1
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Gable JA, Poulos TL, Follmer AH. Redox partner recognition and selectivity of cytochrome P450lin (CYP111A1). J Inorg Biochem 2023; 244:112212. [PMID: 37058990 PMCID: PMC10519177 DOI: 10.1016/j.jinorgbio.2023.112212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 04/16/2023]
Abstract
The strict requirement of cytochrome P450cam for its native ferredoxin redox partner, putidaredoxin (Pdx), is not exhibited by any other known cytochrome P450 (CYP) system and the molecular details of redox partner selectivity are still not completely understood. We therefore examined the selectivity of a related Pseudomonas cytochrome P450, P450lin, by testing its activity with non-native redox partners. We found that P450lin could utilize Arx, the native redox partner of CYP101D1, to enable turnover of its substrate, linalool, while Pdx showed limited activity. Arx exhibited a higher sequence similarity to P450lins native redox partner, linredoxin (Ldx) than Pdx, including several residues that are believed to be at the interface of the two proteins, based on the P450cam-Pdx complex structure. We therefore mutated Pdx to resemble Ldx and Arx and found that a double mutant, D38L/∆106, displayed higher activity than Arx. In addition, Pdx D38L/∆106 does not induce a low-spin shift in linalool bound P450lin but does destabilize the P450lin-oxycomplex. Together our results suggest that P450lin and its redox partners may form a similar interface to P450cam-Pdx, but the interactions that allow for productive turnover are different.
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Affiliation(s)
- Jessica A Gable
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Thomas L Poulos
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Alec H Follmer
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.
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2
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Skinner SP, Follmer AH, Ubbink M, Poulos TL, Houwing-Duistermaat JJ, Paci E. Partial Opening of Cytochrome P450cam (CYP101A1) Is Driven by Allostery and Putidaredoxin Binding. Biochemistry 2021; 60:2932-2942. [PMID: 34519197 DOI: 10.1021/acs.biochem.1c00406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the regio- and stereo-specific 5-exo-hydroxylation of camphor via a multistep catalytic cycle that involves two-electron transfer steps, with an absolute requirement that the second electron be donated by the ferrodoxin, putidaredoxin (Pdx). Whether P450cam, once camphor has bound to the active site and the substrate entry channel has closed, opens up upon Pdx binding, during the second electron transfer step, or it remains closed is still a matter of debate. A potential allosteric site for camphor binding has been identified and postulated to play a role in the binding of Pdx. Here, we have revisited paramagnetic NMR spectroscopy data and determined a heterogeneous ensemble of structures that explains the data, provides a complete representation of the P450cam/Pdx complex in solution, and reconciles alternative hypotheses. The allosteric camphor binding site is always present, and the conformational changes induced by camphor binding to this site facilitates Pdx binding. We also determined that the state to which Pdx binds comprises an ensemble of structures that have features of both the open and closed state. These results demonstrate that there is a finely balanced interaction between allosteric camphor binding and the binding of Pdx at high camphor concentrations.
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Affiliation(s)
- Simon P Skinner
- School of Molecular and Cell Biology and Astbury Centre, University of Leeds, Leeds LS2 9JT, U.K
| | - Alec H Follmer
- Department of Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Thomas L Poulos
- Department of Chemistry, University of California, Irvine, California 92697-3900, United States.,Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3900, United States
| | | | - Emanuele Paci
- School of Molecular and Cell Biology and Astbury Centre, University of Leeds, Leeds LS2 9JT, U.K
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3
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Zhan J, Shou C, Zheng Y, Chen Q, Pan J, Li C, Xu J. Discovery and Engineering of Bacterial (−)‐Isopiperitenol Dehydrogenases to Enhance (−)‐Menthol Precursor Biosynthesis. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jing‐Ru Zhan
- Laboratory of Biocatalysis and Synthetic Biotechnology State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Chao Shou
- Laboratory of Biocatalysis and Synthetic Biotechnology State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Yu‐Cong Zheng
- Laboratory of Biocatalysis and Synthetic Biotechnology State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Qi Chen
- Laboratory of Biocatalysis and Synthetic Biotechnology State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Center for Biomanufacturing School of Biotechnology East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Jiang Pan
- Laboratory of Biocatalysis and Synthetic Biotechnology State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Center for Biomanufacturing School of Biotechnology East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Chun‐Xiu Li
- Laboratory of Biocatalysis and Synthetic Biotechnology State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Center for Biomanufacturing School of Biotechnology East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
| | - Jian‐He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
- Shanghai Collaborative Innovation Center for Biomanufacturing School of Biotechnology East China University of Science and Technology 130 Meilong Road Shanghai 200237 People's Republic of China
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4
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Sushko T, Kavaleuski A, Grabovec I, Kavaleuskaya A, Vakhrameev D, Bukhdruker S, Marin E, Kuzikov A, Masamrekh R, Shumyantseva V, Tsumoto K, Borshchevskiy V, Gilep A, Strushkevich N. A new twist of rubredoxin function in M. tuberculosis. Bioorg Chem 2021; 109:104721. [PMID: 33618255 DOI: 10.1016/j.bioorg.2021.104721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/19/2021] [Accepted: 02/02/2021] [Indexed: 11/27/2022]
Abstract
Electron transfer mediated by metalloproteins drives many biological processes. Rubredoxins are a ubiquitous [1Fe-0S] class of electron carriers that play an important role in bacterial adaptation to changing environmental conditions. In Mycobacterium tuberculosis, oxidative and acidic stresses as well as iron starvation induce rubredoxins expression. However, their functions during M. tuberculosis infection are unknown. In the present work, we show that rubredoxin B (RubB) is able to efficiently shuttle electrons from cognate reductases, FprA and FdR to support catalytic activity of cytochrome P450s, CYP124, CYP125, and CYP142, which are important for bacterial viability and pathogenicity. We solved the crystal structure of RubB and characterized the interaction between RubB and CYPs using site-directed mutagenesis. Mutations that not only neutralize single charge but also change the specific residues on the surface of RubB did not dramatically decrease activity of studied CYPs. Together with isothermal calorimetry (ITC) experiments, the obtained results suggest that interactions are transient and not highly specific. The redox potential of RubB is -264 mV vs. Ag/AgCl and the measured extinction coefficients are 9931 M-1cm-1 and 8371 M-1cm-1 at 380 nm and 490 nm, respectively. Characteristic parameters of RubB along with the discovered function might be useful for biotechnological applications. Our findings suggest that a switch from ferredoxins to rubredoxins might be crucial for M. tuberculosis to support CYPs activity during the infection.
