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Babicz JT, Rogers MS, DeWeese DE, Sutherlin KD, Banerjee R, Böttger LH, Yoda Y, Nagasawa N, Saito M, Kitao S, Kurokuzu M, Kobayashi Y, Tamasaku K, Seto M, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage. J Am Chem Soc 2023; 145:15230-15250. [PMID: 37414058 PMCID: PMC10804917 DOI: 10.1021/jacs.3c02242] [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] [Indexed: 07/08/2023]
Abstract
The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.
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Affiliation(s)
- Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Nobumoto Nagasawa
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo 679-5148, Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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The Conformation of the N-Terminal Tails of Deinococcus grandis Dps Is Modulated by the Ionic Strength. Int J Mol Sci 2022; 23:ijms23094871. [PMID: 35563263 PMCID: PMC9103930 DOI: 10.3390/ijms23094871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
DNA-binding proteins from starved cells (Dps) are homododecameric nanocages, with N- and C-terminal tail extensions of variable length and amino acid composition. They accumulate iron in the form of a ferrihydrite mineral core and are capable of binding to and compacting DNA, forming low- and high-order condensates. This dual activity is designed to protect DNA from oxidative stress, resulting from Fenton chemistry or radiation exposure. In most Dps proteins, the DNA-binding properties stem from the N-terminal tail extensions. We explored the structural characteristics of a Dps from Deinococcus grandis that exhibits an atypically long N-terminal tail composed of 52 residues and probed the impact of the ionic strength on protein conformation using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism and small-angle X-ray scattering. A novel high-spin ferrous iron-binding site was identified in the N-terminal tails, using Mössbauer spectroscopy. Our data reveals that the N-terminal tails are structurally dynamic and alter between compact and extended conformations, depending on the ionic strength of the buffer. This prompts the search for other physiologically relevant modulators of tail conformation and hints that the DNA-binding properties of Dps proteins may be affected by external factors.
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Shapterhasmi T, Palani N, Velusamy M, Bhuvanesh NS, Sundaravel K, Easwaramoorthi S. Iron(III) Complexes of Pyrrolidine and Piperidine Appended Tridentate 3N Donor Ligands as Models for Catechol Dioxygenase Enzymes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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4
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Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW, Rahman S. Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country. Sci Rep 2021; 11:2618. [PMID: 33514807 PMCID: PMC7846579 DOI: 10.1038/s41598-021-82311-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/19/2021] [Indexed: 02/08/2023] Open
Abstract
No studies have investigated the influence of ethnicity in a multi-ethnic middle-income country with a long-standing history of co-habitation. Stool samples from 214 Malaysian community members (46 Malay, 65 Chinese, 49 Indian, and 54 Jakun) were collected. The gut microbiota of the participants was investigated using 16S amplicon sequencing. Ethnicity exhibited the largest effect size across participants (PERMANOVA Pseudo-F = 4.24, R2 = 0.06, p = 0.001). Notably, the influence of ethnicity on the gut microbiota was retained even after controlling for all demographic, dietary factors and other covariates which were significantly associated with the gut microbiome (PERMANOVA Pseudo-F = 1.67, R2 = 0.02, p = 0.002). Our result suggested that lifestyle, dietary, and uncharacterized differences collectively drive the gut microbiota variation across ethnicity, making ethnicity a reliable proxy for both identified and unidentified lifestyle and dietary variation across ethnic groups from the same community.
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Affiliation(s)
- Jacky Dwiyanto
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - M H Hussain
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - D Reidpath
- Health System and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.,South East Asia Community Observatory, Segamat, Malaysia
| | - K S Ong
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - A Qasim
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Genomics Facility, Monash University Malaysia, Bandar Sunway, Malaysia
| | - S W H Lee
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - S M Lee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - S C Foo
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - C W Chong
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, Malaysia.
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5
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Todorova Y, Yotinov I, Topalova Y, Benova E, Marinova P, Tsonev I, Bogdanov T. Evaluation of the effect of cold atmospheric plasma on oxygenases' activities for application in water treatment technologies. ENVIRONMENTAL TECHNOLOGY 2019; 40:3783-3792. [PMID: 29923777 DOI: 10.1080/09593330.2018.1491631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Plasma-based technologies take an increasing place in the new conceptions of wastewater management as a promising tool for the treatment of persistent organic pollutants with low biodegradability. Plasma major advantage is the synergy of diverse active components with high oxidative action and additional benefits as disinfection of treated water. But the bactericidal effect of plasma can influence the treatment effectiveness when this technology is used in combination with biological methods for the removal of pollutants. The aim of this paper is to study the effect of non-thermal atmospheric plasma torch on key enzymes from phenol biodegradation pathways in Pseudomonas aureofaciens (chlororaphis) AP-9. The strain was isolated from contaminated soils and had a high potential for biodegradation of aromatic compounds. The used plasma source is surface-wave-sustained discharge operating at 2.45 GHz in argon produced by an electromagnetic wave launcher surfatron type. The enzyme activities of phenol 2-monooxygenase (P2MO), catechol 1,2-dioxygenase (C12DO), catechol 2,3-dioxygenase (C23DO), protocatechuate 3,4-dioxygenase (P34DO) and succinate dehydrogenase (SDH) were measured in control and after plasma treatment of 10, 30 and 60 s. At short-time treatment, the activities of intradiol dioxygenases increased with 26% and 59% for C12DO and P34DO, respectively. Other oxygenases and SDH were inhibited with 35% even at 10 s treatment. Longer treatment times had a clear negative effect but SDH kept the higher activity at 60 s treatment compared to the oxygenases. Our data suggest that plasma-based technologies are a useful approach for post-treatment of aryl-containing wastewater in order to increase the effectiveness of biological removal.
