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Wang Q, Li H, Bujupi U, Gröning J, Stolz A, Bongiorno A, Gupta R. Oxygen Activation in Aromatic Ring Cleaving Salicylate Dioxygenase: Detection of Reaction Intermediates with a Nitro-substituted Substrate Analog. Chembiochem 2024; 25:e202400023. [PMID: 38363551 DOI: 10.1002/cbic.202400023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/17/2024]
Abstract
Cupin dioxygenases such as salicylate 1,2-dioxygense (SDO) perform aromatic C-C bond scission via a 3-His motif tethered iron cofactor. Here, transient kinetics measurements are used to monitor the catalytic cycle of SDO by using a nitro-substituted substrate analog, 3-nitrogentisate. Compared to the natural substrate, the nitro group reduces the enzymatic kcat by 500-fold, thereby facilitating the detection and kinetic characterization of reaction intermediates. Sums and products of reciprocal relaxation times derived from kinetic measurements were found to be linearly dependent on O2 concentration, suggesting reversible formation of two distinct intermediates. Dioxygen binding to the metal cofactor takes place with a forward rate of 5.9×103 M-1 s-1: two orders of magnitude slower than other comparable ring-cleaving dioxygenses. Optical chromophore of the first intermediate is distinct from the in situ generated SDO Fe(III)-O2⋅- complex but closer to the enzyme-substrate precursor.
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Affiliation(s)
- Qian Wang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
| | - Hanbin Li
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
| | - Uran Bujupi
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
| | - Janosch Gröning
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Angelo Bongiorno
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
| | - Rupal Gupta
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Biochemistry, The Graduate Center of the City University of New York, New York, 10016, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
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2
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BUYUKTEMIZ M, DEDE Y. Homoprotocatechuate dioxygenase active site: Imitating the secondary sphere base via computational design. Turk J Chem 2023; 47:1116-1124. [PMID: 38173743 PMCID: PMC10760822 DOI: 10.55730/1300-0527.3598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 10/31/2023] [Accepted: 09/30/2023] [Indexed: 01/05/2024] Open
Abstract
Oxidative ring cleavage reactions have attracted great interest and various studies on the catechol ring-cleaving enzyme homoprotocatechuate dioxygenase (HPCD) have been reported in the literature. The available data on how the proton transfer takes place led us to design a potential HPCD model structure. A secondary sphere effect of utmost importance, the assistance of His200, which is critical for the catechol proton to migrate to dioxygen, was cautiously included on the first coordination shell. This was done mainly by modifying the axial ligands in the first coordination shell of HPCD such that the dual basic/acidic role in the proton transfer pathway of His200 was reproduced. Model systems with mono-, bi-, and tridentate ligands are reported. Energetically feasible reaction channels on synthetically promising ligand structures are identified. Key structural and electronic principles for obtaining viable proton transfer paths are outlined.
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Affiliation(s)
- Muhammed BUYUKTEMIZ
- Department of Chemistry, Faculty of Science, Gazi University, Ankara,
Turkiye
| | - Yavuz DEDE
- Department of Chemistry, Faculty of Science, Gazi University, Ankara,
Turkiye
- Department of Chemistry, Faculty of Science, University of Helsinki, Helsinki,
Finland
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3
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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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4
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Jeong D, Selverstone Valentine J, Cho J. Bio-inspired mononuclear nonheme metal peroxo complexes: Synthesis, structures and mechanistic studies toward understanding enzymatic reactions. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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5
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Goldberg AM, Robinson MK, Starr ES, Marasco RN, Alana AC, Cochrane CS, Klugh KL, Strzeminski DJ, Du M, Colabroy KL, Peterson LW. L-DOPA Dioxygenase Activity on 6-Substituted Dopamine Analogues. Biochemistry 2021; 60:2492-2507. [PMID: 34324302 DOI: 10.1021/acs.biochem.1c00310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dioxygenase enzymes are essential protein catalysts for the breakdown of catecholic rings, structural components of plant woody tissue. This powerful chemistry is used in nature to make antibiotics and other bioactive materials or degrade plant material, but we have a limited understanding of the breadth and depth of substrate space for these potent catalysts. Here we report steady-state and pre-steady-state kinetic analysis of dopamine derivatives substituted at the 6-position as substrates of L-DOPA dioxygenase, and an analysis of that activity as a function of the electron-withdrawing nature of the substituent. Steady-state and pre-steady-state kinetic data demonstrate the dopamines are impaired in binding and catalysis with respect to the cosubstrate molecular oxygen, which likely afforded spectroscopic observation of an early reaction intermediate, the semiquinone of dopamine. The reaction pathway of dopamine in the pre-steady state is consistent with a nonproductive mode of binding of oxygen at the active site. Despite these limitations, L-DOPA dioxygenase is capable of binding all of the dopamine derivatives and catalyzing multiple turnovers of ring cleavage for dopamine, 6-bromodopamine, 6-carboxydopamine, and 6-cyanodopamine. 6-Nitrodopamine was a single-turnover substrate. The variety of substrates accepted by the enzyme is consistent with an interplay of factors, including the capacity of the active site to bind large, negatively charged groups at the 6-position and the overall oxidizability of each catecholamine, and is indicative of the utility of extradiol cleavage in semisynthetic and bioremediation applications.
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Affiliation(s)
- Alexander M Goldberg
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Miranda K Robinson
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Erykah S Starr
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Ryan N Marasco
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Alexa C Alana
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - C Skyler Cochrane
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - Kameron L Klugh
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
| | - David J Strzeminski
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Muxue Du
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Keri L Colabroy
- Department of Chemistry, Muhlenberg College, 2400 Chew Street, Allentown, Pennsylvania 18104, United States
| | - Larryn W Peterson
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, United States
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6
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Downing AN, Coggins MK, Poon PCY, Kovacs JA. Influence of Thiolate versus Alkoxide Ligands on the Stability of Crystallographically Characterized Mn(III)-Alkylperoxo Complexes. J Am Chem Soc 2021; 143:6104-6113. [PMID: 33851827 DOI: 10.1021/jacs.0c13001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The work described herein demonstrates the exquisite control that the inner coordination sphere of metalloenzymes and transition-metal complexes can have on reactivity. We report one of few crystallographically characterized Mn-peroxo complexes and show that the tight correlations between metrical and spectroscopic parameters, established previously by our group for thiolate-ligated RS-Mn(III)-OOR complexes, can be extended to include an alkoxide-ligated RO-Mn(III)-OOR complex. We show that the alkoxide-ligated RO-Mn(III)-OOR complex is an order of magnitude more stable (t1/2298 K = 6730 s, kobs298 K = 1.03 × 10-4 s-1) than its thiolate-ligated RS-Mn(III)-OOR derivative (t1/2293 K = 249 s, k1293 K = 2.78 × 10-3 s-1). Electronic structure calculations provide insight regarding these differences in stability. The highest occupied orbital of the thiolate-ligated derivative possesses significant sulfur character and π-backdonation from the thiolate competes with π-backdonation from the peroxo π*(O-O). DFT-calculated Mulliken charges show that the Mn ion Lewis acidity of alkoxide-ligated RO-Mn(III)-OOR (+0.451) is greater than that of thiolate-ligated RS-Mn(III)-OOR (+0.306), thereby facilitating π-backdonation from the antibonding peroxo π*(O-O) orbital and increasing its stability. This helps to explain why the photosynthetic oxygen-evolving Mn complex, which catalyzes O-O bond formation as opposed to cleavage, incorporates O- and/or N-ligands as opposed to cysS-ligands.