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Affiliation(s)
- Tatsiana Sushko
- The Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Anton Kavaleuski
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Anna Kavaleuskaya
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Daniil Vakhrameev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; ESRF - The European Synchrotron, 38000 Grenoble, France
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia
| | - Alexey Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - Rami Masamrekh
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - Victoria Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - Kouhei Tsumoto
- The Institute of Medical Science, the University of Tokyo, Tokyo, Japan; Department of Bioengineering, School of Engineering, the University of Tokyo, Tokyo, Japan
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow, Institute of Physics and Technology (MIPT), Dolgoprudny, Russia; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus; Institute of Biomedical Chemistry, Moscow, Russia
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5
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Murarka VC, Batabyal D, Amaya JA, Sevrioukova IF, Poulos TL. Unexpected Differences between Two Closely Related Bacterial P450 Camphor Monooxygenases. Biochemistry 2020; 59:2743-2750. [PMID: 32551522 DOI: 10.1021/acs.biochem.0c00366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The bacterial cytochrome P450cam catalyzes the oxidation of camphor to 5-exo-hydroxycamphor as the first step in the oxidative assimilation of camphor as a carbon/energy source. CYP101D1 is another bacterial P450 that catalyzes the same reaction. A third P450 (P450tcu) has recently been discovered that has ≈86% sequence identity to P450cam as well as very similar enzymatic properties. P450tcu, however, exhibits three unusual features not found in P450cam. First, we observe product in at least two orientations in the X-ray structure that indicates that, unlike the case for P450cam, X-ray-generated reducing equivalents can drive substrate hydroxylation in crystallo. We postulate, on the basis of molecular dynamics simulations, that greater flexibility in P450tcu enables easier access of protons to the active site and, together with X-ray driven reduction, results in O2 activation and substrate hydroxylation. Second, the characteristic low-spin to high-spin transition when camphor binds occurs immediately with P450cam but is very slow in P450tcu. Third, isothermal titration calorimetry shows that in P450cam substrate binding is entropically driven with a ΔH of >0 while in P450tcu with a ΔH of <0 with a more modest change in -TΔS. These results indicate that despite nearly identical structures and enzymatic properties, these two P450s exhibit quite different properties most likely related to differences in conformational dynamics.
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Affiliation(s)
- Vidhi C Murarka
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Jose A Amaya
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Irina F Sevrioukova
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
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6
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Amaya JA, Batabyal D, Poulos TL. Proton Relay Network in the Bacterial P450s: CYP101A1 and CYP101D1. Biochemistry 2020; 59:2896-2902. [DOI: 10.1021/acs.biochem.0c00329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- José A. Amaya
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
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7
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Liou SH, Chuo SW, Qiu Y, Wang LP, Goodin DB. Linkage between Proximal and Distal Movements of P450cam Induced by Putidaredoxin. Biochemistry 2020; 59:2012-2021. [PMID: 32369344 PMCID: PMC9749489 DOI: 10.1021/acs.biochem.0c00294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Putidaredoxin (Pdx) is the exclusive reductase and a structural effector for P450cam (CYP101A1). However, the mechanism of how Pdx modulates the conformational states of P450cam remains elusive. Here we report a putative communication pathway for the Pdx-induced conformational change in P450cam using results of double electron-electron resonance (DEER) spectroscopy and molecular dynamics simulations. Use of solution state DEER measurements allows us to observe subtle conformational changes in the internal helices in P450cam among closed, open, and P450cam-Pdx complex states. Molecular dynamics simulations and dynamic network analysis suggest that Pdx binding is coupled to small coordinated movements of several regions of P450cam, including helices C, B', I, G, and F. These changes provide a linkage between the Pdx binding site on the proximal side of the enzyme and helices F/G on the distal side and the site of the largest movement resulting from the Pdx-induced closed-to-open transition. This study provides a detailed rationale for how Pdx exerts its long-recognized effector function at the active site from its binding site on the opposite face of the enzyme.
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Affiliation(s)
| | | | - Yudong Qiu
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - David B. Goodin
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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8
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Erdogan H. One small step for cytochrome P450 in its catalytic cycle, one giant leap for enzymology. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The intermediates operating in the cytochrome P450 catalytic cycle have been investigated for more than half a century, fascinating many enzymologists. Each intermediate has its unique role to carry out diverse oxidations. Natural time course of the catalytic cycle is quite fast, hence, not all of the reactive intermediates could be isolated during physiological catalysis. Different high-valent iron intermediates have been proposed as primary oxidants: the candidates are compound 0 (Cpd 0, [FeOOH][Formula: see text]P450) and compound I (Cpd I, Fe(IV)[Formula: see text]O por[Formula: see text]P450). Among them, the role of Cpd I in hydroxylation is fairly well understood due the discovery of the peroxide shunt. This review endeavors to put the outstanding research efforts conducted to isolate and characterize the intermediates together. In addition to spectral features of each intermediate in the catalytic cycle, the oxidizing powers of Cpd 0 and Cpd I will be discussed along with most recent scientific findings.
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Affiliation(s)
- Huriye Erdogan
- Department of Chemistry, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
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9
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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10
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Ramos S, Basom EJ, Thielges MC. Conformational Change Induced by Putidaredoxin Binding to Ferrous CO-ligated Cytochrome P450cam Characterized by 2D IR Spectroscopy. Front Mol Biosci 2018; 5:94. [PMID: 30483514 PMCID: PMC6243089 DOI: 10.3389/fmolb.2018.00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 11/16/2022] Open
Abstract
The importance of conformational dynamics to protein function is now well-appreciated. An outstanding question is whether they are involved in the effector role played by putidaredoxin (Pdx) in its reduction of the O2 complex of cytochrome P450cam (P450cam), an archetypical member of the cytochrome P450 superfamily. Recent studies have reported that binding of Pdx induces a conformational change from a closed to an open state of ferric P450cam, but a similar conformational change does not appear to occur for the ferrous, CO-ligated enzyme. To better understand the effector role of Pdx when binding the ferrous, CO-ligated P450cam, we applied 2D IR spectroscopy to compare the conformations and dynamics of the wild-type (wt) enzyme in the absence and presence of Pdx, as well as of L358P P450cam (L358P), which has served as a putative model for the Pdx complex. The CO vibrations of the Pdx complex and L358P report population of two conformational states in which the CO experiences distinct environments. The dynamics among the CO frequencies indicate that the energy landscape of substates within one conformation are reflective of the closed state of P450cam, and for the other conformation, differ from the free wt enzyme, but are equivalent between the Pdx complex and L358P. The two states co-populated by the Pdx complex are postulated to reflect a loosely bound encounter complex and a more tightly bound state, as is commonly observed for the dynamic complexes of redox partners. Significantly, this study shows that the binding of Pdx to ferrous, CO-ligated P450cam does perturb the conformational ensemble in a way that might underlie the effector role of Pdx.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Edward J Basom
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN, United States
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11
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Follmer AH, Mahomed M, Goodin DB, Poulos TL. Substrate-Dependent Allosteric Regulation in Cytochrome P450cam (CYP101A1). J Am Chem Soc 2018; 140:16222-16228. [DOI: 10.1021/jacs.8b09441] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alec H. Follmer
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Mavish Mahomed
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - David B. Goodin
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
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12
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Parisi G, Montemiglio LC, Giuffrè A, Macone A, Scaglione A, Cerutti G, Exertier C, Savino C, Vallone B. Substrate-induced conformational change in cytochrome P450 OleP. FASEB J 2018; 33:1787-1800. [PMID: 30207799 DOI: 10.1096/fj.201800450rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The regulation of cytochrome P450 activity is often achieved by structural transitions induced by substrate binding. We describe the conformational transition experienced upon binding by the P450 OleP, an epoxygenase involved in oleandomycin biosynthesis. OleP bound to the substrate analog 6DEB crystallized in 2 forms: one with an ensemble of open and closed conformations in the asymmetric unit and another with only the closed conformation. Characterization of OleP-6DEB binding kinetics, also using the P450 inhibitor clotrimazole, unveiled a complex binding mechanism that involves slow conformational rearrangement with the accumulation of a spectroscopically detectable intermediate where 6DEB is bound to open OleP. Data reported herein provide structural snapshots of key precatalytic steps in the OleP reaction and explain how structural rearrangements induced by substrate binding regulate activity.-Parisi, G., Montemiglio, L. C., Giuffrè, A., Macone, A., Scaglione, A., Cerutti, G., Exertier, C., Savino, C., Vallone, B. Substrate-induced conformational change in cytochrome P450 OleP.