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Affiliation(s)
- Yovana Todorova
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Ivaylo Yotinov
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Yana Topalova
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Evgenia Benova
- DLTIS, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Plamena Marinova
- Faculty of Physics, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Ivan Tsonev
- Faculty of Physics, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Todor Bogdanov
- Faculty of Medicine, Medical University Sofia, Sofia, Bulgaria
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6
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A monomeric manganese(II) catecholato complex: Synthesis, crystal structure, and reactivity toward molecular oxygen. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Sciortino G, Garribba E, Maréchal JD. Validation and Applications of Protein-Ligand Docking Approaches Improved for Metalloligands with Multiple Vacant Sites. Inorg Chem 2018; 58:294-306. [PMID: 30475597 DOI: 10.1021/acs.inorgchem.8b02374] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Decoding the interaction between coordination compounds and proteins is of fundamental importance in biology, pharmacy, and medicine. In this context, protein- ligand docking represents a particularly interesting asset to predict how small compounds could interact with biomolecules, but to date, very little information is available to adapt these methodologies to metal-containing ligands. Here, we assessed the predictive capability of a metal-compatible parameter set for the docking program GOLD for metallo ligands with multiple vacant sites and different geometries. The study first presents a benchmark of 25 well-characterized X-ray metallo ligand-protein adducts. In 100% of the cases, the docking solutions are superimposable to the X-ray determination, and in 92% the value of the root-mean-square deviation between the experimental and calculated structures is lower than 1.5 Å. After the validation step, we applied these methods to five case studies for the prediction of the binding of pharmacological active metal species to proteins: (i) the anticancer copper(II) complex [CuII(Br)(2-hydroxy-1-naphthaldehyde benzoyl hydrazine)(indazole)] to human serum albumin (HSA); (ii) one of the active species of antidiabetic and antitumor vanadium compounds, VIVO2+ ion, to carboxypeptidase; (iii) the antiarthritic species [AuI(PEt3)]+ to HSA; (iv) the antitumor oxaliplatin to ubiquitin; (v) the antitumor ruthenium(II) compound RAPTA-PentaOH to cathepsin B. The calculations suggested that the binding modes are in good agreement with the partial information retrieved from spectroscopic and spectrometric analysis and allowed us, in certain cases, to propose additional hypotheses. This method is an important update in protein-metallo ligand docking, which could have a wide field of application, from biology and inorganic biochemistry to medicinal chemistry and pharmacology.
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Affiliation(s)
- Giuseppe Sciortino
- Departament de Química , Universitat Autònoma de Barcelona , Cerdanyola del Vallés , Barcelona 08193 , Spain.,Dipartimento di Chimica e Farmacia , Università di Sassari , Via Vienna 2 , Sassari I-07100 , Italy
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia , Università di Sassari , Via Vienna 2 , Sassari I-07100 , Italy
| | - Jean-Didier Maréchal
- Departament de Química , Universitat Autònoma de Barcelona , Cerdanyola del Vallés , Barcelona 08193 , Spain
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8
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Garai M, Dey D, Yadav HR, Choudhury AR, Maji M, Biswas B. Catalytic Fate of Two Copper Complexes towards Phenoxazinone Synthase and Catechol Dioxygenase Activity. ChemistrySelect 2017. [DOI: 10.1002/slct.201702113] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mamoni Garai
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
| | - Dhananjay Dey
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
| | - Hare Ram Yadav
- Department of Chemical Sciences; Indian Institute of Science Education and Research, S.A.S. Nagar, Sector 81, Manauli PO; Mohali 140 306 India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences; Indian Institute of Science Education and Research, S.A.S. Nagar, Sector 81, Manauli PO; Mohali 140 306 India
| | - Milan Maji
- Department of Chemistry; National Institute of Technology; Durgapur 713209, West Bengal India
| | - Bhaskar Biswas
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
- Present Address: Department of Chemistry; Surendranath College; 24/2 M.G. Road, Kolkata 700009, West Bengal India
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9
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Catalytic aspects of a nickel(II)–bipyridine complex towards phosphatase and catechol dioxygenase activity. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.03.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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Long Y, Yang S, Xie Z, Cheng L. Cloning, expression, and characterization of catechol 1,2-dioxygenase from a phenol-degrading Candida tropicalis JH8 strain. Prep Biochem Biotechnol 2016; 46:673-8. [DOI: 10.1080/10826068.2015.1135449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yan Long
- College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), State Key Laboratory of Virology, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan University, Wuhan, China
| | - Sheng Yang
- College of Life Sciences, Hubei University, Wuhan, China
| | - Zhixiong Xie
- College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), State Key Laboratory of Virology, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan University, Wuhan, China
| | - Li Cheng
- College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), State Key Laboratory of Virology, Wuhan University, Wuhan, China
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11
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De A, Garai M, Yadav HR, Choudhury AR, Biswas B. Catalytic promiscuity of an iron(II)-phenanthroline complex. Appl Organomet Chem 2016. [DOI: 10.1002/aoc.3551] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Abhranil De
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
| | - Mamoni Garai
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
| | - Hare Ram Yadav
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; Sector 81, S. A. S. Nagar, Manauli PO Mohali 140306 India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; Sector 81, S. A. S. Nagar, Manauli PO Mohali 140306 India
| | - Bhaskar Biswas
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
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12
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Yamanashi T, Kim SY, Hara H, Funa N. In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1. Biosci Biotechnol Biochem 2015; 79:830-5. [PMID: 25558786 DOI: 10.1080/09168451.2014.993915] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The β-ketoadipate pathway is a major pathway involved in the catabolism of the aromatic compounds in microbes. The recent progress in genome sequencing has led to a rapid accumulation of genes from the β-ketoadipate pathway in the available genetic database, yet the functions of these genes remain uncharacterized. In this study, the protocatechuate branch of the β-ketoadipate pathway of Rhodococcus jostii was reconstituted in vitro. Analysis of the reaction products of PcaHG, PcaB, and PcaL was achieved by high-performance liquid chromatography. These reaction products, β-ketoadipate enol-lactone, 3-carboxy-cis,cis-muconate, γ-carboxymuconolactone, muconolactone, and β-ketoadipate, were further characterized using LC-MS and nuclear magnetic resonance. In addition, the in vitro reaction of PcaL, a bidomain protein consisting of γ-carboxy-muconolactone decarboxylase and β-ketoadipate enol-lactone hydrolase activities, was demonstrated for the first time. This work provides a basis for analyzing the catalytic properties of enzymes involved in the growing number of β-ketoadipate pathways deposited in the genetic database.