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Affiliation(s)
- Alexandra N Downing
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Michael K Coggins
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Penny Chaau Yan Poon
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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7
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Tu N, Zhang D, Niu X, Du C, Zhang L, Xie W, Niu X, Liu Y, Li Y. A novel concept for the biodegradation mechanism of dianionic catechol with homoprotocatechuate 2,3-dioxygenase: A non-proton-assisted process. CHEMOSPHERE 2020; 246:125796. [PMID: 31918103 DOI: 10.1016/j.chemosphere.2019.125796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/15/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
The theory of "proton-assisted process" can well explain the catalytic mechanism of homoprotocatechuate 2,3-dioxygenase (2,3-HPCD) with a monoanionic substrate (homoprotocatechuate, HPCA). Here a "non-proton-assisted process" is presented to interpret catalytic mechanism of 2,3-HPCD with a dianionic substrate (4-nitrocatechol, 4NC). The ONIOM calculation is performed to investigate the reaction pathway of a wild-type 2,3-HPCD with 4NC (H200H-4NC system). The catalytic reaction is comprised of four steps: (1) A dioxygen attacks the aromatic ring to produce an alkylperoxo species. (2) O-O bond cleavage and the formation of an epoxide species occur. (3) A seven-membered O-heterocyclic compound is generated by the extinction of the epoxy structure. (4) The seven-membered ring undergoes ring opening to form the final product (C2-C3 cleavage product). The effective free energy barrier of the catalytic reaction of the H200H-4NC system is 26.2 kcal mol-1, which is much higher than that of the H200H-HPCA system. Furthermore, two calculated electronic configurations (Fe(III)-O2•- and Fe(III)-SQ•) have a high similarity to previously detected ones, which demonstrates that the Asn200 variant (H200N-4NC variant system) employs a C4 (para-carbon) pathway to produce a C4-C5 cleavage product. Our findings provide an in-depth understanding of the catalytic mechanisms of dianionic catechol and its derivatives.
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Affiliation(s)
- Ningyu Tu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Dongmei Zhang
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Xianchun Niu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Cheng Du
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Li Zhang
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Wenyu Xie
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Xiaojun Niu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China; School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yang Liu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China.
| | - Youming Li
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, China
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8
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Substrate promiscuity and active site differences in gentisate 1,2-dioxygenases: electron paramagnetic resonance study. J Biol Inorg Chem 2019; 24:287-296. [PMID: 30712085 DOI: 10.1007/s00775-019-01646-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/28/2019] [Indexed: 10/27/2022]
Abstract
Gentisate 1,2-dioxygenases (GDOs) are non-heme iron enzymes that catalyze the oxidation of dihydroxylated aromatic substrate, gentisate (2,5-dihydroxybenzoate). Salicylate 1,2-dioxygenase (SDO), a member of the GDO family, performs the ring scission of monohydroxylated substrates such as salicylate, thereby oxidizing a broader range of substrates compared to GDOs. Although the two types of enzymes share a high degree of sequence similarity, the origin of substrate specificity between SDO and GDOs is not understood. We present electron paramagnetic resonance (EPR) investigation of ferrous-nitrosyl complexes of SDO and a GDO from the bacterium Corynebacterium glutamicum (GDOCg). The EPR spectra of these complexes, which mimic the Fe-substrate-O2 intermediates in the catalytic cycle, show unexpected differences in the substrate binding mode and the coordination geometry of the metal cofactor in the two enzymes. Binding of substrate to the ferrous center increases the symmetry of the Fe(II)-NO complex in SDO, while a reverse trend is observed in GDOCg where substrate ligation reduces the symmetry of the nitrosyl complex. Identical EPR spectra were obtained for the NO derivatives of a variant of GDOCg(A112G), which can oxidize salicylate, and wild-type GDOCg revealing that the A112G mutation does not alter the nature of the Fe-substrate-O2 ternary complex.
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9
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Sutherlin KD, Wasada-Tsutsui Y, Mbughuni MM, Rogers MS, Park K, Liu LV, Kwak Y, Srnec M, Böttger LH, Frenette M, Yoda Y, Kobayashi Y, Kurokuzu M, Saito M, Seto M, Hu M, Zhao J, Alp EE, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity. J Am Chem Soc 2018; 140:16495-16513. [PMID: 30418018 DOI: 10.1021/jacs.8b06517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O2. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O2-4NC species and a Fe-O2-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as FeIII-superoxo-catecholate and FeIII-peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on FeIII-superoxo-catecholate and an end-on FeIII-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a FeIII-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of FeIII-superoxo and FeIII-hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.
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Affiliation(s)
- Kyle D Sutherlin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yuko Wasada-Tsutsui
- Department of Life Science and Applied Chemistry, Graduate School of Engineering , Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya 466-8555 , Japan
| | - Michael M Mbughuni
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Melanie S Rogers
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Kiyoung Park
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Lei V Liu
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yeonju Kwak
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Martin Srnec
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Lars H Böttger
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Mathieu Frenette
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute , Hyogo 679-5198 , Japan
| | | | - Masayuki Kurokuzu
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Makina Saito
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Michael Hu
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - E Ercan Alp
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States.,SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
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10
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Gordon JB, McGale JP, Prendergast JR, Shirani-Sarmazeh Z, Siegler MA, Jameson GNL, Goldberg DP. Structures, Spectroscopic Properties, and Dioxygen Reactivity of 5- and 6-Coordinate Nonheme Iron(II) Complexes: A Combined Enzyme/Model Study of Thiol Dioxygenases. J Am Chem Soc 2018; 140:14807-14822. [PMID: 30346746 PMCID: PMC6596423 DOI: 10.1021/jacs.8b08349] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The synthesis of four new FeII(N4S(thiolate)) complexes as models of the thiol dioxygenases are described. They are composed of derivatives of the neutral, tridentate ligand triazacyclononane (R3TACN; R = Me, iPr) and 2-aminobenzenethiolate (abtx; X = H, CF3), a non-native substrate for thiol dioxygenases. The coordination number of these complexes depends on the identity of the TACN derivative, giving 6-coordinate (6-coord) complexes for FeII(Me3TACN)(abtx)(OTf) (1: X = H; 2: X = CF3) and 5-coordinate (5-coord) complexes for [FeII(iPr3TACN)(abtx)](OTf) (3: X = H; 4: X = CF3). Complexes 1-4 were examined by UV-vis, 1H/19F NMR, and Mössbauer spectroscopies, and density functional theory (DFT) calculations were employed to support the data. Mössbauer spectroscopy reveals that the 6-coord 1-2 and 5-coord 3- 4 exhibit distinct spectra, and these data are compared with that for cysteine-bound CDO, helping to clarify the coordination environment of the cys-bound FeII active site. Reaction of 1 or 2 with O2 at -95 °C leads to S-oxygenation of the abt ligand, and in the case of 2, a rare di(sulfinato)-bridged complex, [Fe2III(μ-O)((2-NH2) p-CF3C6H3SO2)2](OTf)2 ( 5), was obtained. Parallel enzymatic studies on the CDO variant C93G were carried out with the abt substrate and show that reaction with O2 leads to disulfide formation, as opposed to S-oxygenation. The combined model and enzyme studies show that the thiol dioxygenases can operate via a 6-coord FeII center, in contrast to the accepted mechanism for nonheme iron dioxygenases, and that proper substrate chelation to Fe appears to be critical for S-oxygenation.