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Affiliation(s)
- Giacomo Parisi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Linda Celeste Montemiglio
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Alessandro Giuffrè
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Alberto Macone
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Antonella Scaglione
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Gabriele Cerutti
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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13
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Haga T, Hirakawa H, Nagamune T. Artificial Self‐Sufficient Cytochrome P450 Containing Multiple Auxiliary Proteins Demonstrates Improved Monooxygenase Activity. Biotechnol J 2018; 13:e1800088. [DOI: 10.1002/biot.201800088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Tomoaki Haga
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Teruyuki Nagamune
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
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14
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Batabyal D, Poulos TL. Effect of redox partner binding on CYP101D1 conformational dynamics. J Inorg Biochem 2018; 183:179-183. [PMID: 29550100 PMCID: PMC5976445 DOI: 10.1016/j.jinorgbio.2018.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/13/2018] [Accepted: 02/18/2018] [Indexed: 11/27/2022]
Abstract
We have compared the thermodynamics of substrate and redox partner binding of P450cam to its close homologue, CYP101D1, using isothermal titration calorimetry (ITC). CYP101D1 binds camphor about 10-fold more weakly than P450cam which is consistent with the inability of camphor to cause a complete low- to high-spin shift in CYP101D1. Even so molecular dynamics simulations show that camphor is very stable in the CYP101D1 active site similar to P450cam. ITC data on the binding of the CYP101D1 ferredoxin redox partner (abbreviated Arx) shows that the substrate-bound closed state of CYP101D1 binds Arx more tightly than the substrate-free open form. This is just the opposite to P450cam where Pdx (ferredoxin redox partner of P450cam) favors binding to the P450cam open state. In addition, CYP101D1-Arx binding has a large negative ΔS while the P450cam-Pdx has a much smaller ΔS indicating that interactions at the docking interface are different. The most obvious difference is that PDXD38 which forms an important ion pair with P450camR112 at the center of the interface is ArxL39 in Arx. This suggests that Arx may adopt a different orientation than Pdx in order to optimize nonpolar interactions with ArxL39.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900, USA
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900, USA.
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15
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Mao Z, Liou SH, Khadka N, Jenney FE, Goodin DB, Seefeldt LC, Adams MWW, Cramer SP, Larsen DS. Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins. Biochemistry 2018; 57:978-990. [PMID: 29303562 DOI: 10.1021/acs.biochem.7b01159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin, the 2Fe-2S cluster in Pseudomonas putida putidaredoxin, the 4Fe-4S cluster in nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein. Laser excitation promotes the iron-sulfur clusters to excited electronic states that relax to lower states. The electronic relaxation lifetimes of the 1Fe-4S, 8Fe-7S, and 7Fe-9S-1Mo clusters are on the picosecond time scale, although the dynamics of the MoFe protein is a mixture of the dynamics of the latter two clusters. The lifetimes of the 2Fe-2S and 4Fe-4S clusters, however, extend to several nanoseconds. A competition between reorganization energies and the density of electronic states (thus electronic coupling between states) mediates the charge-transfer lifetimes, with the 2Fe-2S cluster of Pdx and the 4Fe-4S cluster of Fe protein lying at the optimum leading to them having significantly longer lifetimes. Their long lifetimes make them the optimal candidates for long-range electron transfer and as external photosensitizers for other photoactivated chemical reactions like solar hydrogen production. Potential electron-transfer and hole-transfer pathways that possibly facilitate these charge transfers are proposed.
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Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Shu-Hao Liou
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine , Suwanee, Georgia 30024, United States
| | - David B Goodin
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Michael W W Adams
- Department of Biochemistry, The University of Georgia , Athens, Georgia 30602, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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17
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Erdogan H, Vandemeulebroucke A, Nauser T, Bounds PL, Koppenol WH. Jumpstarting the cytochrome P450 catalytic cycle with a hydrated electron. J Biol Chem 2017; 292:21481-21489. [PMID: 29109145 DOI: 10.1074/jbc.m117.813683] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/25/2017] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450cam (CYP101Fe3+) regioselectively hydroxylates camphor. Possible hydroxylating intermediates in the catalytic cycle of this well-characterized enzyme have been proposed on the basis of experiments carried out at very low temperatures and shunt reactions, but their presence has not yet been validated at temperatures above 0 °C during a normal catalytic cycle. Here, we demonstrate that it is possible to mimic the natural catalytic cycle of CYP101Fe3+ by using pulse radiolysis to rapidly supply the second electron of the catalytic cycle to camphor-bound CYP101[FeO2]2+ Judging by the appearance of an absorbance maximum at 440 nm, we conclude that CYP101[FeOOH]2+ (compound 0) accumulates within 5 μs and decays rapidly to CYP101Fe3+, with a k440 nm of 9.6 × 104 s-1 All processes are complete within 40 μs at 4 °C. Importantly, no transient absorbance bands could be assigned to CYP101[FeO2+por•+] (compound 1) or CYP101[FeO2+] (compound 2). However, indirect evidence for the involvement of compound 1 was obtained from the kinetics of formation and decay of a tyrosyl radical. 5-Hydroxycamphor was formed quantitatively, and the catalytic activity of the enzyme was not impaired by exposure to radiation during the pulse radiolysis experiment. The rapid decay of compound 0 enabled calculation of the limits for the Gibbs activation energies for the conversions of compound 0 → compound 1 → compound 2 → CYP101Fe3+, yielding a ΔG‡ of 45, 39, and 39 kJ/mol, respectively. At 37 °C, the steps from compound 0 to the iron(III) state would take only 4 μs. Our kinetics studies at 4 °C complement the canonical mechanism by adding the dimension of time.
