strains on different substrates and iv) genetic complementation and biotransformation assays with those strains. Our results show that KshA2 isoform is needed for the degradation of steroid substrates with short side chain, while KshA3 works on those molecules with longer side chains. KshA1 is a more versatile enzyme related to the cholic acid catabolism, although it also collaborates with KshA2 or KshA3 activities in the catabolism of steroids. Accordingly to what it is described for other Rhodococcus strains, our results also suggest that the side chain degradation is KshAB-independent.
Collapse
Affiliation(s)
- Govinda Guevara
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | | | - Julián Perera
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology I, Universidad Complutense de Madrid, 28040, Madrid, Spain.
| |
Collapse
|
7
|
Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center. PLoS One 2016; 11:e0162031. [PMID: 27656882 PMCID: PMC5033481 DOI: 10.1371/journal.pone.0162031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
Abstract
Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.
Collapse
|
8
|
Jagger BR, Koval AM, Wheeler RA. Distinguishing Protonation States of Histidine Ligands to the Oxidized Rieske Iron-Sulfur Cluster through (15) N Vibrational Frequency Shifts. Chemphyschem 2016; 17:216-20. [PMID: 26603967 DOI: 10.1002/cphc.201500838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/07/2022]
Abstract
The Rieske [2Fe-2S] cluster is a vital component of many oxidoreductases, including mitochondrial cytochrome bc1; its chloroplast equivalent, cytochrome b6f; one class of dioxygenases; and arsenite oxidase. The Rieske cluster acts as an electron shuttle and its reduction is believed to couple with protonation of one of the cluster's His ligands. In cytochromes bc1 and b6f, for example, the Rieske cluster acts as the first electron acceptor in a modified Q cycle. The protonation states of the cluster's His ligands determine its ability to accept a proton and possibly an electron through a hydrogen bond to the electron carrier, ubiquinol. Experimental determination of the protonation states of a Rieske cluster's two His ligands by NMR spectroscopy is difficult, due to the close proximity of the two paramagnetic iron atoms of the cluster. Therefore, this work reports density functional calculations and proposes that difference vibrational spectroscopy with (15) N isotopic substitution may be used to assign the protonation states of the His ligands of the oxidized Rieske [2Fe-2S] complex.
Collapse
Affiliation(s)
- Benjamin R Jagger
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA
| | - Ashlyn M Koval
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA
| | - Ralph A Wheeler
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA.
| |
Collapse
|
9
|
Rivard BS, Rogers MS, Marell DJ, Neibergall MB, Chakrabarty S, Cramer CJ, Lipscomb JD. Rate-Determining Attack on Substrate Precedes Rieske Cluster Oxidation during Cis-Dihydroxylation by Benzoate Dioxygenase. Biochemistry 2015; 54:4652-64. [PMID: 26154836 DOI: 10.1021/acs.biochem.5b00573] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rieske dearomatizing dioxygenases utilize a Rieske iron-sulfur cluster and a mononuclear Fe(II) located 15 Å across a subunit boundary to catalyze O2-dependent formation of cis-dihydrodiol products from aromatic substrates. During catalysis, O2 binds to the Fe(II) while the substrate binds nearby. Single-turnover reactions have shown that one electron from each metal center is required for catalysis. This finding suggested that the reactive intermediate is Fe(III)-(H)peroxo or HO-Fe(V)═O formed by O-O bond scission. Surprisingly, several kinetic phases were observed during the single-turnover Rieske cluster oxidation. Here, the Rieske cluster oxidation and product formation steps of a single turnover of benzoate 1,2-dioxygenase are investigated using benzoate and three fluorinated analogues. It is shown that the rate constant for product formation correlates with the reciprocal relaxation time of only the fastest kinetic phase (RRT-1) for each substrate, suggesting that the slower phases are not mechanistically relevant. RRT-1 is strongly dependent on substrate type, suggesting a role for substrate in electron transfer from the Rieske cluster to the mononuclear iron site. This insight, together with the substrate and O2 concentration dependencies of RRT-1, indicates that a reactive species is formed after substrate and O2 binding but before electron transfer from the Rieske cluster. Computational studies show that RRT-1 is correlated with the electron density at the substrate carbon closest to the Fe(II), consistent with initial electrophilic attack by an Fe(III)-superoxo intermediate. The resulting Fe(III)-peroxo-aryl radical species would then readily accept an electron from the Rieske cluster to complete the cis-dihydroxylation reaction.