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Affiliation(s)
- Tomoya Yamanashi
- a Graduate Division of Nutritional and Environmental Sciences , University of Shizuoka , Shizuoka , Japan
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14
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Balamurugan M, Vadivelu P, Palaniandavar M. Iron(iii) complexes of tripodal tetradentate 4N ligands as functional models for catechol dioxygenases: the electronic vs. steric effect on extradiol cleavage. Dalton Trans 2014; 43:14653-68. [DOI: 10.1039/c3dt52145a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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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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Sankaralingam M, Saravanan N, Anitha N, Suresh E, Palaniandavar M. Biomimetic iron(iii) complexes of facially and meridionally coordinating tridentate 3N ligands: tuning of regioselective extradiol dioxygenase activity in organized assemblies. Dalton Trans 2014; 43:6828-41. [DOI: 10.1039/c3dt52350k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Guzik U, Hupert-Kocurek K, Sitnik M, Wojcieszyńska D. High activity catechol 1,2-dioxygenase from Stenotrophomonas maltophilia strain KB2 as a useful tool in cis,cis-muconic acid production. Antonie van Leeuwenhoek 2013; 103:1297-307. [PMID: 23536173 PMCID: PMC3656225 DOI: 10.1007/s10482-013-9910-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/22/2013] [Indexed: 10/31/2022]
Abstract
This is the first report of a catechol 1,2-dioxygenase from Stenotrophomonas maltophilia strain KB2 with high activity against catechol and its methyl derivatives. This enzyme was maximally active at pH 8.0 and 40 °C and the half-life of the enzyme at this temperature was 3 h. Kinetic studies showed that the value of K m and V max was 12.8 μM and 1,218.8 U/mg of protein, respectively. During our studies on kinetic properties of the catechol 1,2-dioxygenase we observed substrate inhibition at >80 μM. The nucleotide sequence of the gene encoding the S. maltophilia strain KB2 catechol 1,2-dioxygenase has high identity with other catA genes from members of the genus Pseudomonas. The deduced 314-residue sequence of the enzyme corresponds to a protein of molecular mass 34.5 kDa. This enzyme was inhibited by competitive inhibitors (phenol derivatives) only by ca. 30 %. High tolerance against condition changes is desirable in industrial processes. Our data suggest that this enzyme could be of use as a tool in production of cis,cis-muconic acid and its derivatives.
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Affiliation(s)
- Urszula Guzik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland.
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Abstract
Ring-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. Many pathways converge to catecholic intermediates, which are subject to ortho or meta cleavage by intradiol or extradiol dioxygenases, respectively. However, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. The ring-cleaving dioxygenases active toward these compounds belong to the cupin superfamily, which is characterized by a six-stranded β-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. Most cupin-type ring cleavage dioxygenases use an Fe(II) center for catalysis, and the proposed mechanism is very similar to that of the canonical (type I) extradiol dioxygenases. The metal ion is presumed to act as an electron conduit for single electron transfer from the metal-bound substrate anion to O(2), resulting in activation of both substrates to radical species. The family of cupin-type dioxygenases also involves quercetinase (flavonol 2,4-dioxygenase), which opens up two C-C bonds of the heterocyclic ring of quercetin, a wide-spread plant flavonol. Remarkably, bacterial quercetinases are capable of using different divalent metal ions for catalysis, suggesting that the redox properties of the metal are relatively unimportant for the catalytic reaction. The major role of the active-site metal ion could be to correctly position the substrate and to stabilize transition states and intermediates rather than to mediate electron transfer. The tentative hypothesis that quercetinase catalysis involves direct electron transfer from metal-bound flavonolate to O(2) is supported by model chemistry.