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Affiliation(s)
| | - An Vandemeulebroucke
- Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland
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18
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Batabyal D, Richards LS, Poulos TL. Effect of Redox Partner Binding on Cytochrome P450 Conformational Dynamics. J Am Chem Soc 2017; 139:13193-13199. [PMID: 28823160 DOI: 10.1021/jacs.7b07656] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Previous crystal structures of cytochrome P450cam complexed with its redox partner, putidaredoxin (Pdx), shows that P450cam adopts the open conformation. It has been hypothesized that the Pdx-induced shift toward the open state frees the essential Asp251 from salt bridges with Arg186 and Lys178 so that Asp251 can participate in a proton relay network required for O2 activation. This in part explains why P450cam has such a strict requirement for Pdx. One problem with this view is that looser substrate-protein interactions in the open state may not be compatible with the observed regio- and stereoselective hydroxylation. In the present study, molecular dynamics simulations show that Pdx binding favors a conformation that stabilizes the active site and decreases camphor mobility yet retains a partially open conformation compatible with the required proton relay network. The R186A mutant which frees Asp251 in the absence of Pdx retains good enzyme activity, and the crystal structure shows that product, 5-exo-hydroxycamphor, is bound. This indicates that rupture of the Asp251-Arg186 relaxes selectivity with respect to source of electrons and enables X-ray generated reducing equivalents to support substrate hydroxylation. These combined computational and experimental results are consistent with the proposed role of Pdx in assisting the release of Asp251 from ion pairs so that it can participate in proton-coupled electron transfer.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Logan S Richards
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
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Batabyal D, Lewis-Ballester A, Yeh SR, Poulos TL. A Comparative Analysis of the Effector Role of Redox Partner Binding in Bacterial P450s. Biochemistry 2016; 55:6517-6523. [PMID: 27808504 DOI: 10.1021/acs.biochem.6b00913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The camphor monooxygenase, cytochrome P450cam, exhibits a strict requirement for its own redox partner, putidaredoxin (Pdx), a two-iron-sulfur ferredoxin. The closest homologue to P450cam, CYP101D1, is structurally very similar, uses a similar redox partner, and exhibits nearly identical enzymatic properties in the monooxygenation of camphor to give the same single 5-exo-hydroxy camphor product. However, CYP101D1 does not strictly require its own ferredoxin (Arx) for activity because Pdx can support CYP101D1 catalysis but Arx cannot support P450cam catalysis. We have further examined the differences between these two P450s by determining the effect of spin equilibrium, redox properties, and stability of oxygen complexes. We find that Arx shifts the spin state equilibrium toward high-spin, which is the opposite of the effect of Pdx on P450cam. In both P450s, redox partner binding destabilizes the oxy-P450 complex but this effect is much weaker with CYP101D1. In addition, resonance Raman data show that structural perturbations observed in P450cam upon addition of Pdx are absent in CYP101D1. These data indicate that Arx does not play the same effector role in catalysis as Pdx does with P450cam. The most relevant structural difference between these two P450s centers on a catalytically important Asp residue required for proton-coupled electron transfer. We postulate that with P450cam larger Pdx-assisted motions are required to free this Asp for catalysis while the smaller number of restrictions in CYP101D1 precludes the need for redox partner-assisted structural changes.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
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20
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Johnson EO, Wong LL. Partial fusion of a cytochrome P450 system by carboxy-terminal attachment of putidaredoxin reductase to P450cam (CYP101A1). Catal Sci Technol 2016; 6:7549-7560. [PMID: 28944003 PMCID: PMC5609660 DOI: 10.1039/c6cy01042c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome P450 (CYP) enzymes catalyze the insertion of oxygen into carbon-hydrogen bonds and have great potential for enzymatic synthesis. Application development of class I CYPs is hampered by their dependence on two redox partners (a ferredoxin and ferredoxin reductase), slowing catalysis compared to self-sufficient CYPs such as CYP102A1 (P450BM3). Previous attempts to address this have fused all three components in several permutations and geometries, with much reduced activity compared to the native system. We report here the new approach of fusing putidaredoxin reductase (PdR) to the carboxy-terminus of CYP101A1 (P450cam) via a linker peptide and reconstituting camphor hydroxylase activity with free putidaredoxin (Pdx). Initial purification of a P450cam-PdR fusion yielded 2.0% heme incorporation. Co-expression of E. coli ferrochelatase, lengthening the linker from 5 to 20 residues, and altering culture conditions for enzyme production furnished 85% heme content. Fusion co-expression with Pdx gave a functional system with comparable in vivo camphor oxidation activity as the native system. In vitro, the fused system's steady state NADH oxidation rate was two-fold faster than that of the native system. In contrast to the native system, NADH oxidation rates for the fusion enzyme showed non-hyperbolic dependence on Pdx concentration, suggesting a role for the PdR domain; these data were consistent with a kinetic model based on two-site binding of Pdx by P450cam-PdR and inactive dimer formation of the fusion. P450cam-PdR is the first example of a class I P450 fusion that exhibits significantly more favorable behavior than that of the native system.
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Affiliation(s)
| | - Luet-Lok Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
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21
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Duan Y, Ba L, Gao J, Gao X, Zhu D, de Jong RM, Mink D, Kaluzna I, Lin Z. Semi-rational engineering of cytochrome CYP153A from Marinobacter aquaeolei for improved ω-hydroxylation activity towards oleic acid. Appl Microbiol Biotechnol 2016; 100:8779-88. [DOI: 10.1007/s00253-016-7634-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 04/10/2016] [Accepted: 05/14/2016] [Indexed: 12/25/2022]
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22
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Identification, characterization and molecular adaptation of class I redox systems for the production of hydroxylated diterpenoids. Microb Cell Fact 2016; 15:86. [PMID: 27216162 PMCID: PMC4877809 DOI: 10.1186/s12934-016-0487-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/11/2016] [Indexed: 12/31/2022] Open
Abstract
Background De novo production of multi-hydroxylated diterpenoids is challenging due to the lack of efficient redox systems. Results In this study a new reductase/ferredoxin system from Streptomyces afghaniensis (AfR·Afx) was identified, which allowed the Escherichia coli-based production of the trihydroxylated diterpene cyclooctatin, a potent inhibitor of human lysophospholipase. This production system provides a 43-fold increase in cyclooctatin yield (15 mg/L) compared to the native producer. AfR·Afx is superior in activating the cylcooctatin-specific class I P450s CotB3/CotB4 compared to the conventional Pseudomonas putida derived PdR·Pdx model. To enhance the activity of the PdR·Pdx system, the molecular basis for these activity differences, was examined by molecular engineering. Conclusion We demonstrate that redox system engineering can boost and harmonize the catalytic efficiency of class I hydroxylase enzyme cascades. Enhancing CotB3/CotB4 activities also provided for identification of CotB3 substrate promiscuity and sinularcasbane D production, a functionalized diterpenoid originally isolated from the soft coral Sinularia sp. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0487-6) contains supplementary material, which is available to authorized users.
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23
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Vandemeulebroucke A, Aldag C, Stiebritz MT, Reiher M, Hilvert D. Kinetic Consequences of Introducing a Proximal Selenocysteine Ligand into Cytochrome P450cam. Biochemistry 2015; 54:6692-703. [DOI: 10.1021/acs.biochem.5b00939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- An Vandemeulebroucke
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Caroline Aldag
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin T. Stiebritz
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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Abstract
The energy landscapes of proteins are highly complex and can be influenced by changes in physical and chemical conditions under which the protein is studied. The redox enzyme cytochrome P450cam undergoes a multistep catalytic cycle wherein two electrons are transferred to the heme group and the enzyme visits several conformational states. Using paramagnetic NMR spectroscopy with a lanthanoid tag, we show that the enzyme bound to its redox partner, putidaredoxin, is in a closed state at ambient temperature in solution. This result contrasts with recent crystal structures of the complex, which suggest that the enzyme opens up when bound to its partner. The closed state supports a model of catalysis in which the substrate is locked in the active site pocket and the enzyme acts as an insulator for the reactive intermediates of the reaction.
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25
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Hlavica P. Mechanistic basis of electron transfer to cytochromes p450 by natural redox partners and artificial donor constructs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:247-97. [PMID: 26002739 DOI: 10.1007/978-3-319-16009-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochromes P450 (P450s) are hemoproteins catalyzing oxidative biotransformation of a vast array of natural and xenobiotic compounds. Reducing equivalents required for dioxygen cleavage and substrate hydroxylation originate from different redox partners including diflavin reductases, flavodoxins, ferredoxins and phthalate dioxygenase reductase (PDR)-type proteins. Accordingly, circumstantial analysis of structural and physicochemical features governing donor-acceptor recognition and electron transfer poses an intriguing challenge. Thus, conformational flexibility reflected by togging between closed and open states of solvent exposed patches on the redox components was shown to be instrumental to steered electron transmission. Here, the membrane-interactive tails of the P450 enzymes and donor proteins were recognized to be crucial to proper orientation toward each other of surface sites on the redox modules steering functional coupling. Also, mobile electron shuttling may come into play. While charge-pairing mechanisms are of primary importance in attraction and complexation of the redox partners, hydrophobic and van der Waals cohesion forces play a minor role in docking events. Due to catalytic plasticity of P450 enzymes, there is considerable promise in biotechnological applications. Here, deeper insight into the mechanistic basis of the redox machinery will permit optimization of redox processes via directed evolution and DNA shuffling. Thus, creation of hybrid systems by fusion of the modified heme domain of P450s with proteinaceous electron carriers helps obviate the tedious reconstitution procedure and induces novel activities. Also, P450-based amperometric biosensors may open new vistas in pharmaceutical and clinical implementation and environmental monitoring.