Collapse
Affiliation(s)
- Brent S Rivard
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Melanie S Rogers
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel J Marell
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Matthew B Neibergall
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sarmistha Chakrabarty
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J Cramer
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D Lipscomb
- †Department of Biochemistry, Molecular Biology, and Biophysics and the Center for Metals in Biocatalysis, ‡Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
10
|
Penfield JS, Worrall LJ, Strynadka NC, Eltis LD. Substrate specificities and conformational flexibility of 3-ketosteroid 9α-hydroxylases. J Biol Chem 2014; 289:25523-36. [PMID: 25049233 DOI: 10.1074/jbc.m114.575886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >10(5) s(-1) M(-1) for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (Ki S ∼100 μM). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue "mouth loop," which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450.
Collapse
Affiliation(s)
| | - Liam J Worrall
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
11
|
3-Ketosteroid 9α-hydroxylase enzymes: Rieske non-heme monooxygenases essential for bacterial steroid degradation. Antonie van Leeuwenhoek 2014; 106:157-72. [PMID: 24846050 PMCID: PMC4064121 DOI: 10.1007/s10482-014-0188-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/25/2014] [Indexed: 12/26/2022]
Abstract
Various micro-organisms are able to use sterols/steroids as carbon- and energy sources for growth. 3-Ketosteroid 9α-hydroxylase (KSH), a two component Rieske non-heme monooxygenase comprised of the oxygenase KshA and the reductase KshB, is a key-enzyme in bacterial steroid degradation. It initiates opening of the steroid polycyclic ring structure. The enzyme has industrial relevance in the synthesis of pharmaceutical steroids. Deletion of KSH activity in sterol degrading bacteria results in blockage of steroid ring opening and is used to produce valuable C19-steroids such as 4-androstene-3,17-dione and 1,4-androstadiene-3,17-dione. Interestingly, KSH activity is essential for the pathogenicity of Mycobacterium tuberculosis. Detailed information about KSH thus is of medical relevance, and KSH inhibitory compounds may find application in combatting tuberculosis. In recent years, the 3D structure of the KshA protein of M. tuberculosis H37Rv has been elucidated and various studies report biochemical characteristics and possible physiological roles of KSH. The current knowledge is reviewed here and forms a solid basis for further studies on this highly interesting enzyme. Future work may result in the construction of KSH mutants capable of production of specific bioactive steroids. Furthermore, KSH provides an promising target for drugs against the pathogenic agent M. tuberculosis.
Collapse
|
12
|
Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
13
|
Ashikawa Y, Fujimoto Z, Usami Y, Inoue K, Noguchi H, Yamane H, Nojiri H. Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase. BMC STRUCTURAL BIOLOGY 2012; 12:15. [PMID: 22727022 PMCID: PMC3423008 DOI: 10.1186/1472-6807-12-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 06/24/2012] [Indexed: 01/11/2023]
Abstract
BACKGROUND Dihydroxylation of tandemly linked aromatic carbons in a cis-configuration, catalyzed by multicomponent oxygenase systems known as Rieske nonheme iron oxygenase systems (ROs), often constitute the initial step of aerobic degradation pathways for various aromatic compounds. Because such RO reactions inherently govern whether downstream degradation processes occur, novel oxygenation mechanisms involving oxygenase components of ROs (RO-Os) is of great interest. Despite substantial progress in structural and physicochemical analyses, no consensus exists on the chemical steps in the catalytic cycles of ROs. Thus, determining whether conformational changes at the active site of RO-O occur by substrate and/or oxygen binding is important. Carbazole 1,9a-dioxygenase (CARDO), a RO member consists of catalytic terminal oxygenase (CARDO-O), ferredoxin (CARDO-F), and ferredoxin reductase. We have succeeded in determining the crystal structures of oxidized CARDO-O, oxidized CARDO-F, and both oxidized and reduced forms of the CARDO-O: CARDO-F binary complex. RESULTS In the present study, we determined the crystal structures of the reduced carbazole (CAR)-bound, dioxygen-bound, and both CAR- and dioxygen-bound CARDO-O: CARDO-F binary complex structures at 1.95, 1.85, and 2.00 Å resolution. These structures revealed the conformational changes that occur in the catalytic cycle. Structural comparison between complex structures in each step of the catalytic mechanism provides several implications, such as the order of substrate and dioxygen bindings, the iron-dioxygen species likely being Fe(III)-(hydro)peroxo, and the creation of room for dioxygen binding and the promotion of dioxygen binding in desirable fashion by preceding substrate binding. CONCLUSIONS The RO catalytic mechanism is proposed as follows: When the Rieske cluster is reduced, substrate binding induces several conformational changes (e.g., movements of the nonheme iron and the ligand residue) that create room for oxygen binding. Dioxygen bound in a side-on fashion onto nonheme iron is activated by reduction to the peroxo state [Fe(III)-(hydro)peroxo]. This state may react directly with the bound substrate, or O-O bond cleavage may occur to generate Fe(V)-oxo-hydroxo species prior to the reaction. After producing a cis-dihydrodiol, the product is released by reducing the nonheme iron. This proposed scheme describes the catalytic cycle of ROs and provides important information for a better understanding of the mechanism.