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Affiliation(s)
- Jesse B Gordon
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
| | - Jeremy P McGale
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
| | - Joshua R Prendergast
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
| | - Zahra Shirani-Sarmazeh
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
| | - Maxime A Siegler
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
| | - Guy N L Jameson
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
| | - David P Goldberg
- Department of Chemistry , The Johns Hopkins University , 3400 North Charles Street , Baltimore , Maryland 21218 , United States
- School of Chemistry , Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
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11
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Gupta R, Stringer J, Struppe J, Rehder D, Polenova T. Direct detection and characterization of bioinorganic peroxo moieties in a vanadium complex by 17O solid-state NMR and density functional theory. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 91:15-20. [PMID: 29506770 PMCID: PMC6267778 DOI: 10.1016/j.ssnmr.2018.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Electronic and structural properties of short-lived metal-peroxido complexes, which are key intermediates in many enzymatic reactions, are not fully understood. While detected in various enzymes, their catalytic properties remain elusive because of their transient nature, making them difficult to study spectroscopically. We integrated 17O solid-state NMR and density functional theory (DFT) to directly detect and characterize the peroxido ligand in a bioinorganic V(V) complex mimicking intermediates non-heme vanadium haloperoxidases. 17O chemical shift and quadrupolar tensors, measured by solid-state NMR spectroscopy, probe the electronic structure of the peroxido ligand and its interaction with the metal. DFT analysis reveals the unusually large chemical shift anisotropy arising from the metal orbitals contributing towards the magnetic shielding of the ligand. The results illustrate the power of an integrated approach for studies of oxygen centers in enzyme reaction intermediates.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
| | - John Stringer
- PhoenixNMR, 4921 Eagle Lake Drive, Fort Collins, CO, USA
| | | | - Dieter Rehder
- Department of Chemistry, University of Hamburg, D-20146, Hamburg, Germany
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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12
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Guengerich FP, Yoshimoto FK. Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions. Chem Rev 2018; 118:6573-6655. [PMID: 29932643 DOI: 10.1021/acs.chemrev.8b00031] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O2 in systems in which the binding of a substrate facilitates O2 activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
| | - Francis K Yoshimoto
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
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13
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Tchesnokov EP, Faponle AS, Davies CG, Quesne MG, Turner R, Fellner M, Souness RJ, Wilbanks SM, de Visser SP, Jameson GNL. An iron-oxygen intermediate formed during the catalytic cycle of cysteine dioxygenase. Chem Commun (Camb) 2018; 52:8814-7. [PMID: 27297454 PMCID: PMC5043143 DOI: 10.1039/c6cc03904a] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Combined spectroscopic, kinetic and computational studies provide first evidence of a short-lived intermediate in the catalytic cycle of cysteine dioxygenase.
Cysteine dioxygenase is a key enzyme in the breakdown of cysteine, but its mechanism remains controversial. A combination of spectroscopic and computational studies provides the first evidence of a short-lived intermediate in the catalytic cycle. The intermediate decays within 20 ms and has absorption maxima at 500 and 640 nm.
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Affiliation(s)
- E P Tchesnokov
- Department of Chemistry & MacDiarmid Institute for Advanced Materials and Nanotechnology University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - A S Faponle
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - C G Davies
- Department of Chemistry & MacDiarmid Institute for Advanced Materials and Nanotechnology University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - M G Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - R Turner
- Centre for Free Radical Research, University of Otago, 2 Riccarton Ave, PO Box 4345, Christchurch, New Zealand
| | - M Fellner
- Department of Chemistry & MacDiarmid Institute for Advanced Materials and Nanotechnology University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - R J Souness
- Department of Chemistry & MacDiarmid Institute for Advanced Materials and Nanotechnology University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - S M Wilbanks
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - S P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - G N L Jameson
- Department of Chemistry & MacDiarmid Institute for Advanced Materials and Nanotechnology University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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14
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Roy S, Kästner J. Catalytic Mechanism of Salicylate Dioxygenase: QM/MM Simulations Reveal the Origin of Unexpected Regioselectivity of the Ring Cleavage. Chemistry 2017; 23:8949-8962. [DOI: 10.1002/chem.201701286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Subhendu Roy
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
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15
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Wang Y, Li J, Liu A. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J Biol Inorg Chem 2017; 22:395-405. [PMID: 28084551 DOI: 10.1007/s00775-017-1436-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/03/2017] [Indexed: 11/25/2022]
Abstract
Molecular oxygen is utilized in numerous metabolic pathways fundamental for life. Mononuclear nonheme iron-dependent oxygenase enzymes are well known for their involvement in some of these pathways, activating O2 so that oxygen atoms can be incorporated into their primary substrates. These reactions often initiate pathways that allow organisms to use stable organic molecules as sources of carbon and energy for growth. From the myriad of reactions in which these enzymes are involved, this perspective recounts the general mechanisms of aromatic dihydroxylation and oxidative ring cleavage, both of which are ubiquitous chemical reactions found in life-sustaining processes. The organic substrate provides all four electrons required for oxygen activation and insertion in the reactions mediated by extradiol and intradiol ring-cleaving catechol dioxygenases. In contrast, two of the electrons are provided by NADH in the cis-dihydroxylation mechanism of Rieske dioxygenases. The catalytic nonheme Fe center, with the aid of active site residues, facilitates these electron transfers to O2 as key elements of the activation processes. This review discusses some general questions for the catalytic strategies of oxygen activation and insertion into aromatic compounds employed by mononuclear nonheme iron-dependent dioxygenases. These include: (1) how oxygen is activated, (2) whether there are common intermediates before oxygen transfer to the aromatic substrate, and (3) are these key intermediates unique to mononuclear nonheme iron dioxygenases?