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Affiliation(s)
- Peter Hlavica
- Walther-Straub-Institut für Pharmakologie und Toxikologie der LMU, Goethestrasse 33, 80336, München, Germany,
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26
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Hollingsworth SA, Poulos TL. Molecular dynamics of the P450cam-Pdx complex reveals complex stability and novel interface contacts. Protein Sci 2014; 24:49-57. [PMID: 25307478 DOI: 10.1002/pro.2583] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/02/2014] [Accepted: 10/05/2014] [Indexed: 11/07/2022]
Abstract
Cytochrome P450cam catalyzes the stereo and regiospecific hydroxylation of camphor to 5-exo-hydroxylcamphor. The two electrons for the oxidation of camphor are provided by putidaredoxin (Pdx), a Fe2 S2 containing protein. Two recent crystal structures of the P450cam-Pdx complex, one solved with the aid of covalent cross-linking and one without, have provided a structural picture of the redox partner interaction. To study the stability of the complex structure and the minor differences between the recent crystal structures, a 100 nanosecond molecular dynamics (MD) simulation of the cross-linked structure, mutated in silico to wild type and the linker molecule removed, was performed. The complex was stable over the course of the simulation though conformational changes including the movement of the C helix of P450cam further toward Pdx allowed for the formation of a number of new contacts at the complex interface that remained stable throughout the simulation. While several minor crystal contacts were lost in the simulation, all major contacts that had been experimentally studied previously were maintained. The equilibrated MD structure contained a mixture of contacts resembling both the cross-linked and noncovalent structures and the newly identified interactions. Finally, the reformation of the P450cam Asp251-Arg186 ion pair in the MD simulation mirrors the ion pair observed in the more promiscuous CYP101D1 and suggests that the Asp251-Arg186 ion pair may be important.
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Affiliation(s)
- Scott A Hollingsworth
- Departments of Chemistry, Pharmaceutical Sciences, and Molecular Biology and Biochemistry, University of California, Irvine, California, 92697
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27
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Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California Irvine, Irvine, California 92697-3900
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28
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Hiruma Y, Gupta A, Kloosterman A, Olijve C, Ölmez B, Hass MAS, Ubbink M. Hot-Spot Residues in the Cytochrome P450cam-Putidaredoxin Binding Interface. Chembiochem 2013; 15:80-6. [DOI: 10.1002/cbic.201300582] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 11/09/2022]
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29
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Structural insights into the mechanism for recognizing substrate of the cytochrome P450 enzyme TxtE. PLoS One 2013; 8:e81526. [PMID: 24282603 PMCID: PMC3840065 DOI: 10.1371/journal.pone.0081526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 10/14/2013] [Indexed: 11/19/2022] Open
Abstract
Thaxtomins, a family of phytotoxins produced by Streptomyces spp., can cause dramatic plant cell hypertrophy and seedling stunting. Thaxtomin A is the dominant form from Streptomyces scabies and has demonstrated herbicidal action. TxtE, a cytochrome P450 enzyme from Streptomyces scabies 87.22, catalyzes direct nitration of the indolyl moiety of L-tryptophan to L-4-nitrotryptophan using nitric oxide, dioxygen and NADPH. The crystal structure of TxtE was determined at 2.1 Å resolution and described in this work. A clearly defined substrate access channel is observed and can be classified as channel 2a, which is common in bacteria cytochrome P450 enzymes. A continuous hydrogen bond chain from the active site to the external solvent is observed. Compared with other cytochrome P450 enzymes, TxtE shows a unique proton transfer pathway which crosses the helix I distortion. Polar contacts of Arg59, Tyr89, Asn293, Thr296, and Glu394 with L-tryptophan are seen using molecular docking analysis, which are potentially important for substrate recognition and binding. After mutating Arg59, Asn293, Thr296 or Glu394 to leucine, the substrate binding ability of TxtE was lost or decreased significantly. Based on the docking and mutation results, a possible mechanism for substrate recognition and binding is proposed.
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30
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Hiruma Y, Hass MA, Kikui Y, Liu WM, Ölmez B, Skinner SP, Blok A, Kloosterman A, Koteishi H, Löhr F, Schwalbe H, Nojiri M, Ubbink M. The Structure of the Cytochrome P450cam–Putidaredoxin Complex Determined by Paramagnetic NMR Spectroscopy and Crystallography. J Mol Biol 2013; 425:4353-65. [DOI: 10.1016/j.jmb.2013.07.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/03/2013] [Accepted: 07/08/2013] [Indexed: 11/27/2022]
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31
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Haga T, Hirakawa H, Nagamune T. Fine tuning of spatial arrangement of enzymes in a PCNA-mediated multienzyme complex using a rigid poly-L-proline linker. PLoS One 2013; 8:e75114. [PMID: 24040392 PMCID: PMC3764174 DOI: 10.1371/journal.pone.0075114] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
Inspired by natural multienzyme complexes, many types of artificial multienzyme complexes have recently been constructed. We previously constructed a self-assembled complex of a bacterial cytochrome P450 and its ferredoxin and ferredoxin reductase partners using heterotrimerization of proliferating cell nuclear antigen (PCNA) from Sulfolobus solfataricus. In this study, we inserted different peptide linkers between ferredoxin and the PCNA subunit, and examined the effect on activity of the self-assembled multienzyme complex. Although the activity was affected by the lengths of both the rigid poly-L-proline-rich linkers and the flexible Gly4-Ser repeating linkers, the poly-L-proline-rich linkers provided the greatest activity enhancement. The optimized poly-L-proline-rich linker enhanced the activity 1.9-fold compared with the GGGGSLVPRGSGGGGS linker used in the previously reported complex, while the Gly4-Ser repeating linkers, (G4S)n (n = 1–6), did not yield higher activity than the maximum activity by the optimized poly-L-proline linker. Both the rigidity/flexibility and length of the peptide linker were found to be important for enhancing the overall activity of the multienzyme complex.
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Affiliation(s)
- Tomoaki Haga
- Department of Chemistry and Biotechnology, School of Engineering, the University of Tokyo, Hongo, Tokyo, Japan
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32
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Batabyal D, Li H, Poulos TL. Synergistic effects of mutations in cytochrome P450cam designed to mimic CYP101D1. Biochemistry 2013; 52:5396-402. [PMID: 23865948 PMCID: PMC3790332 DOI: 10.1021/bi400676d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A close orthologue to cytochrome P450cam (CYP101A1) that catalyzes the same hydroxylation of camphor to 5-exo-hydroxycamphor is CYP101D1. There are potentially important differences in and around the active site that could contribute to subtle functional differences. Adjacent to the heme iron ligand, Cys357, is Leu358 in P450cam, whereas this residue is Ala in CYP101D1. Leu358 plays a role in binding of the P450cam redox partner, putidaredoxin (Pdx). On the opposite side of the heme, about 15-20 Å away, Asp251 in P450cam plays a critical role in a proton relay network required for O2 activation but forms strong ion pairs with Arg186 and Lys178. In CYP101D1 Gly replaces Lys178. Thus, the local electrostatic environment and ion pairing are substantially different in CYP101D1. These sites have been systematically mutated in P450cam to the corresponding residues in CYP101D1 and the mutants analyzed by crystallography, kinetics, and UV-vis spectroscopy. Individually, the mutants have little effect on activity or structure, but in combination there is a major drop in enzyme activity. This loss in activity is due to the mutants being locked in the low-spin state, which prevents electron transfer from the P450cam redox partner, Pdx. These studies illustrate the strong synergistic effects on well-separated parts of the structure in controlling the equilibrium between the open (low-spin) and closed (high-spin) conformational states.