Collapse
Affiliation(s)
- Yuji Ashikawa
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | | | | | | | | | | | | |
Collapse
|
14
|
Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation. J Mol Biol 2009; 392:498-510. [PMID: 19616011 DOI: 10.1016/j.jmb.2009.07.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 07/04/2009] [Accepted: 07/09/2009] [Indexed: 11/20/2022]
Abstract
Dicamba (3,6-dichloro-2-methoxybenzoic acid) is a widely used herbicide that is efficiently degraded by soil microbes. These microbes use a novel Rieske nonheme oxygenase, dicamba monooxygenase (DMO), to catalyze the oxidative demethylation of dicamba to 3,6-dichlorosalicylic acid (DCSA) and formaldehyde. We have determined the crystal structures of DMO in the free state, bound to its substrate dicamba, and bound to the product DCSA at 2.10-1.75 A resolution. The structures show that the DMO active site uses a combination of extensive hydrogen bonding and steric interactions to correctly orient chlorinated, ortho-substituted benzoic-acid-like substrates for catalysis. Unlike other Rieske aromatic oxygenases, DMO oxygenates the exocyclic methyl group, rather than the aromatic ring, of its substrate. This first crystal structure of a Rieske demethylase shows that the Rieske oxygenase structural scaffold can be co-opted to perform varied types of reactions on xenobiotic substrates.
Collapse
|
15
|
Distal end of 105-125 loop--a putative reductase binding domain of phthalate dioxygenase. Arch Biochem Biophys 2009; 487:10-8. [PMID: 19464996 DOI: 10.1016/j.abb.2009.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/14/2009] [Accepted: 05/17/2009] [Indexed: 11/21/2022]
Abstract
The phthalate dioxygenase system consists of the dioxygenase, PDO, which contains a Rieske [2Fe-2S] center and a Fe(II)-mononuclear center, and the reductase, PDR. Involvement of the distal end of the 105-125 loop of PDO in its interaction with PDR was tested by substituting charged residues in the loop with alanines and by replacing the conserved tryptophan-94. Compared to wild-type PDO, all variants had lower catalytic activity and the Rieske centers were reduced more slowly by reduced PDR. The rates of oxidation of the Rieske centers by oxygen, which represent electron transfer between the Rieske and mononuclear centers, were essentially unaffected. These results suggest that positively charged residues of the distal end of the 105-125 loop are collectively involved in PDR binding with the PDO. Contrary to expectations, Trp94 variants were not directly involved in electron transfer between PDR and PDO. The tryptophan appears to have mainly a structural role, apparently preserving the hydrophilic environment of the Rieske center.
Collapse
|
16
|
Capyk JK, D'Angelo I, Strynadka NC, Eltis LD. Characterization of 3-ketosteroid 9{alpha}-hydroxylase, a Rieske oxygenase in the cholesterol degradation pathway of Mycobacterium tuberculosis. J Biol Chem 2009; 284:9937-46. [PMID: 19234303 DOI: 10.1074/jbc.m900719200] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
KshAB (3-Ketosteroid 9alpha-hydroxylase) is a two-component Rieske oxygenase (RO) in the cholesterol catabolic pathway of Mycobacterium tuberculosis. Although the enzyme has been implicated in pathogenesis, it has largely been characterized by bioinformatics and molecular genetics. Purified KshB, the reductase component, was a monomeric protein containing a plant-type [2Fe-2S] cluster and FAD. KshA, the oxygenase, was a homotrimer containing a Rieske [2Fe-2S] cluster and mononuclear ferrous iron. Of two potential substrates, reconstituted KshAB had twice the specificity for 1,4-androstadiene-3,17-dione as for 4-androstene-3,17-dione. The transformation of both substrates was well coupled to the consumption of O(2). Nevertheless, the reactivity of KshAB with O(2) was low in the presence of 1,4-androstadiene-3,17-dione, with a k(cat)/K(m)(O(2)) of 2450 +/- 80 m(-1) s(-1). The crystallographic structure of KshA, determined to 2.3A(,) revealed an overall fold and a head-to-tail subunit arrangement typical of ROs. The central fold of the catalytic domain lacks all insertions found in characterized ROs, consistent with a minimal and perhaps archetypical RO catalytic domain. The structure of KshA is further distinguished by a C-terminal helix, which stabilizes subunit interactions in the functional trimer. Finally, the substrate-binding pocket extends farther into KshA than in other ROs, consistent with the large steroid substrate, and the funnel accessing the active site is differently orientated. This study provides a solid basis for further studies of a key steroid-transforming enzyme of biotechnological and medical importance.