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Visvaganesan K, Ramachitra S, Palaniandavar M. Functional models for enzyme–substrate adducts of catechol dioxygenase enzymes: The Lewis basicity of facially coordinating tridentate phenolate ligands tunes the rate of dioxygenation and product selectivity. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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Comba P, Wadepohl H, Wunderlich S. Oxidation versus Dioxygenation of Catechol: The Iron-Bispidine System. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100802] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Aslam AM, Rajagopal S, Vairamani M, Ravikumar M. Iron(III)–salen–H2O2 as a peroxidase model: electron transfer reactions with anilines. TRANSIT METAL CHEM 2011. [DOI: 10.1007/s11243-011-9529-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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PALANIANDAVAR MALLAYAN, VISVAGANESAN KUSALENDIRAN. Mononuclear non-heme iron(III) complexes of linear and tripodal tridentate ligands as functional models for catechol dioxygenases: Effect of N-alkyl substitution on regioselectivity and reaction rate. J CHEM SCI 2011. [DOI: 10.1007/s12039-011-0110-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wójcik A, Borowski T, Broclawik E. The mechanism of the reaction of intradiol dioxygenase with hydroperoxy probe. Catal Today 2011. [DOI: 10.1016/j.cattod.2010.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nakatani N, Hitomi Y, Sakaki S. Multistate CASPT2 Study of Native Iron(III)-Dependent Catechol Dioxygenase and Its Functional Models: Electronic Structure and Ligand-to-Metal Charge-Transfer Excitation. J Phys Chem B 2011; 115:4781-9. [DOI: 10.1021/jp110045f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Naoki Nakatani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yutaka Hitomi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Shigeyoshi Sakaki
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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25
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Safaei E, Sheykhi H, Wojtczak A, Jagličić Z, Kozakiewicz A. Synthesis and characterization of an iron(III) complex of glycine derivative of bis(phenol)amine ligand in relevance to catechol dioxygenase active site. Polyhedron 2011. [DOI: 10.1016/j.poly.2011.01.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Anitha N, Palaniandavar M. Mononuclear iron(iii) complexes of 3N ligands in organized assemblies: spectral and redox properties and attainment of regioselective extradiol dioxygenase activity. Dalton Trans 2011; 40:1888-901. [DOI: 10.1039/c0dt01012j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Sundaravel K, Sankaralingam M, Suresh E, Palaniandavar M. Biomimetic iron(iii) complexes of N3O and N3O2 donor ligands: protonation of coordinated ethanolate donor enhances dioxygenase activity. Dalton Trans 2011; 40:8444-58. [PMID: 21785763 DOI: 10.1039/c1dt10495k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Karuppasamy Sundaravel
- Centre for Bioinorganic Chemistry, School of Chemistry, Bharathidasan University, Tiruchirappalli, 620 024, India
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28
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Sundaravel K, Suresh E, Saminathan K, Palaniandavar M. Iron(III) complexes of N2O and N3O donor ligands as functional models for catechol dioxygenase enzymes: ether oxygen coordination tunes the regioselectivity and reactivity. Dalton Trans 2011; 40:8092-107. [DOI: 10.1039/c0dt01598a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Karuppasamy Sundaravel
- Centre for Bioinorganic Chemistry, School of Chemistry, Bharathidasan University, Tiruchirappalli, 620 024, Tamilnadu, India
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29
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Sundaravel K, Suresh E, Palaniandavar M. Iron(III) complexes of tridentate N3 ligands as models for catechol dioxygenases: Stereoelectronic effects of pyrazole coordination. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kendall AJ, Zakharov LN, Gilbertson JD. Synthesis and Stabilization of a Monomeric Iron(II) Hydroxo Complex via Intramolecular Hydrogen Bonding in the Secondary Coordination Sphere. Inorg Chem 2010; 49:8656-8. [PMID: 20799715 DOI: 10.1021/ic101408e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander J. Kendall
- Department of Chemistry, Western Washington University, Bellingham, Washington 98225
| | - Lev N. Zakharov
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403
| | - John D. Gilbertson
- Department of Chemistry, Western Washington University, Bellingham, Washington 98225
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31
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Melo FA, Araújo AP, Costa-Filho AJ. Role of cis–cis muconic acid in the catalysis of Pseudomonas putida chlorocatechol 1,2-dioxygenase. Int J Biol Macromol 2010; 47:233-7. [DOI: 10.1016/j.ijbiomac.2010.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/22/2010] [Accepted: 04/23/2010] [Indexed: 11/15/2022]
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32
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Mayilmurugan R, Sankaralingam M, Suresh E, Palaniandavar M. Novel square pyramidal iron(iii) complexes of linear tetradentate bis(phenolate) ligands as structural and reactive models for intradiol-cleaving 3,4-PCD enzymes: Quinone formation vs. intradiol cleavage. Dalton Trans 2010; 39:9611-25. [DOI: 10.1039/c0dt00171f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Dhanalakshmi T, Suresh E, Palaniandavar M. Synthesis, structure, spectra and reactivity of iron(III) complexes of imidazole and pyrazole containing ligands as functional models for catechol dioxygenases. Dalton Trans 2009:8317-28. [PMID: 19789784 DOI: 10.1039/b903602d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of new 1 : 1 iron(iii) complexes of the type [Fe()Cl(3)], where is a tridentate 3N donor ligand, has been isolated and studied as functional models for catechol dioxygenases. The ligands (1-methyl-1H-imidazol-2-ylmethyl)pyrid-2-ylmethyl-amine (), N,N-dimethyl-N'-(1-methyl-1H-imidazol-2-ylmethyl)ethane-1,2-diamine () and N-(1-methyl-1H-imidazol-2-ylmethyl)-N'-phenylethane-1,2-diamine () are linear while the ligands tris(1-pyrazolyl)methane (), tris(3,5-dimethyl-1-pyrazolyl)methane () and tris(3-iso-propylpyrazolyl)methane () are tripodal ones. All the complexes have been characterized by spectral and electrochemical methods. The X-ray crystal structure of the dinuclear catecholate adduct [Fe()(TCC)](2)O, where TCC(2-) is a tetrachlorocatecholate dianion, has been successfully determined. In this complex both the iron(iii) atoms are bridged by a mu-oxo group and each iron(iii) center possesses a distorted octahedral coordination geometry in which the ligand is facially coordinated and the remaining coordination sites are occupied by the TCC(2-) dianion. Spectral studies suggest that addition of a base like Et(3)N induces the mononuclear complex species [Fe()(TCC)Cl] to dimerize forming a mu-oxo-bridged complex. The spectral and electrochemical properties of the catecholate adducts of the complexes generated in situ reveal that a systematic variation in the ligand donor atom type significantly influences the Lewis acidity of the iron(iii) center and hence the interaction of the complexes with simple and substituted catechols. The 3,5-di-tert-butylcatecholate (DBC(2-)) adducts of the type [Fe()(DBC)Cl], where is a linear tridentate ligand (), undergo mainly oxidative intradiol cleavage of the catechol in the presence of dioxygen. Also, the extradiol-to-intradiol product selectivity (E : I) is enhanced upon removal of the coordinated chloride ion in these adducts to obtain [Fe()(DBC)(Sol)](+) and upon incorporating coordinated N-methylimidazolyl nitrogen in them. In contrast to the iron(iii) complexes of imidazole-based ligands, those of the tripodal pyrazole-based ligands yield major amounts of the oxidized product benzoquinone and small amounts of both intra- and extradiol products. One of the pyrazole arms coordinated in the equatorial plane of these sterically constrained complexes is substituted by a solvent molecule upon adduct formation with DBC(2-), which encourages molecular oxygen to attack this site leading to benzoquinone formation. The DBSQ/DBC(2-) redox potentials of both the imidazole- and pyrazole-based complexes fall in the narrow range of -0.186 to -0.214 V supporting this proposal.