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Jiasong Li
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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16
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Liu Y, Tu N, Xie W, Li Y. Theoretical investigation on proton transfer mechanism of extradiol dioxygenase. RSC Adv 2017. [DOI: 10.1039/c7ra08080h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The formation mechanism of alkyl(hydro)peroxo species is performed via two parallel pathways.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Pulp and Paper Engineering
- South China University of Technology
- Guangzhou 510640
- P. R. China
- Faculty of Environmental & Biological Engineering
| | - Ningyu Tu
- Faculty of Environmental & Biological Engineering
- Guangdong University of Petrochemical Technology
- Maoming 525000
- P. R. China
| | - Wenyu Xie
- Faculty of Environmental & Biological Engineering
- Guangdong University of Petrochemical Technology
- Maoming 525000
- P. R. China
| | - Youming Li
- State Key Laboratory of Pulp and Paper Engineering
- South China University of Technology
- Guangzhou 510640
- P. R. China
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17
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Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes. J Biol Inorg Chem 2016; 22:407-424. [PMID: 27853875 DOI: 10.1007/s00775-016-1402-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
The active sites of metalloenzymes that catalyze O2-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O2 at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O2 reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O2 activation at these three "overlooked" metals.
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18
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Abstract
The non-heme Fe enzymes are ubiquitous in nature and perform a wide range of functions involving O2 activation. These had been difficult to study relative to heme enzymes; however, spectroscopic methods that provide significant insight into the correlation of structure with function have now been developed. This Current Topics article summarizes both the molecular mechanism these enzymes use to control O2 activation in the presence of cosubstrates and the oxygen intermediates these reactions generate. Three types of O2 activation are observed. First, non-heme reactivity is shown to be different from heme chemistry where a low-spin FeIII-OOH non-heme intermediate directly reacts with substrate. Also, two subclasses of non-heme Fe enzymes generate high-spin FeIV═O intermediates that provide both σ and π frontier molecular orbitals that can control selectivity. Finally, for several subclasses of non-heme Fe enzymes, binding of the substrate to the FeII site leads to the one-electron reductive activation of O2 to an FeIII-superoxide capable of H atom abstraction and electrophilic attack.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States.,SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Serra Goudarzi
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Kyle D Sutherlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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19
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Sutherlin KD, Liu LV, Lee YM, Kwak Y, Yoda Y, Saito M, Kurokuzu M, Kobayashi Y, Seto M, Que L, Nam W, Solomon EI. Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites. J Am Chem Soc 2016; 138:14294-14302. [PMID: 27726349 DOI: 10.1021/jacs.6b07227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FeIII-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on FeIII-peroxy and end-on FeIII-hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of FeIII-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.
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Affiliation(s)
- Kyle D Sutherlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Lei V Liu
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Yong-Min Lee
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University , Seoul 120-750, Korea
| | - Yeonju Kwak
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | | | - Makina Saito
- Research Reactor Institute, Kyoto University , Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Research Reactor Institute, Kyoto University , Osaka 590-0494, Japan
| | | | - Makoto Seto
- Research Reactor Institute, Kyoto University , Osaka 590-0494, Japan
| | - Lawrence Que
- Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University , Seoul 120-750, Korea
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States.,SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
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20
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Meier KK, Rogers MS, Kovaleva EG, Lipscomb JD, Bominaar EL, Münck E. Enzyme Substrate Complex of the H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Mössbauer and Computational Studies. Inorg Chem 2016; 55:5862-70. [PMID: 27275865 PMCID: PMC4924929 DOI: 10.1021/acs.inorgchem.6b00148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The extradiol, aromatic ring-cleaving enzyme homoprotocatechuate 2,3-dioxygenase (HPCD) catalyzes a complex chain of reactions that involve second sphere residues of the active site. The importance of the second-sphere residue His200 was demonstrated in studies of HPCD variants, such as His200Cys (H200C), which revealed significant retardations of certain steps in the catalytic process as a result of the substitution, allowing novel reaction cycle intermediates to be trapped for spectroscopic characterization. As the H200C variant largely retains the wild-type active site structure and produces the correct ring-cleaved product, this variant presents a valuable target for mechanistic HPCD studies. Here, the high-spin Fe(II) states of resting H200C and the H200C-homoprotocatechuate enzyme-substrate (ES) complex have been characterized with Mössbauer spectroscopy to assess the electronic structures of the active site in these states. The analysis reveals a high-spin Fe(II) center in a low symmetry environment that is reflected in the values of the zero-field splitting (ZFS) (D ≈ - 8 cm(-1), E/D ≈ 1/3 in ES), as well as the relative orientations of the principal axes of the (57)Fe magnetic hyperfine (A) and electric field gradient (EFG) tensors relative to the ZFS tensor axes. A spin Hamiltonian analysis of the spectra for the ES complex indicates that the magnetization axis of the integer-spin S = 2 Fe(II) system is nearly parallel to the symmetry axis, z, of the doubly occupied dxy ground orbital deduced from the EFG and A-values, an observation, which cannot be rationalized by DFT assisted crystal-field theory. In contrast, ORCA/CASSCF calculations for the ZFS tensor in combination with DFT calculations for the EFG- and A-tensors describe the experimental data remarkably well.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Elena G. Kovaleva
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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21
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Tearing down to build up: Metalloenzymes in the biosynthesis lincomycin, hormaomycin and the pyrrolo [1,4]benzodiazepines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:724-737. [DOI: 10.1016/j.bbapap.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 11/21/2022]
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22
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Thermodynamics of substrate binding to the metal site in homoprotocatechuate 2,3-dioxygenase: Using ITC under anaerobic conditions to study enzyme–substrate interactions. Biochim Biophys Acta Gen Subj 2016; 1860:910-916. [DOI: 10.1016/j.bbagen.2015.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/17/2015] [Accepted: 07/24/2015] [Indexed: 11/24/2022]
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23
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Christian GJ, Neese F, Ye S. Unravelling the Molecular Origin of the Regiospecificity in Extradiol Catechol Dioxygenases. Inorg Chem 2016; 55:3853-64. [PMID: 27050565 DOI: 10.1021/acs.inorgchem.5b02978] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many factors have been suggested to control the selectivity for extradiol or intradiol cleavage in catechol dioxygenases. The varied selectivity of model complexes and the ability to force an extradiol enzyme to do intradiol cleavage indicate that the problem may be complex. In this paper we focus on the regiospecificity of the proximal extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase (HPCD), for which considerable advances have been made in our understanding of the mechanism from an experimental and computational standpoint. Two key steps in the reaction mechanism were investigated: (1) attack of the substrate by the superoxide moiety and (2) attack of the substrate by the oxyl radical generated by O-O bond cleavage. The selectivity at both steps was investigated through a systematic study of the role of the substrate and the first and second coordination spheres. For the isolated native substrate, intradiol cleavage is calculated to be both kinetically and thermodynamically favored, therefore nature must use the enzyme environment to reverse this preference. Two second sphere residues were found to play key roles in controlling the regiospecificity of the reaction: Tyr257 and His200. Tyr257 controls the selectivity by modulating the electronic structure of the substrate, while His200 controls selectivity through steric effects and by preventing alternative pathways to intradiol cleavage.