Collapse
Affiliation(s)
- Jenna K Capyk
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver V6 1Z3, Canada
| | | | | | | |
Collapse
|
17
|
Léger C, Bertrand P. Direct Electrochemistry of Redox Enzymes as a Tool for Mechanistic Studies. Chem Rev 2008; 108:2379-438. [DOI: 10.1021/cr0680742] [Citation(s) in RCA: 594] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
Ohta T, Chakrabarty S, Lipscomb JD, Solomon EI. Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases. J Am Chem Soc 2008; 130:1601-10. [PMID: 18189388 DOI: 10.1021/ja074769o] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Near-IR MCD and variable temperature, variable field (VTVH) MCD have been applied to naphthalene 1,2-dioxygenase (NDO) to describe the coordination geometry and electronic structure of the mononuclear nonheme ferrous catalytic site in the resting and substrate-bound forms with the Rieske 2Fe2S cluster oxidized and reduced. The structural results are correlated with the crystallographic studies of NDO and other related Rieske nonheme iron oxygenases to develop molecular level insights into the structure/function correlation for this class of enzymes. The MCD data for resting NDO with the Rieske center oxidized indicate the presence of a six-coordinate high-spin ferrous site with a weak axial ligand which becomes more tightly coordinated when the Rieske center is reduced. Binding of naphthalene to resting NDO (Rieske oxidized and reduced) converts the six-coordinate sites into five-coordinate (5c) sites with elimination of a water ligand. In the Rieske oxidized form the 5c sites are square pyramidal but transform to a 1:2 mixture of trigonal bipyramial/square pyramidal sites when the Rieske center is reduced. Thus the geometric and electronic structure of the catalytic site in the presence of substrate can be significantly affected by the redox state of the Rieske center. The catalytic ferrous site is primed for the O2 reaction when substrate is bound in the active site in the presence of the reduced Rieske site. These structural changes ensure that two electrons and the substrate are present before the binding and activation of O2, which avoids the uncontrolled formation and release of reactive oxygen species.
Collapse
Affiliation(s)
- Takehiro Ohta
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | |
Collapse
|
19
|
Bruijnincx PCA, van Koten G, Klein Gebbink RJM. Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies. Chem Soc Rev 2008; 37:2716-44. [DOI: 10.1039/b707179p] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
20
|
Tarasev M, Kaddis CS, Yin S, Loo JA, Burgner J, Ballou DP. Similar enzymes, different structures: phthalate dioxygenase is an alpha3alpha3 stacked hexamer, not an alpha3beta3 trimer like "normal" Rieske oxygenases. Arch Biochem Biophys 2007; 466:31-9. [PMID: 17764654 PMCID: PMC2084370 DOI: 10.1016/j.abb.2007.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 07/05/2007] [Accepted: 07/06/2007] [Indexed: 11/24/2022]
Abstract
Phthalate dioxygenase (PDO) is a member of a class of bacterial oxygenases that contain both Rieske [2Fe-2S] and Fe(II) mononuclear centers. Recent crystal structures of several Rieske dioxygenases showed that they exist as alpha(3)beta(3) multimers with subunits arranged head-to-tail in alpha and beta stacked planar rings. The structure of PDO, which consists of only alpha-subunits, remains to be solved. Although similar to other Rieske dioxygenases in many aspects, PDO was shown to differ in the mechanism of catalysis. Gel filtration and analytical centrifugation experiments, supplemented with mass spectrometric analysis (both ESI-MS and ESI-GEMMA), in this work showed a hexameric arrangement of subunits in the PDO multimer. Our proposed model for the subunit arrangement in PDO postulates two alpha(3) planar rings one on top the other, similar to the alpha(3)beta(3) arrangement in other Rieske dioxygenases. Unlike other Rieske dioxygenases, this arrangement brings two Rieske and two mononuclear centers, all on separate subunits, into proximity, allowing their cooperation for catalysis. Potential reasons necessitating this unusual structural arrangement are discussed.
Collapse
Affiliation(s)
- Michael Tarasev
- Department of Biological Chemistry, University of Michigan, 1301 Catherine Street, Ann Arbor, MI 48109-0606, USA
| | | | | | | | | | | |
Collapse
|