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Mayilmurugan R, Visvaganesan K, Suresh E, Palaniandavar M. Iron(III) Complexes of Tripodal Monophenolate Ligands as Models for Non-Heme Catechol Dioxygenase Enzymes: Correlation of Dioxygenase Activity with Ligand Stereoelectronic Properties. Inorg Chem 2009; 48:8771-83. [DOI: 10.1021/ic900969n] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Eringathodi Suresh
- Analytical Science Discipline, Central Salt and Marine Chemicals Research Institute, Bhavnagar − 364 002, India
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35
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Nakatani N, Nakao Y, Sato H, Sakaki S. Theoretical study of dioxygen binding process in iron(III) catechol dioxygenase: "oxygen activation" vs "substrate activation". J Phys Chem B 2009; 113:4826-36. [PMID: 19284795 DOI: 10.1021/jp806507k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dioxygen binding process of nonheme iron(III) center in intradiol catechol dioxygenase was investigated with CASSCF/CASPT2 method to incorporate multiconfigurational character participating in Fe-O(2) interaction. In this process, two alternative mechanisms were proposed: one is called "oxygen activation" and the other is called "substrate activation". Our CASSCF/CASPT2-calculated results support the oxygen activation. Potential energy curves and electronic structure evaluated with SA(state-averaged)-CASSCF/CASPT2 method indicate that the charge transfer directly occurs from the catecholate moiety to the dioxygen moiety in the O(2) binding process, to produce eta(1)-end-on type iron(III)-superoxo complex. This is the key step of the dioxygen activation. Interestingly, the iron center always keeps high spin d(5) character during the O(2) binding process, indicating the iron(III) center does not receive charge transfer from the catecholate moiety. However, this does not mean that the iron(III) center is not necessary to the dioxygen activation. The important role which the iron(III) center plays in catechol dioxygenase is to adjust the energy level of O(2) to induce the charge transfer from the catecholate moiety to the dioxygen moiety. Besides the eta(1)-end-on iron(III)-superoxo complex, eta(2)-side-on type iron(III)-superoxo complex is also optimized. This species is more stable than the eta(1)-end-on type iron(III)-superoxo complex, suggesting that this is considered as a stable isomer in the early stage of the catalytic cycle.
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Affiliation(s)
- Naoki Nakatani
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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36
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Boudalis AK, Clemente-Juan JM, Dahan F, Psycharis V, Raptopoulou CP, Donnadieu B, Sanakis Y, Tuchagues JP. Reversible Core-Interconversion of an Iron(III) Dihydroxo Bridged Complex. Inorg Chem 2008; 47:11314-23. [DOI: 10.1021/ic800716r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Athanassios K. Boudalis
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
| | - Juan Modesto Clemente-Juan
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
| | - Françoise Dahan
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
| | - Vassilis Psycharis
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
| | - Catherine P. Raptopoulou
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
| | - Bruno Donnadieu
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
| | - Yiannis Sanakis
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
| | - Jean-Pierre Tuchagues
- Institute of Materials Science, NCSR “Demokritos”, 153 10 Aghia Paraskevi Attikis, Greece, Laboratoire de Chimie de Coordination du CNRS, UPR 8241, 205, route de Narbonne, 31077 Toulouse Cedex 04, France, Instituto de Ciencia Molecular, Universidad de Valencia, c/ Doctor Moliner, 50, 46100 Burjassot, Spain, and Department of Chemistry, University of California at Riverside, Riverside, California 92521
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Abstract
Ring-cleaving dioxygenases catalyze the oxygenolytic fission of catecholic compounds, a critical step in the aerobic degradation of aromatic compounds by bacteria. Two classes of these enzymes have been identified, based on the mode of ring cleavage: intradiol dioxygenases utilize non-heme Fe(III) to cleave the aromatic nucleus ortho to the hydroxyl substituents; and extradiol dioxygenases utilize non-heme Fe(II) or other divalent metal ions to cleave the aromatic nucleus meta to the hydroxyl substituents. Recent genomic, structural, spectroscopic, and kinetic studies have increased our understanding of the distribution, evolution, and mechanisms of these enzymes. Overall, extradiol dioxygenases appear to be more versatile than their intradiol counterparts. Thus, the former cleave a wider variety of substrates, have evolved on a larger number of structural scaffolds, and occur in a wider variety of pathways, including biosynthetic pathways and pathways that degrade non-aromatic compounds. The catalytic mechanisms of the two enzymes proceed via similar iron-alkylperoxo intermediates. The ability of extradiol enzymes to act on a variety of non-catecholic compounds is consistent with proposed differences in the breakdown of this iron-alkylperoxo intermediate in the two enzymes, involving alkenyl migration in extradiol enzymes and acyl migration in intradiol enzymes. Nevertheless, despite recent advances in our understanding of these fascinating enzymes, the major determinant of the mode of ring cleavage remains unknown.