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Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697-3900
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697-3900
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697-3900
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Ba L, Li P, Zhang H, Duan Y, Lin Z. Engineering of a hybrid biotransformation system for cytochrome P450sca-2 in Escherichia coli. Biotechnol J 2013; 8:785-93. [PMID: 23744742 DOI: 10.1002/biot.201200097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/24/2013] [Accepted: 05/29/2013] [Indexed: 11/09/2022]
Abstract
P450sca-2 is an industrially important enzyme that stereoselectively converts mevastatin into pravastatin. However, little information or engineering efforts have been reported for this enzyme or its redox partner. In this study, we successfully reconstituted the P450sca-2 activity in Escherichia coli by co-expression with putidaredoxin reductase (Pdr) and putidaredoxin (Pdx) from the Pseudomonas putida cytochrome P450cam system. With an HPLC-based screening assay, random mutagenesis was applied to yield a mutant (R8-5C) with a pravastatin yield of the whole-cell biotransformation 4.1-fold that of the wild type. P450sca-2 wild-type and R8-5C were characterized in terms of mevastatin binding and hydroxylation, electron transfer, and circular dichroism spectroscopy. R8-5C showed an active P450 expression level that was 3.8-fold that of the wild type, with relatively smaller changes in the apparent k(cat)/K(M) with respect to the substrate mevastatin (1.3-fold) or Pdx (1.5-fold) compared with the wild type. Thus, the increase in the pravastatin yield of the whole-cell biotransformation primarily came from the improved active P450 expression, which has resulted largely from better heme incorporation, although none of the six mutations of R8-5C are located near the heme active site. These results will facilitate further engineering of this P450sca-2 system and provide useful clues for improving other hybrid P450 systems.
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Affiliation(s)
- Lina Ba
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes, Tsinghua University, Beijing, P.R. China
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Ba L, Li P, Zhang H, Duan Y, Lin Z. Semi-rational engineering of cytochrome P450sca-2 in a hybrid system for enhanced catalytic activity: Insights into the important role of electron transfer. Biotechnol Bioeng 2013; 110:2815-25. [DOI: 10.1002/bit.24960] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/28/2013] [Accepted: 05/06/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Lina Ba
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes; Tsinghua University; One Tsinghua Garden Road Beijing 100084 China
| | - Pan Li
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes; Tsinghua University; One Tsinghua Garden Road Beijing 100084 China
| | - Hui Zhang
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes; Tsinghua University; One Tsinghua Garden Road Beijing 100084 China
| | - Yan Duan
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes; Tsinghua University; One Tsinghua Garden Road Beijing 100084 China
| | - Zhanglin Lin
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes; Tsinghua University; One Tsinghua Garden Road Beijing 100084 China
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Poulos TL, Madrona Y. Oxygen activation and redox partner binding in cytochromes P450. Biotechnol Appl Biochem 2013; 60:128-33. [DOI: 10.1002/bab.1056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/25/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences; University of California; Irvine, Irvine; CA; USA
| | - Yarrow Madrona
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences; University of California; Irvine, Irvine; CA; USA
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Bell SG, Yang W, Yorke JA, Zhou W, Wang H, Harmer J, Copley R, Zhang A, Zhou R, Bartlam M, Rao Z, Wong LL. Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:277-91. [PMID: 22349230 DOI: 10.1107/s090744491200145x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/12/2012] [Indexed: 11/11/2022]
Abstract
CYP108D1 from Novosphingobium aromaticivorans DSM12444 binds a range of aromatic hydrocarbons such as phenanthrene, biphenyl and phenylcyclohexane. Its structure, which is reported here at 2.2 Å resolution, is closely related to that of CYP108A1 (P450terp), an α-terpineol-oxidizing enzyme. The compositions and structures of the active sites of these two enzymes are very similar; the most significant changes are the replacement of Glu77 and Thr103 in CYP108A1 by Thr79 and Val105 in CYP108D1. Other residue differences lead to a larger and more hydrophobic access channel in CYP108D1. These structural features are likely to account for the weaker α-terpineol binding by CYP108D1 and, when combined with the presence of three hydrophobic phenylalanine residues in the active site, promote the binding of aromatic hydrocarbons. The haem-proximal surface of CYP108D1 shows a different charge distribution and topology to those of CYP101D1, CYP101A1 and CYP108A1, including a pronounced kink in the proximal loop of CYP108D1, which may result in poor complementarity with the [2Fe-2S] ferredoxins Arx, putidaredoxin and terpredoxin that are the respective redox partners of these three P450 enzymes. The unexpectedly low reduction potential of phenylcyclohexane-bound CYP108D1 (-401 mV) may also contribute to the low activity observed with these ferredoxins. CYP108D1 appears to function as an aromatic hydrocarbon hydroxylase that requires a different electron-transfer cofactor protein.
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Affiliation(s)
- Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford,South Parks Road, Oxford OX1 3QR, England.
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Bell SG, McMillan JHC, Yorke JA, Kavanagh E, Johnson EOD, Wong LL. Tailoring an alien ferredoxin to support native-like P450 monooxygenase activity. Chem Commun (Camb) 2012; 48:11692-4. [DOI: 10.1039/c2cc35968e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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NMR basis for interprotein electron transfer gating between cytochrome c and cytochrome c oxidase. Proc Natl Acad Sci U S A 2011; 108:12271-6. [PMID: 21746907 DOI: 10.1073/pnas.1108320108] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The final interprotein electron transfer (ET) in the mammalian respiratory chain, from cytochrome c (Cyt c) to cytochrome c oxidase (CcO) is investigated by (1)H-(15)N heteronuclear single quantum coherence spectral analysis. The chemical shift perturbation in isotope-labeled Cyt c induced by addition of unlabeled CcO indicates that the hydrophobic heme periphery and adjacent hydrophobic amino acid residues of Cyt c dominantly contribute to the complex formation, whereas charged residues near the hydrophobic core refine the orientation of Cyt c to provide well controlled ET. Upon oxidation of Cyt c, the specific line broadening of N-H signals disappeared and high field (1)H chemical shifts of the N-terminal helix were observed, suggesting that the interactions of the N-terminal helix with CcO are reduced by steric constraint in oxidized Cyt c, while the chemical shift perturbations in the C-terminal helix indicate notable interactions of oxidized Cyt c with CcO. These results suggest that the overall affinity of oxidized Cyt c for CcO is significantly, but not very much weaker than that of reduced Cyt c. Thus, electron transfer is gated by dissociation of oxidized Cyt c from CcO, the rate of which is controlled by the affinity of oxidized Cyt c to CcO for providing an appropriate electron transfer rate for the most effective energy coupling. The conformational changes in Lys13 upon CcO binding to oxidized Cyt c, shown by (1)H- and (1)H, (15)N-chemical shifts, are also expected to gate intraprotein ET by a polarity control of heme c environment.