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Affiliation(s)
- Gemma J Christian
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.,Avondale College of Higher Education , Cooranbong, New South Wales 2265, Australia
| | - Frank Neese
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Shengfa Ye
- Max-Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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24
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Roy S, Kästner J. QM/MM-Simulationen ergeben synergetische Substrat- und Sauerstoffaktivierung in Salicylat-Dioxygenase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Subhendu Roy
- Institut für Theoretische Chemie; Universität Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Deutschland
| | - Johannes Kästner
- Institut für Theoretische Chemie; Universität Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Deutschland
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25
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Roy S, Kästner J. Synergistic Substrate and Oxygen Activation in Salicylate Dioxygenase Revealed by QM/MM Simulations. Angew Chem Int Ed Engl 2015; 55:1168-72. [DOI: 10.1002/anie.201506363] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/18/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Subhendu Roy
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
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26
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Meier KK, Rogers MS, Kovaleva EG, Mbughuni MM, Bominaar EL, Lipscomb JD, Münck E. A Long-Lived Fe(III)-(Hydroperoxo) Intermediate in the Active H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Characterization by Mössbauer, Electron Paramagnetic Resonance, and Density Functional Theory Methods. Inorg Chem 2015; 54:10269-80. [PMID: 26485328 DOI: 10.1021/acs.inorgchem.5b01576] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The extradiol-cleaving dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) binds substrate homoprotocatechuate (HPCA) and O2 sequentially in adjacent ligand sites of the active site Fe(II). Kinetic and spectroscopic studies of HPCD have elucidated catalytic roles of several active site residues, including the crucial acid-base chemistry of His200. In the present study, reaction of the His200Cys (H200C) variant with native substrate HPCA resulted in a decrease in both kcat and the rate constants for the activation steps following O2 binding by >400 fold. The reaction proceeds to form the correct extradiol product. This slow reaction allowed a long-lived (t1/2 = 1.5 min) intermediate, H200C-HPCAInt1 (Int1), to be trapped. Mössbauer and parallel mode electron paramagnetic resonance (EPR) studies show that Int1 contains an S1 = 5/2 Fe(III) center coupled to an SR = 1/2 radical to give a ground state with total spin S = 2 (J > 40 cm(-1)) in Hexch = JŜ1·ŜR. Density functional theory (DFT) property calculations for structural models suggest that Int1 is a (HPCA semiquinone(•))Fe(III)(OOH) complex, in which OOH is protonated at the distal O and the substrate hydroxyls are deprotonated. By combining Mössbauer and EPR data of Int1 with DFT calculations, the orientations of the principal axes of the (57)Fe electric field gradient and the zero-field splitting tensors (D = 1.6 cm(-1), E/D = 0.05) were determined. This information was used to predict hyperfine splittings from bound (17)OOH. DFT reactivity analysis suggests that Int1 can evolve from a ferromagnetically coupled Fe(III)-superoxo precursor by an inner-sphere proton-coupled-electron-transfer process. Our spectroscopic and DFT results suggest that a ferric hydroperoxo species is capable of extradiol catalysis.
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Affiliation(s)
- Katlyn K Meier
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Melanie S Rogers
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Michael M Mbughuni
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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27
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Kovaleva EG, Rogers MS, Lipscomb JD. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Biochemistry 2015; 54:5329-39. [PMID: 26267790 DOI: 10.1021/acs.biochem.5b00709] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady-state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures determined at 1.35-1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild-type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second-sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in the steric bulk and charge of the residue at position 200 appear to be capable of altering the rate-limiting step in catalysis and, perhaps, the nature of the reactive species.
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Affiliation(s)
- Elena G Kovaleva
- Institute of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Melanie S Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
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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.
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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
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Bittner MM, Lindeman SV, Popescu CV, Fiedler AT. Dioxygen reactivity of biomimetic Fe(II) complexes with noninnocent catecholate, o-aminophenolate, and o-phenylenediamine ligands. Inorg Chem 2014; 53:4047-61. [PMID: 24697567 PMCID: PMC3998776 DOI: 10.1021/ic403126p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Indexed: 11/28/2022]
Abstract
This study describes the O2 reactivity of a series of high-spin mononuclear Fe(II) complexes each containing the facially coordinating tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine ((Ph2)TIP) ligand and one of the following bidentate, redox-active ligands: 4-tert-butylcatecholate ((tBu)CatH(-)), 4,6-di-tert-butyl-2-aminophenolate ((tBu2)APH(-)), or 4-tert-butyl-1,2-phenylenediamine ((tBu)PDA). The preparation and X-ray structural characterization of [Fe(2+)((Ph2)TIP)((tBu)CatH)]OTf, [3]OTf and [Fe(2+)((Ph2)TIP)((tBu)PDA)](OTf)2, [4](OTf)2 are described here, whereas [Fe(2+)((Ph2)TIP)((tBu2)APH)]OTf, [2]OTf was reported in our previous paper [Bittner et al., Chem.-Eur. J. 2013, 19, 9686-9698]. These complexes mimic the substrate-bound active sites of nonheme iron dioxygenases, which catalyze the oxidative ring-cleavage of aromatic substrates like catechols and aminophenols. Each complex is oxidized in the presence of O2, and the geometric and electronic structures of the resulting complexes were examined with spectroscopic (absorption, EPR, Mössbauer, resonance Raman) and density functional theory (DFT) methods. Complex [3]OTf reacts rapidly with O2 to yield the ferric-catecholate species [Fe(3+)((Ph2)TIP)((tBu)Cat)](+) (3(ox)), which undergoes further oxidation to generate an extradiol cleavage product. In contrast, complex [4](2+) experiences a two-electron (2e(-)), ligand-based oxidation to give [Fe(2+)((Ph2)TIP)((tBu)DIBQ)](2+) (4(ox)), where DIBQ is o-diiminobenzoquinone. The reaction of [2](+) with O2 is also a 2e(-) process, yet in this case both the Fe center and (tBu2)AP ligand are oxidized; the resulting complex (2(ox)) is best described as [Fe(3+)((Ph2)TIP)((tBu2)ISQ)](+), where ISQ is o-iminobenzosemiquinone. Thus, the oxidized complexes display a remarkable continuum of electronic structures ranging from [Fe(3+)(L(2-))](+) (3(ox)) to [Fe(3+)(L(•-))](2+) (2(ox)) to [Fe(2+)(L(0))](2+) (4(ox)). Notably, the O2 reaction rates vary by a factor of 10(5) across the series, following the order [3](+) > [2](+) > [4](2+), even though the complexes have similar structures and Fe(3+/2+) redox potentials. To account for the kinetic data, we examined the relative abilities of the title complexes to bind O2 and participate in H-atom transfer reactions. We conclude that the trend in O2 reactivity can be rationalized by accounting for the role of proton transfer(s) in the overall reaction.