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Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Mayilmurugan R, Stoeckli-Evans H, Palaniandavar M. Novel Iron(III) Complexes of Sterically Hindered 4N Ligands: Regioselectivity in Biomimetic Extradiol Cleavage of Catechols. Inorg Chem 2008; 47:6645-58. [DOI: 10.1021/ic702410d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ramasamy Mayilmurugan
- School of Chemistry, Bharathidasan University, Tiruchirapalli 620 024, India, and Department of Chemistry, University of Neuchatel, Neuchatel, Switzerland
| | - Helen Stoeckli-Evans
- School of Chemistry, Bharathidasan University, Tiruchirapalli 620 024, India, and Department of Chemistry, University of Neuchatel, Neuchatel, Switzerland
| | - Mallayan Palaniandavar
- School of Chemistry, Bharathidasan University, Tiruchirapalli 620 024, India, and Department of Chemistry, University of Neuchatel, Neuchatel, Switzerland
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39
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Strautmann JBH, George SD, Bothe E, Bill E, Weyhermüller T, Stammler A, Bögge H, Glaser T. Molecular and Electronic Structures of Mononuclear Iron Complexes Using Strongly Electron-Donating Ligands and their Oxidized Forms. Inorg Chem 2008; 47:6804-24. [DOI: 10.1021/ic800335t] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Julia B. H. Strautmann
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Serena DeBeer George
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Eberhard Bothe
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Eckhard Bill
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Thomas Weyhermüller
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Anja Stammler
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Hartmut Bögge
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Thorsten Glaser
- Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany, Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Stanford, California 94309, and Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim, Germany
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40
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Sundaravel K, Dhanalakshmi T, Suresh E, Palaniandavar M. Synthesis, structure, spectra and reactivity of iron(iii) complexes of facially coordinating and sterically hindering 3N ligands as models for catechol dioxygenases. Dalton Trans 2008:7012-25. [DOI: 10.1039/b809142k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Substrate activation for O2 reactions by oxidized metal centers in biology. Proc Natl Acad Sci U S A 2007; 104:18355-62. [PMID: 18003930 DOI: 10.1073/pnas.0704191104] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The uncatalyzed reactions of O(2) (S = 1) with organic substrates (S = 0) are thermodynamically favorable but kinetically slow because they are spin-forbidden and the one-electron reduction potential of O(2) is unfavorable. In nature, many of these important O(2) reactions are catalyzed by metalloenzymes. In the case of mononuclear non-heme iron enzymes, either Fe(II) or Fe(III) can play the catalytic role in these spin-forbidden reactions. Whereas the ferrous enzymes activate O(2) directly for reaction, the ferric enzymes activate the substrate for O(2) attack. The enzyme-substrate complex of the ferric intradiol dioxygenases exhibits a low-energy catecholate to Fe(III) charge transfer transition that provides a mechanism by which both the Fe center and the catecholic substrate are activated for the reaction with O(2). In this Perspective, we evaluate how the coupling between this experimentally observed charge transfer and the change in geometry and ligand field of the oxidized metal center along the reaction coordinate can overcome the spin-forbidden nature of the O(2) reaction.
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Visvaganesan K, Mayilmurugan R, Suresh E, Palaniandavar M. Iron(III) Complexes of Tridentate 3N Ligands as Functional Models for Catechol Dioxygenases: The Role of Ligand N-alkyl Substitution and Solvent on Reaction Rate and Product Selectivity. Inorg Chem 2007; 46:10294-306. [DOI: 10.1021/ic700822y] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kusalendiran Visvaganesan
- School of Chemistry, Bharathidasan University, Tiruchirappalli-620 024, India, Analytical Science Discipline, Central Salt and Marine Chemicals Research Institute, Bhavnagar-364 002, India
| | - Ramasamy Mayilmurugan
- School of Chemistry, Bharathidasan University, Tiruchirappalli-620 024, India, Analytical Science Discipline, Central Salt and Marine Chemicals Research Institute, Bhavnagar-364 002, India
| | - Eringathodi Suresh
- School of Chemistry, Bharathidasan University, Tiruchirappalli-620 024, India, Analytical Science Discipline, Central Salt and Marine Chemicals Research Institute, Bhavnagar-364 002, India
| | - Mallayan Palaniandavar
- School of Chemistry, Bharathidasan University, Tiruchirappalli-620 024, India, Analytical Science Discipline, Central Salt and Marine Chemicals Research Institute, Bhavnagar-364 002, India
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43
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Li F, Wang M, Li P, Zhang T, Sun L. Iron(III) Complexes with a Tripodal N3O Ligand Containing an Internal Base as a Model for Catechol Intradiol-Cleaving Dioxygenases. Inorg Chem 2007; 46:9364-71. [DOI: 10.1021/ic700664u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fei Li
- State Key Laboratory of Fine Chemicals, DUT-KTH Joint Education and Research Center on Molecular Devices, Dalian University of Technology (DUT), Dalian 116012, China, and Organic Chemistry, KTH Chemical Science and Engineering, Stockholm 10044, Sweden
| | - Mei Wang
- State Key Laboratory of Fine Chemicals, DUT-KTH Joint Education and Research Center on Molecular Devices, Dalian University of Technology (DUT), Dalian 116012, China, and Organic Chemistry, KTH Chemical Science and Engineering, Stockholm 10044, Sweden
| | - Ping Li
- State Key Laboratory of Fine Chemicals, DUT-KTH Joint Education and Research Center on Molecular Devices, Dalian University of Technology (DUT), Dalian 116012, China, and Organic Chemistry, KTH Chemical Science and Engineering, Stockholm 10044, Sweden