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Ma M, Bell SG, Yang W, Hao Y, Rees NH, Bartlam M, Zhou W, Wong LL, Rao Z. Structural Analysis of CYP101C1 from Novosphingobium aromaticivorans DSM12444. Chembiochem 2011; 12:88-99. [PMID: 21154803 DOI: 10.1002/cbic.201000537] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
CYP101C1 from Novosphingobium aromaticivorans DSM12444 is a homologue of CYP101D1 and CYP101D2 enzymes from the same bacterium and CYP101A1 from Pseudomonas putida. CYP101C1 does not bind camphor but is capable of binding and hydroxylating ionone derivatives including α- and β-ionone and β-damascone. The activity of CYP101C1 was highest with β-damascone (k(cat)=86 s(-1)) but α-ionone oxidation was the most regioselective (98 % at C3). The crystal structures of hexane-2,5-diol- and β-ionone-bound CYP101C1 have been solved; both have open conformations and the hexanediol-bound form has a clear access channel from the heme to the bulk solvent. The entrance of this channel is blocked when β-ionone binds to the enzyme. The heme moiety of CYP101C1 is in a significantly different environment compared to the other structurally characterised CYP101 enzymes. The likely ferredoxin binding site on the proximal face of CYP101C1 has a different topology but a similar overall positive charge compared to CYP101D1 and CYP101D2, all of which accept electrons from the ArR/Arx class I electron transfer system.
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Affiliation(s)
- Ming Ma
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
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41
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Strushkevich NV, Harnastai IN, Usanov SA. Mechanism of steroidogenic electron transport: role of conserved Glu429 in destabilization of CYP11A1-adrenodoxin complex. BIOCHEMISTRY (MOSCOW) 2010; 75:570-8. [PMID: 20632935 DOI: 10.1134/s0006297910050056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present work the role of conserved residue E429 of cytochrome P45011A1 has been studied. The charge neutralization of E429Q results in 3-fold decrease of K(d) as well as V(max) compared to the wild type hemoprotein indicating tighter binding and, as the result, the impaired dissociation of oxidized adrenodoxin from the complex. As cytochrome P45011A1-adrenodoxin complex formation is driven primarily by electrostatic interactions, the low activity of E429Q mutant is completely restored to that of wild type hemoprotein by increasing of ionic strength. The charge neutralization of the corresponding residue of rat cytochrome P45011B2 has the same effect: the activity is 10-fold decreased but it is restored by increasing of ionic strength without effect on the ratio of products formed. Thus, this is the first report on identification of residues involved in modulation of dissociation of redox partner from the complex with cytochrome P450s.
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Affiliation(s)
- N V Strushkevich
- Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Minsk, 220141, Belarus
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42
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Structural biology of redox partner interactions in P450cam monooxygenase: a fresh look at an old system. Arch Biochem Biophys 2010; 507:66-74. [PMID: 20816746 DOI: 10.1016/j.abb.2010.08.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 08/28/2010] [Accepted: 08/31/2010] [Indexed: 11/21/2022]
Abstract
The P450cam monooxygenase system consists of three separate proteins: the FAD-containing, NADH-dependent oxidoreductase (putidaredoxin reductase or Pdr), cytochrome P450cam and the 2Fe2S ferredoxin (putidaredoxin or Pdx), which transfers electrons from Pdr to P450cam. Over the past few years our lab has focused on the interaction between these redox components. It has been known for some time that Pdx can serve as an effector in addition to its electron shuttle role. The binding of Pdx to P450cam is thought to induce structural changes in the P450cam active site that couple electron transfer to substrate hydroxylation. The nature of these structural changes has remained unclear until a particular mutant of P450cam (Leu358Pro) was found to exhibit spectral perturbations similar to those observed in wild type P450cam bound to Pdx. The crystal structure of the L358P variant has provided some important insights on what might be happening when Pdx docks. In addition to these studies, many Pdx mutants have been analyzed to identify regions important for electron transfer. Somewhat surprisingly, we found that Pdx residues predicted to be at the P450cam-Pdx interface play different roles in the reduction of ferric P450cam and the ferrous P450-O(2) complex. More recently we have succeeded in obtaining the structure of a chemically cross-linked Pdr-Pdx complex. This fusion protein represents a valid model for the noncovalent Pdr-Pdx complex as it retains the redox activities of native Pdr and Pdx and supports monooxygenase reactions catalyzed by P450cam. The insights gained from these studies will be summarized in this review.
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Yang W, Bell SG, Wang H, Zhou W, Hoskins N, Dale A, Bartlam M, Wong LL, Rao Z. Molecular characterization of a class I P450 electron transfer system from Novosphingobium aromaticivorans DSM12444. J Biol Chem 2010; 285:27372-27384. [PMID: 20576606 DOI: 10.1074/jbc.m110.118349] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (CYP) enzymes of the CYP101 and CYP111 families from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 are heme monooxygenases that receive electrons from NADH via Arx, a [2Fe-2S] ferredoxin, and ArR, a ferredoxin reductase. These systems show fast NADH turnovers (k(cat) = 39-91 s(-1)) that are efficiently coupled to product formation. The three-dimensional structures of ArR, Arx, and CYP101D1, which form a physiological class I P450 electron transfer chain, have been resolved by x-ray crystallography. The general structural features of these proteins are similar to their counterparts in other class I systems such as putidaredoxin reductase (PdR), putidaredoxin (Pdx), and CYP101A1 of the camphor hydroxylase system from Pseudomonas putida, and adrenodoxin (Adx) of the mitochondrial steroidogenic CYP11 and CYP24A1 systems. However, significant differences in the proposed protein-protein interaction surfaces of the ferredoxin reductase, ferredoxin, and P450 enzyme are found. There are regions of positive charge on the likely interaction face of ArR and CYP101D1 and a corresponding negatively charged area on the surface of Arx. The [2Fe-2S] cluster binding loop in Arx also has a neutral, hydrophobic patch on the surface. These surface characteristics are more in common with those of Adx than Pdx. The observed structural features are consistent with the ionic strength dependence of the activity.
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Affiliation(s)
- Wen Yang
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Stephen G Bell
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.
| | - Hui Wang
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Weihong Zhou
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Nicola Hoskins
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Alison Dale
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Mark Bartlam
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
| | - Luet-Lok Wong
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Zihe Rao
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
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44
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Sevrioukova IF, Poulos TL, Churbanova IY. Crystal structure of the putidaredoxin reductase x putidaredoxin electron transfer complex. J Biol Chem 2010; 285:13616-20. [PMID: 20179327 DOI: 10.1074/jbc.m110.104968] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the camphor monooxygenase system from Pseudomonas putida, the [2Fe-2S]-containing putidaredoxin (Pdx) shuttles electrons between the NADH-dependent putidaredoxin reductase (Pdr) and cytochrome P450(cam). The mechanism of the Pdr.Pdx redox couple has been investigated by a variety of techniques. One of the exceptions is x-ray crystallography as the native partners associate weakly and resist co-crystallization. Here, we present the 2.6-A x-ray structure of a catalytically active complex between Pdr and Pdx C73S/C85S chemically cross-linked via the Lys(409Pdr)-Glu(72Pdx) pair. The 365 A(2) Pdr-Pdx interface is predominantly hydrophobic with one central Arg(310Pdr)-Asp(38Pdx) salt bridge, likely assisting docking and orienting the partners optimally for electron transfer, and a few peripheral hydrogen bonds. A predicted 12-A-long electron transfer route between FAD and [2Fe-2S] includes flavin flanking Trp(330Pdr) and the iron ligand Cys(39Pdx). The x-ray model agrees well with the experimental and theoretical results and suggests that the linked Pdx must undergo complex movements during turnover to accommodate P450(cam), which could limit the Pdx-to-P450(cam) electron transfer reaction.