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Affiliation(s)
- Michael M. Bittner
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Sergey V. Lindeman
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Codrina V. Popescu
- Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Adam T. Fiedler
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
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30
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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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Fielding AJ, Lipscomb JD, Que L. A two-electron-shell game: intermediates of the extradiol-cleaving catechol dioxygenases. J Biol Inorg Chem 2014; 19:491-504. [PMID: 24615282 DOI: 10.1007/s00775-014-1122-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/13/2014] [Indexed: 11/29/2022]
Abstract
Extradiol-cleaving catechol dioxygenases function by binding both the organic substrate and O2 at a divalent metal center in the active site. They have proven to be a particularly versatile group of enzymes with which to study the O2 activation process. Here, recent studies of homoprotocatechuate 2,3-dioxygenase are summarized, showing how nature can utilize the enzyme structure and the properties of the metal and the substrate to select among many possible chemical paths to achieve both specificity and efficiency. Possible intermediates in the mechanism have been trapped by swapping active-site metals, introducing active-site amino acid substituted variants, and using substrates with different electron-donating capacities. Although each of these intermediates could form part of a viable reaction pathway, kinetic measurements significantly limit the likely candidates. Structural, kinetic, spectroscopic, and computational analyses of the various intermediates shed light on how catalytic efficiency can be achieved.
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Affiliation(s)
- Andrew J Fielding
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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32
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Dong G, Lai W. Reaction mechanism of homoprotocatechuate 2,3-dioxygenase with 4-nitrocatechol: implications for the role of substrate. J Phys Chem B 2014; 118:1791-8. [PMID: 24467596 DOI: 10.1021/jp411812m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The reaction mechanism of the dioxygen activation by homoprotocatechuate 2,3-dioxygenase (HPCD) with the substrate 4-nitrocatechol was investigated by quantum mechanical/molecular mechanical calculations. Our results demonstrated that the experimentally determined side-on iron-oxygen complex in crystallo is a semiquinone substrate radical (SQ(•))-Fe(III)-hydroperoxo species, which could not act as the reactive species. In fact, the Fe(III)-superoxo species with a hydrogen bond between His200 and the proximal oxygen is the reactive oxygen species. The second-sphere His200 residue was found to play an important role in manipulating the orientation of the superoxide in the Fe-O2 adduct for the further reaction. The rate-limiting step is the attack of the superoxo group on the substrate with a barrier of 17.2 kcal/mol, in good agreement with the experimental value of 16.8 kcal/mol. The reaction mechanism was then compared with the one for HPCD with its native substrate homoprotocatechuate studied recently by the same methods, in which a hybrid SQ(•)-Fe(II)-O2(•-)/Fe(III)-O2(•-) was suggested to be the reactive species. Therefore, our studies suggested that the substrate plays important roles in the dioxygen activation by HPCD.
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Affiliation(s)
- Geng Dong
- Department of Chemistry, Renmin University of China , Beijing 100872, China
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33
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Barry KP, Taylor EA. Characterizing the promiscuity of LigAB, a lignin catabolite degrading extradiol dioxygenase from Sphingomonas paucimobilis SYK-6. Biochemistry 2013; 52:6724-36. [PMID: 23977959 DOI: 10.1021/bi400665t] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LigAB from Sphingomonas paucimobilis SYK-6 is the only structurally characterized dioxygenase of the largely uncharacterized superfamily of Type II extradiol dioxygenases (EDO). This enzyme catalyzes the oxidative ring-opening of protocatechuate (3,4-dihydroxybenzoic acid or PCA) in a pathway allowing the degradation of lignin derived aromatic compounds (LDACs). LigAB has also been shown to utilize two other LDACs from the same metabolic pathway as substrates, gallate, and 3-O-methyl gallate; however, kcat/KM had not been reported for any of these compounds. In order to assess the catalytic efficiency and get insights into the observed promiscuity of this enzyme, steady-state kinetic analyses were performed for LigAB with these and a library of related compounds. The dioxygenation of PCA by LigAB was highly efficient, with a kcat of 51 s(-1) and a kcat/KM of 4.26 × 10(6) M(-1)s(-1). LigAB demonstrated the ability to use a variety of catecholic molecules as substrates beyond the previously identified gallate and 3-O-methyl gallate, including 3,4-dihydroxybenzamide, homoprotocatechuate, catechol, and 3,4-dihydroxybenzonitrile. Interestingly, 3,4-dihydroxybenzamide (DHBAm) behaves in a manner similar to that of the preferred benzoic acid substrates, with a kcat/Km value only ∼4-fold lower than that for gallate and ∼10-fold higher than that for 3-O-methyl gallate. All of these most active substrates demonstrate mechanistic inactivation of LigAB. Additionally, DHBAm exhibits potent product inhibition that leads to an inactive enzyme, being more highly deactivating at lower substrate concentration, a phenomena that, to our knowledge, has not been reported for another dioxygenase substrate/product pair. These results provide valuable catalytic insight into the reactions catalyzed by LigAB and make it the first Type II EDO that is fully characterized both structurally and kinetically.
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Affiliation(s)
- Kevin P Barry
- Department of Chemistry, Wesleyan University , 52 Lawn Avenue, Middletown, Connecticut 06459, United States
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Bittner MM, Kraus D, Lindeman SV, Popescu CV, Fiedler AT. Synthetic, spectroscopic, and DFT studies of iron complexes with iminobenzo(semi)quinone ligands: implications for o-aminophenol dioxygenases. Chemistry 2013; 19:9686-98. [PMID: 23744733 PMCID: PMC3965334 DOI: 10.1002/chem.201300520] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/17/2013] [Indexed: 11/10/2022]
Abstract
The oxidative C-C bond cleavage of o-aminophenols by nonheme Fe dioxygenases is a critical step in both human metabolism (the kynurenine pathway) and the microbial degradation of nitroaromatic pollutants. The catalytic cycle of o-aminophenol dioxygenases (APDOs) has been proposed to involve formation of an Fe(II)/O2/iminobenzosemiquinone complex, although the presence of a substrate radical has been called into question by studies of related ring-cleaving dioxygenases. Recently, we reported the first synthesis of an iron(II) complex coordinated to an iminobenzosemiquinone (ISQ) ligand, namely, [Fe((Ph2)Tp)((tBu)ISQ)] (2a; where (Ph2)Tp=hydrotris(3,5-diphenylpyrazol-1-yl)borate and (tBu)ISQ is the radical anion derived from 2-amino-4,6-di-tert-butylphenol). In the current manuscript, density functional theory (DFT) calculations and a wide variety of spectroscopic methods (electronic absorption, Mössbauer, magnetic circular dichroism, and resonance Raman) were employed to obtain detailed electronic-structure descriptions of 2a and its one-electron oxidized derivative [3a](+). In addition, we describe the synthesis and characterization of a parallel series of complexes featuring the neutral supporting ligand tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine ((Ph2)TIP). The isomer shifts of about 0.97 mm s(-1) obtained through Mössbauer experiments confirm that 2a (and its (Ph2)TIP-based analogue [2b](+)) contain Fe(II) centers, and the presence of an ISQ radical was verified by analysis of the absorption spectra in light of time-dependent DFT calculations. The collective spectroscopic data indicate that one-electron oxidation of the Fe(II)-ISQ complexes yields complexes ([3a](+) and [3b](2+)) with electronic configurations between the Fe(III)-ISQ and Fe(II)-IBQ limits (IBQ=iminobenzoquinone), highlighting the ability of o-amidophenolates to access multiple oxidation states. The implications of these results for the mechanism of APDOs and other ring-cleaving dioxygenases are discussed.