| | - Tingting Zhang
- State Key Laboratory of Fine Chemicals, DUT-KTH Joint Education and Research Center on Molecular Devices, Dalian University of Technology (DUT), Dalian 116012, China, and Organic Chemistry, KTH Chemical Science and Engineering, Stockholm 10044, Sweden
| | - Licheng Sun
- State Key Laboratory of Fine Chemicals, DUT-KTH Joint Education and Research Center on Molecular Devices, Dalian University of Technology (DUT), Dalian 116012, China, and Organic Chemistry, KTH Chemical Science and Engineering, Stockholm 10044, Sweden
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44
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Bruijnincx PCA, Lutz M, Spek AL, Hagen WR, van Koten G, Gebbink RJMK. Iron(III)-catecholato complexes as structural and functional models of the intradiol-cleaving catechol dioxygenases. Inorg Chem 2007; 46:8391-402. [PMID: 17722878 DOI: 10.1021/ic700741v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural and spectroscopic characterization of mononuclear iron(III)-catecholato complexes of ligand L4 (methyl bis(1-methylimidazol-2-yl)(2-hydroxyphenyl)methyl ether, HL4) are described, which closely mimic the enzyme-substrate complex of the intradiol-cleaving catechol dioxygenases. The tridentate, tripodal monoanionic ligand framework of L4 incorporates one phenolato and two imidazole donor groups and thus well reproduces the His2Tyr endogenous donor set. In fact, regarding the structural features of [FeIII(L4)(tcc)(H2O)] (5.H2O, tcc = tetrachlorocatechol) in the solid state, the complex constitutes the closest structural model reported to date. The iron(III)-catecholato complexes mimic both the structural features of the active site and its spectroscopic characteristics. As part of its spectroscopic characterization, the electron paramagnetic resonance (EPR) spectra were successfully simulated using a simple model that accounts for D strain. The simulation procedure showed that the observed g = 4.3 line is an intrinsic part of the EPR envelope of the studied complexes and should not necessarily be attributed to a highly rhombic impurity. [FeIII(L4)(dtbc)(H2O)] (dtbc = 3,5-di-tert-butylcatechol) was studied with respect to its dioxygen reactivity, and oxidative cleavage of the substrate was observed. Intradiol- and extradiol-type cleavage products were found in roughly equal amounts. This shows that an accurate structural model of the first-coordination sphere of the active site is not sufficient for obtaining regioselectivity.
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Affiliation(s)
- Pieter C A Bruijnincx
- Chemical Biology & Organic Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Mayilmurugan R, Suresh E, Palaniandavar M. A New Tripodal Iron(III) Monophenolate Complex: Effects of Ligand Basicity, Steric Hindrance, and Solvent on Regioselective Extradiol Cleavage. Inorg Chem 2007; 46:6038-49. [PMID: 17589990 DOI: 10.1021/ic700646m] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The new iron(III) complex [Fe(L3)Cl(2)], where H(L3) is the tripodal monophenolate ligand N,N-dimethyl-N'-(pyrid-2-ylmethyl)-N'-(2-hydroxy-3,5-dimethylbenzyl)ethylenediamine, has been isolated and studied as a structural and functional model for catechol dioxygenase enzymes. The complex possesses a distorted octahedral iron(III) coordination geometry constituted by the phenolate oxygen, pyridine nitrogen and two amine nitrogens of the tetradentate ligand, and two cis-coordinated chloride ions. The Fe-O-C bond angle (134.0 degrees) and Fe-O bond length (1.889 Angstrom) are very close to those (Fe-O-C, 133 degrees and 148 degrees, Fe-O(tyrosinate), 1.81 and 1.91 Angstrom) of protocatechuate 3,4-dioxygenase enzymes. When the complex is treated with AgNO(3), the ligand-to-metal charge transfer (LMCT) band around 650 nm (epsilon, 2390 M(-1) cm(-1)) is red shifted to 665 nm with an increase in absorptivity (epsilon, 2630 M(-1) cm(-1)) and the Fe(III)/Fe(II) redox couple is shifted to a slightly more positive potential (-0.329 to -0.276 V), suggesting an increase in the Lewis acidity of the iron(III) center upon the removal of coordinated chloride ions. Furthermore, when 3,5-di-tert-butylcatechol (H(2)DBC) pretreated with 2 mol of Et(3)N is added to the complex [Fe(L3)Cl(2)] treated with 2 equiv of AgNO(3), two intense catecholate-to-iron(III) LMCT bands (719 nm, epsilon, 3150 M(-1) cm(-1); 494 nm, epsilon, 3510 M(-1) cm(-1)) are observed. Similar observations are made when H(2)DBC pretreated with 2 mol of piperidine is added to [Fe(L3)Cl(2)], suggesting the formation of [Fe(L3)(DBC)] with bidentate coordination of DBC(2-). On the other hand, when H(2)DBC pretreated with 2 mol of Et(3)N is added to [Fe(L3)Cl(2)], only one catecholate-to-iron(III) LMCT band (617 nm; epsilon, 4380 M(-1) cm(-1)) is observed, revealing the formation of [Fe(L3)(HDBC)(Cl)] involving monodentate coordination of the catecholate. The appearance of the DBSQ/H(2)DBC couple for [Fe(L3)(DBC)] at a potential (-0.083 V) more positive than that (-0.125 V) for [Fe(L3)(HDBC)(Cl)] reveals that chelated DBC(2-) in the former is stabilized toward oxidation more than the coordinated HDBC(-). It is remarkable that the complex [Fe(L3)(HDBC)(Cl)] undergoes slow selective extradiol cleavage (17.3%) of H(2)DBC in the presence of O(2), unlike the iron(III)-phenolate complexes known to yield only intradiol products. It is probable that the weakly coordinated (2.310 Angstrom) -NMe(2) group rather than chloride in the substrate-bound complex is displaced, facilitating O(2) attack on the iron(III) center and, hence, the extradiol cleavage. In contrast, when the cleavage reaction was performed in the presence of a stronger base-like piperidine before and after the removal of the coordinated chloride ions, a faster intradiol cleavage was favored over extradiol cleavage, suggesting the importance of the bidentate coordination of the catecholate substrate in facilitating intradiol cleavage. Also, intradiol cleavage is favored in dimethylformamide and acetonitrile solvents, with enhanced intradiol cleavage yields of 94 and 40%, respectively.