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Affiliation(s)
- Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.
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45
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Xu F, Bell SG, Peng Y, Johnson EOD, Bartlam M, Rao Z, Wong LL. Crystal structure of a ferredoxin reductase for the CYP199A2 system from Rhodopseudomonas palustris. Proteins 2010; 77:867-80. [PMID: 19626710 DOI: 10.1002/prot.22510] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cytochrome P450-199A2 from Rhodopseudomonas palustris oxidizes para-substituted benzoic acids and may play a role in lignin and aromatic acid degradation pathways in the bacterium. CYP199A2 has an associated [2Fe-2S] ferredoxin, palustrisredoxin (Pux) but not a ferredoxin reductase. A genome search identified the palustrisredoxin reductase (PuR) gene. PuR was produced in Escherichia coli and shown to be a flavin-dependent protein that supports efficient electron transfer from NADH to Pux, thus reconstituting CYP199A2 monooxygenase activity (k(cat) = 37.9 s(-1) with 4-methoxybenzoic acid). The reduction of Pux by PuR shows K(m) = 4.2 microM and k(cat) = 262 s(-1) in 50 mM Tris, pH 7.4. K(m) is increased to 154 microM in the presence of 200 mM KCl, indicating the importance of ionic interactions in PuR/Pux binding. The crystal structure of PuR has been determined at 2.2 A resolution and found to be closely related to that of other oxygenase-coupled NADH-dependent ferredoxin reductases. Residues on the surface that had been proposed to be involved in ferredoxin reductase-ferredoxin binding are conserved in PuR. However, Lys328 in PuR lies over the FAD isoalloxazine ring and, together with His11 and Gln41, render the electrostatic potential of the surface more positive and may account for the greater involvement of electrostatic interactions in ferredoxin binding by PuR. Consistent with these observations the K328G mutation weakened Pux binding and virtually eliminated the dependence of PuR/Pux binding on salt concentration, thus confirming that the FAD si side surface in the vicinity of Lys328 is the ferredoxin binding site.
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Affiliation(s)
- Feng Xu
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Department of Biological Science and Biotechnology, Tsinghua University, Beijing 100084, People's Republic of China
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Annalora AJ, Goodin DB, Hong WX, Zhang Q, Johnson EF, Stout CD. Crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism. J Mol Biol 2009; 396:441-51. [PMID: 19961857 DOI: 10.1016/j.jmb.2009.11.057] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Revised: 11/18/2009] [Accepted: 11/21/2009] [Indexed: 01/08/2023]
Abstract
Cytochrome P450 (CYP) 24A1 catalyzes the side-chain oxidation of the hormonal form of vitamin D. Expression of CYP24A1 is up-regulated to attenuate vitamin D signaling associated with calcium homeostasis and cellular growth processes. The development of therapeutics for disorders linked to vitamin D insufficiency would be greatly facilitated by structural knowledge of CYP24A1. Here, we report the crystal structure of rat CYP24A1 at 2.5 A resolution. The structure exhibits an open cleft leading to the active-site heme prosthetic group on the distal surface that is likely to define the path of substrate access into the active site. The entrance to the cleft is flanked by conserved hydrophobic residues on helices A' and G', suggesting a mode of insertion into the inner mitochondrial membrane. A docking model for 1alpha,25-dihydroxyvitamin D(3) binding in the open form of CYP24A1 that clarifies the structural determinants of secosteroid recognition and validates the predictive power of existing homology models of CYP24A1 is proposed. Analysis of CYP24A1's proximal surface identifies the determinants of adrenodoxin recognition as a constellation of conserved residues from helices K, K'', and L that converge with an adjacent lysine-rich loop for binding the redox protein. Overall, the CYP24A1 structure provides the first template for understanding membrane insertion, substrate binding, and redox partner interaction in mitochondrial P450s.
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Affiliation(s)
- Andrew J Annalora
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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47
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Protein recognition in ferredoxin–P450 electron transfer in the class I CYP199A2 system from Rhodopseudomonas palustris. J Biol Inorg Chem 2009; 15:315-28. [DOI: 10.1007/s00775-009-0604-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
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48
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Zawaira A, Gallotta M, Beeton-Kempen N, Coulson L, Marais P, Kuttel M, Blackburn J. Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450 (CYP) and P450-oxidoreductase (POR) proteins. Comput Biol Chem 2009; 34:42-52. [PMID: 19939736 DOI: 10.1016/j.compbiolchem.2009.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 10/20/2009] [Accepted: 10/21/2009] [Indexed: 10/20/2022]
Abstract
In this work, a model for the interaction between CYP2B4 and the FMN domain of rat P450-oxidoreductase is built using as template the structure of a bacterial redox complex. Amino acid residues identified in the literature as cytochrome P450 (CYP)-redox partner interfacial residues map to the interface in our model. Our model supports the view that the bacterial template represents a specific electron transfer complex and moreover provides a structural framework for explaining previous experimental data. We have used our model in an exhaustive search for complementary pairs of mammalian CYP and P450-oxidoreductase (POR) charge clusters. We quantitatively show that among the previously defined basic clusters, the 433K-434R cluster is the most dominant (32.3% of interactions) and among the acidic clusters, the 207D-208D-209D cluster is the most dominant (29%). Our analysis also reveals the previously not described basic cluster 343R-345K (16.1% of interactions) and 373K (3.2%) and the acidic clusters 113D-115E-116E (25.8%), 92E-93E (12.9%), 101D (3.2%) and 179E (3.2%). Cluster pairings among the previously defined charge clusters include the pairing of cluster 421K-422R to cluster 207D-208D-209D. Moreover, 433K-434R and 207D-208D-209D, respectively the dominant positively and negatively charged clusters, are uncorrelated. Instead our analysis suggests that the newly identified cluster 113D-115E-116E is the main partner of the 433K-434R cluster while the newly described cluster 343R-345K is correlated to the cluster 207D-208D-209D.
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Affiliation(s)
- Alexander Zawaira
- Division of Medical Biochemistry, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa.
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49
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Kumar D, Tahsini L, de Visser SP, Kang HY, Kim SJ, Nam W. Effect of Porphyrin Ligands on the Regioselective Dehydrogenation versus Epoxidation of Olefins by Oxoiron(IV) Mimics of Cytochrome P450. J Phys Chem A 2009; 113:11713-22. [DOI: 10.1021/jp9028694] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Devesh Kumar
- Contribution from Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India, The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Department of Chemistry and Nano Science, Department of Bioinspired Science, Centre for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Laleh Tahsini
- Contribution from Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India, The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Department of Chemistry and Nano Science, Department of Bioinspired Science, Centre for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Sam P. de Visser
- Contribution from Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India, The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Department of Chemistry and Nano Science, Department of Bioinspired Science, Centre for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Hye Yeon Kang
- Contribution from Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India, The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Department of Chemistry and Nano Science, Department of Bioinspired Science, Centre for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Soo Jeong Kim
- Contribution from Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India, The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Department of Chemistry and Nano Science, Department of Bioinspired Science, Centre for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Wonwoo Nam
- Contribution from Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India, The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Department of Chemistry and Nano Science, Department of Bioinspired Science, Centre for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
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Porro CS, Sutcliffe MJ, de Visser SP. Quantum Mechanics/Molecular Mechanics Studies on the Sulfoxidation of Dimethyl Sulfide by Compound I and Compound 0 of Cytochrome P450: Which Is the Better Oxidant? J Phys Chem A 2009; 113:11635-42. [DOI: 10.1021/jp9023926] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cristina S. Porro
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael J. Sutcliffe
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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