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Affiliation(s)
- Michael M. Bittner
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - David Kraus
- Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Sergey V. Lindeman
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Codrina V. Popescu
- Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Adam T. Fiedler
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
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Hayden JA, Farquhar ER, Que L, Lipscomb JD, Hendrich MP. NO binding to Mn-substituted homoprotocatechuate 2,3-dioxygenase: relationship to O₂ reactivity. J Biol Inorg Chem 2013; 18:717-28. [PMID: 23824380 DOI: 10.1007/s00775-013-1016-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
Iron(II)-containing homoprotocatechuate 2,3-dioxygenase (FeHPCD) activates O2 to catalyze the aromatic ring opening of homoprotocatechuate (HPCA). The enzyme requires Fe(II) for catalysis, but Mn(II) can be substituted (MnHPCD) with essentially no change in the steady-state kinetic parameters. Near simultaneous O2 and HPCA activation has been proposed to occur through transfer of an electron or electrons from HPCA to O2 through the divalent metal. In O2 reactions with MnHPCD-HPCA and the 4-nitrocatechol (4NC) complex of the His200Asn (H200N) variant of FeHPCD, this transfer has resulted in the detection of a transient M(III)-O2 (·-) species that is not observed during turnover of the wild-type FeHPCD. The factors governing formation of the M(III)-O2 (·-) species are explored here by EPR spectroscopy using MnHPCD and nitric oxide (NO) as an O2 surrogate. Both the HPCA and the dihydroxymandelic substrate complexes of MnHPCD bind NO, thus representing the first reported stable MnNO complexes of a nonheme enzyme. In contrast, the free enzyme, the MnHPCD-4NC complex, and the MnH200N and MnH200Q variants with or without HPCA bound do not bind NO. The MnHPCD-ligand complexes that bind NO are also active in normal O2-linked turnover, whereas the others are inactive. Past studies have shown that FeHPCD and the analogous variants and catecholic ligand complexes all bind NO, and are active in normal turnover. This contrasting behavior may stem from the ability of the enzyme to maintain the approximately 0.8-V difference in the solution redox potentials of Fe(II) and Mn(II). Owing to the higher potential of Mn, the formation of the NO adduct or the O2 adduct requires both strong charge donation from the bound catecholic ligand and additional stabilization by interaction with the active-site His200. The same nonoptimal electronic and structural forces that prevent NO and O2 binding in MnHPCD variants may lead to inefficient electron transfer from the catecholic substrate to the metal center in variants of FeHPCD during O2-linked turnover. Accordingly, past studies have shown that intermediate Fe(III) species are observed for these mutant enzymes.
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Affiliation(s)
- Joshua A Hayden
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
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36
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Escherichia coli protein YgiD produces the structural unit of plant pigments betalains: characterization of a prokaryotic enzyme with DOPA-extradiol-dioxygenase activity. Appl Microbiol Biotechnol 2013; 98:1165-74. [DOI: 10.1007/s00253-013-4961-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 01/09/2023]
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37
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Dong G, Shaik S, Lai W. Oxygen activation by homoprotocatechuate 2,3-dioxygenase: a QM/MM study reveals the key intermediates in the activation cycle. Chem Sci 2013. [DOI: 10.1039/c3sc51147b] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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38
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Kovaleva EG, Lipscomb JD. Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Biochemistry 2012; 51:8755-63. [PMID: 23066739 DOI: 10.1021/bi301115c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Homoprotocatechuate 2,3-dioxygenase (FeHPCD) utilizes an active site Fe(II) to activate O(2) in a reaction cycle that ultimately results in aromatic ring cleavage. Here, the roles of the conserved active site residue Tyr257 are investigated by solving the X-ray crystal structures of the Tyr257-to-Phe variant (Y257F) in complex with the substrate homoprotocatechuate (HPCA) and the alternative substrate 4-nitrocatechol (4NC). These are compared with structures of the analogous wild type enzyme complexes. In addition, the oxy intermediate of the reaction cycle of Y257F-4NC + O(2) is formed in crystallo and structurally characterized. It is shown that both substrates adopt a previously unrecognized, slightly nonplanar, strained conformation affecting the geometries of all aromatic ring carbons when bound in the FeHPCD active site. This global deviation from planarity is not observed for the Y257F variant. In the Y257F-4NC-oxy complex, the O(2) is bound side-on to the Fe(II), while the 4NC is chelated in two adjacent sites. The ring of the 4NC in this complex is planar, in contrast to the equivalent FeHPCD intermediate, which exhibits substantial local distortion of the substrate hydroxyl moiety (C2-O(-)) that is hydrogen bonded to Tyr257. We propose that Tyr257 induces the global and local distortions of the substrate ring in two different ways. First, van der Waals conflict between the Tyr257-OH substituent and the substrate C2 carbon is relieved by adopting the globally strained structure. Second, Tyr257 stabilizes the localized out-of-plane position of the C2-O(-) by forming a stronger hydrogen bond as the distortion increases. Both types of distortions favor transfer of one electron out of the substrate to form a reactive semiquinone radical. Then, the localized distortion at substrate C2 promotes formation of the key alkylperoxo intermediate of the cycle resulting from oxygen attack on the activated substrate at C2, which becomes sp(3) hybridized. The inability of Y257F to promote the distorted substrate structure may explain the observed 100-fold decrease in the rates of the O(2) activation and insertion steps of the reaction.
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Affiliation(s)
- Elena G Kovaleva
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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39
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Mbughuni MM, Meier KK, Münck E, Lipscomb JD. Substrate-mediated oxygen activation by homoprotocatechuate 2,3-dioxygenase: intermediates formed by a tyrosine 257 variant. Biochemistry 2012; 51:8743-54. [PMID: 23066705 DOI: 10.1021/bi301114x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homoprotocatechuate (HPCA; 3,4-dihydroxyphenylacetate or 4-carboxymethyl catechol) and O(2) bind in adjacent ligand sites of the active site Fe(II) of homoprotocatechuate 2,3-dioxygenase (FeHPCD). We have proposed that electron transfer from the chelated aromatic substrate through the Fe(II) to O(2) gives both substrates radical character. This would promote reaction between the substrates to form an alkylperoxo intermediate as the first step in aromatic ring cleavage. Several active site amino acids are thought to promote these reactions through acid/base chemistry, hydrogen bonding, and electrostatic interactions. Here the role of Tyr257 is explored by using the Tyr257Phe (Y257F) variant, which decreases k(cat) by about 75%. The crystal structure of the FeHPCD-HPCA complex has shown that Tyr257 hydrogen bonds to the deprotonated C2-hydroxyl of HPCA. Stopped-flow studies show that at least two reaction intermediates, termed Y257F(Int1)(HPCA) and Y257F(Int2)(HPCA), accumulate during the Y257F-HPCA + O(2) reaction prior to formation of the ring-cleaved product. Y257F(Int1)(HPCA) is colorless and is formed as O(2) binds reversibly to the HPCA−enzyme complex. Y257F(Int2)(HPCA) forms spontaneously from Y257F(Int1)(HPCA) and displays a chromophore at 425 nm (ε(425) = 10 500 M(−1) cm(−1)). Mössbauer spectra of the intermediates trapped by rapid freeze quench show that both intermediates contain Fe(II). The lack of a chromophore characteristic of a quinone or semiquinone form of HPCA, the presence of Fe(II), and the low O(2) affinity suggest that Y257F(Int1)(HPCA) is an HPCA-Fe(II)-O(2) complex with little electron delocalization onto the O(2). In contrast, the intense spectrum of Y257F(Int2)(HPCA) suggests the intermediate is most likely an HPCA quinone-Fe(II)-(hydro)peroxo species. Steady-state and transient kinetic analyses show that steps of the catalytic cycle are slowed by as much as 100-fold by the mutation. These effects can be rationalized by a failure of Y257F to facilitate the observed distortion of the bound HPCA that is proposed to promote transfer of one electron to O(2).