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Functional model for intradiol-cleaving catechol 1,2-dioxygenase: Synthesis, structure, spectra, and catalytic activity of iron(III) complexes with substituted salicylaldimine ligands. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2007.02.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Palaniandavar M, Mayilmurugan R. Mononuclear non-heme iron(III) complexes as functional models for catechol dioxygenases. CR CHIM 2007. [DOI: 10.1016/j.crci.2007.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Palaniandavar M, Velusamy M, Mayilmurugan R. Iron(III) complexes of certain tetradentate phenolate ligands as functional models for catechol dioxygenases. J CHEM SCI 2006. [DOI: 10.1007/bf02703959] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Borowski T, Siegbahn PEM. Mechanism for Catechol Ring Cleavage by Non-Heme Iron Intradiol Dioxygenases: A Hybrid DFT Study. J Am Chem Soc 2006; 128:12941-53. [PMID: 17002391 DOI: 10.1021/ja0641251] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the catalytic reaction of protocatechuate 3,4-dioxygenase (3,4-PCD), a representative intradiol dioxygenase, was studied with the hybrid density functional method B3LYP. First, a smaller model involving only the iron first-shell ligands (His460, His462, and Tyr408) and the substrates (catechol and dioxygen) was used to probe various a priori plausible reaction mechanisms. Then, an extended model involving also the most important second-shell groups (Arg457, Gln477, and Tyr479) was used for the refinement of the preselected mechanisms. The computational results suggest that the chemical reactions constituting the catalytic cycle of intradiol dioxygenases involve: (1) binding of the substrate as a dianion, in agreement with experimental suggestions, (2) binding of dioxygen to the metal aided by an electron transfer from the substrate to O(2), (3) formation of a bridging peroxo intermediate and its conformational change, which opens the coordination site trans to His462, (4) binding of a neutral XOH ligand (H(2)O or Tyr447) at the open site, (5) proton transfer from XOH to the neighboring peroxo ligand yielding the hydroperoxo intermediate, (6) a Criegee rearrangement leading to the anhydride intermediate, and (7) hydrolysis of the anhydride to the final acyclic product. One of the most important results obtained is that the Criegee mechanism requires an in-plane orientation of the four atoms (two oxygen and two carbon atoms) mainly involved in the reaction. This orientation yields a good overlap between the two sigma orbitals involved, C-C sigma and O-O sigma, allowing an efficient electron flow between them. Another interesting result is that under some conditions, a homolytic O-O bond cleavage might compete with the Criegee rearrangement. The role of the second-shell residues and the substituent effects are also discussed.
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Affiliation(s)
- Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland.
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Dhanalakshmi T, Bhuvaneshwari M, Palaniandavar M. Iron(III) complexes of certain meridionally coordinating tridentate ligands as models for non-heme iron enzymes: The role of carboxylate coordination. J Inorg Biochem 2006; 100:1527-34. [PMID: 16814389 DOI: 10.1016/j.jinorgbio.2006.05.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Revised: 04/13/2006] [Accepted: 05/10/2006] [Indexed: 11/18/2022]
Abstract
The iron(III) complexes [Fe(pda)Cl(H(2)O)(2)] (1), [Fe(tpy)Cl(3)] (2), and [Fe(bbp)Cl(3)] (3), where H(2)pda is pyridine-2,6-dicarboxylic acid, tpy is 2,2':6,2''-terpyridine and bbp is 2,6-bis(benzimidazolyl)pyridine, have been isolated and studied as functional models for the intradiol-cleaving catechol dioxygenase enzymes. Mixed ligand complexes of H(2)pda with the bidentate ligands 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen) have been also prepared and studied. All the complexes have been characterized using absorption spectral and electrochemical methods. The spectral changes in the catecholate adducts of the complexes generated in situ have been investigated. Upon interacting the complexes with catecholate anions a low energy catecholate to iron(III) charge transfer band appears, which is similar to that observed for enzyme-substrate complexes. All the complexes catalyze the oxidative intradiol cleavage of 3,5-di-tert-butylcatechol (H(2)dbc) in the presence of dioxygen. Interestingly, on replacing the pyridyl groups in 2 and the bulky benzimidazole groups in 3 by the carboxylate groups, the yields of the intradiol cleavage products of dioxygenation increases, 1 (50%)>2 (20%)>3 (10%). The higher intradiol yield for 1 has been ascribed to the meridional coordination of two carboxylate groups of pda(2-). In contrast to the trend in the intradiol cleavage yields, a tremendous decrease in the rate (200 times) is observed on replacing the two pyridyl moieties in 2 by two carboxylates as in 1 and a significant decrease in rate is observed on replacing the pyridyl moieties in 2 by strongly sigma-donating benzimidazole moieties as in 3. This is in conformity with the decrease in Lewis acidities of the iron(III) centers.
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