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Affiliation(s)
- Michael M Mbughuni
- Department of Biochemistry, Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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40
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Cotruvo JA, Stubbe J. Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study. Metallomics 2012; 4:1020-36. [PMID: 22991063 PMCID: PMC3488304 DOI: 10.1039/c2mt20142a] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
How cells ensure correct metallation of a given protein and whether a degree of promiscuity in metal binding has evolved are largely unanswered questions. In a classic case, iron- and manganese-dependent superoxide dismutases (SODs) catalyze the disproportionation of superoxide using highly similar protein scaffolds and nearly identical active sites. However, most of these enzymes are active with only one metal, although both metals can bind in vitro and in vivo. Iron(ii) and manganese(ii) bind weakly to most proteins and possess similar coordination preferences. Their distinct redox properties suggest that they are unlikely to be interchangeable in biological systems except when they function in Lewis acid catalytic roles, yet recent work suggests this is not always the case. This review summarizes the diversity of ways in which iron and manganese are substituted in similar or identical protein frameworks. As models, we discuss (1) enzymes, such as epimerases, thought to use Fe(II) as a Lewis acid under normal growth conditions but which switch to Mn(II) under oxidative stress; (2) extradiol dioxygenases, which have been found to use both Fe(II) and Mn(II), the redox role of which in catalysis remains to be elucidated; (3) SODs, which use redox chemistry and are generally metal-specific; and (4) the class I ribonucleotide reductases (RNRs), which have evolved unique biosynthetic pathways to control metallation. The primary focus is the class Ib RNRs, which can catalyze formation of a stable radical on a tyrosine residue in their β2 subunits using either a di-iron or a recently characterized dimanganese cofactor. The physiological roles of enzymes that can switch between iron and manganese cofactors are discussed, as are insights obtained from the studies of many groups regarding iron and manganese homeostasis and the divergent and convergent strategies organisms use for control of protein metallation. We propose that, in many of the systems discussed, "discrimination" between metals is not performed by the protein itself, but it is instead determined by the environment in which the protein is expressed.
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Affiliation(s)
- Joseph A. Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.; Fax: +1 617 324-0505; Tel: +1 617 253-1814
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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Rose MJ, Bellone DE, Di Bilio AJ, Gray HB. Spectroscopic and magnetic properties of an iodo Co(I) tripodal phosphine complex. Dalton Trans 2012; 41:11788-97. [PMID: 22903546 DOI: 10.1039/c2dt31229h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction of the tripodal phosphine ligand 1,1,1-tris((diphenylphosphino)phenyl)ethane (PhP3) with CoI(2) spontaneously generates a one-electron reduced complex, [(PhP3)Co(I)(I)] (1). The crystal structure of 1 reveals a distorted tetrahedral environment, with an apical Co-I bond distance of ~2.52 Å. Co(II/I) redox occurs at an unusually high potential (+0.38 V vs. SCE). The electronic absorption spectrum of 1 exhibits an MLCT peak at 320 nm (ε = 8790 M(-1) cm(-1)) and a d-d feature at 850 nm (ε = 840 M(-1) cm(-1)). Two more d-d bands are observed in the NIR region, 8650 (ε = 450) and 7950 cm(-1) (ε = 430 M(-1) cm(-1)). Temperature dependent magnetic measurements (SQUID) on 1 (solid state, 20-300 K) give μ(eff) = 2.99(6) μ(B), consistent with an S = 1 ground state. Magnetic susceptibilities below 20 K are consistent with a zero field splitting (zfs) |D| = 8 cm(-1). DFT calculations also support a spin-triplet ground state for 1, as optimized (6-31G*/PW91) geometries (S = 1) closely match the X-ray structure. EPR measurements performed in parallel mode (X-band; 0-15,000 G, 15 K) on polycrystalline 1 or frozen solutions of 1 (THF/toluene) exhibit a feature at g≈ 4 that arises from a (Δm = 2) transition within the M(S) = <+1,-1> manifold. Below 10 K, the EPR signal decreases significantly, consistent with a solution zfs parameter (|D|≈ 8 cm(-1)) similar to that obtained from SQUID measurements. Our work provides an EPR signature for high-spin Co(I) in trigonal ligation.
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Affiliation(s)
- Michael J Rose
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Chen H, Cho KB, Lai W, Nam W, Shaik S. Dioxygen Activation by a Non-Heme Iron(II) Complex: Theoretical Study toward Understanding Ferric–Superoxo Complexes. J Chem Theory Comput 2012; 8:915-26. [DOI: 10.1021/ct300015y] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hui Chen
- Beijing National Laboratory for Molecular
Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Kyung-Bin Cho
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Wenzhen Lai
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry
and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
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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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Christian GJ, Ye S, Neese F. Oxygen activation in extradiol catecholate dioxygenases – a density functional study. Chem Sci 2012. [DOI: 10.1039/c2sc00754a] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Fielding AJ, Lipscomb JD, Que L. Characterization of an O2 adduct of an active cobalt-substituted extradiol-cleaving catechol dioxygenase. J Am Chem Soc 2011; 134:796-9. [PMID: 22175783 DOI: 10.1021/ja2095365] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first example of an O(2) adduct of an active Co-substituted oxygenase has been observed in the extradiol ring cleavage of the electron-poor substrate 4-nitrocatechol (4NC) by Co(II)-homoprotocatechuate 2,3-dioxygenase (Co-HPCD). Upon O(2) binding to the high-spin Co(II) (S = (3)/(2)) enzyme-substrate complex, an S = (1)/(2) EPR signal exhibiting (59)Co hyperfine splitting (A = 24 G) typical of a low-spin Co(III)-superoxide complex was observed. Both the formation and decay of the new intermediate are very slow in comparison to the analogous steps for turnover of 4NC by native high-spin Fe(II)-HPCD, which is likely to remain high-spin upon O(2) binding. A similar but effectively stable S = (1)/(2) intermediate was formed by the inactive [H200N-Co-HPCD(4NC)] variant. The observations presented shed light on the key roles played by the substrate, the second-sphere His200 residue, and the spin state of the metal center in facilitating O(2) binding and activation.
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Affiliation(s)
- Andrew J Fielding
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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