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Wu L, Luo H, Xu J, Yu L, Xiong J, Liu Y, Huang X, Zou X. Vital role of CYP450 in the biodegradation of antidiabetic drugs in the aerobic activated sludge system and the mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134056. [PMID: 38522208 DOI: 10.1016/j.jhazmat.2024.134056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
The extensive use of antidiabetic drugs (ADDs) and their detection in high concentrations in the environment have been extensively documented. However, the mechanism of ADDs dissipation in aquatic environments is still not well understood. This study thoroughly investigates the dissipation behavior of ADDs and the underlying mechanisms in the aerobic activated sludge system. The results indicate that the removal efficiencies of ADDs range from 3.98% to 100% within 48 h, largely due to the biodegradation process. Additionally, the gene expression of cytochrome P450 (CYP450) is shown to be significantly upregulated in most ADDs-polluted samples (P < 0.05), indicating the vital role of CYP450 enzymes in the biodegradation of ADDs. Enzyme inhibition experiments validated this hypothesis. Moreover, molecular docking and simulation results indicate that a strong correlation between the biodegradation of ADDs and the interactions between ADDs and CYP450 (Ebinding). The differences in dissipation behavior among the tested ADDs are possibly due to their electrophilic characteristics. Overall, this study makes the initial contribution to a more profound comprehension of the crucial function of CYP450 enzymes in the dissipation behavior of ADDs in a typical aquatic environment.
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Affiliation(s)
- Ligui Wu
- School of Life Science, Jinggangshan University, Ji'an 343009, China; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Hao Luo
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Jingcheng Xu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ling Yu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Jiangtao Xiong
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Yizhi Liu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Xiangfeng Huang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Xiaoming Zou
- School of Life Science, Jinggangshan University, Ji'an 343009, China.
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2
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Giang PD, Churchman LR, Buczynski JB, Bell SG, Stok JE, De Voss JJ. CYP108N14: A Monoterpene Monooxygenase from Rhodococcus globerulus. Arch Biochem Biophys 2024; 752:109852. [PMID: 38072297 DOI: 10.1016/j.abb.2023.109852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/29/2024]
Abstract
Rhodococcus globerulus (R. globerulus) was isolated from the soil beneath a Eucalypt tree. Metabolic growth studies revealed that R. globerulus was capable of living on certain monoterpenes, including 1,8-cineole and p-cymene, as sole sources of carbon and energy. Multiple P450 genes were identified in the R. globerulus genome that shared homology to known bacterial, monoterpene hydroxylating P450s. To date, two of these P450s have been expressed and characterised as 1,8-cineole (CYP176A1) and p-cymene (CYP108N12) monooxygenases that are believed to initiate the biodegradation of these terpenes. In this work, another putative P450 gene (CYP108N14) was identified in R. globerulus genome. Given its amino acid sequence identity to other monoterpene hydroxylating P450s it was hypothesised to catalyse monoterpene hydroxylation. These include CYP108A1 from Pseudomonas sp. (47 % identity, 68 % similarity) which hydroxylates α-terpineol, and CYP108N12 also from R. globerulus (62 % identity, 77 % similarity). Also present in the operon containing CYP108N14 were putative ferredoxin and ferredoxin reductase genes, suggesting a typical Class I P450 system. CYP108N14 was successfully over-expressed heterologously and purified, resulting in a good yield of CYP108N14 holoprotein. However, neither the ferredoxin nor ferredoxin reductase could be produced heterologously. Binding studies with CYP108N14 revealed a preference for the monoterpenes p-cymene, (R)-limonene, (S)-limonene, (S)-α-terpineol and (S)-4-terpineol. An active catalytic system was reconstituted with the non-native redox partners cymredoxin (from the CYP108N12 system) and putidaredoxin reductase (from the CYP101A1 system). CYP108N14 when supported by these redox partners was able to catalyse the hydroxylation of the five aforementioned substrates selectively at the methyl benzylic/allylic positions.
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Affiliation(s)
- Peter D Giang
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Brisbane, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Brisbane, Australia
| | - Julia B Buczynski
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Brisbane, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Brisbane, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Brisbane, Australia.
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3
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Giang PD, Churchman LR, Stok JE, Bell SG, De Voss JJ. Cymredoxin, a [2Fe-2S] ferredoxin, supports catalytic activity of the p-cymene oxidising P450 enzyme CYP108N12. Arch Biochem Biophys 2023; 737:109549. [PMID: 36801262 DOI: 10.1016/j.abb.2023.109549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023]
Abstract
Rhodococcus globerulus is a metabolically active organism that has been shown to utilise eucalypt oil as its sole source of carbon and energy. This oil includes 1,8-cineole, p-cymene and limonene. Two identified and characterised cytochromes P450 (P450s) from this organism initiate the biodegradation of the monoterpenes 1,8-cineole (CYP176A1) and p-cymene (CYP108N12). Extensive characterisation has been completed for CYP176A1 and it has been successfully reconstituted with its immediate redox partner, cindoxin, and E. coli flavodoxin reductase. Two putative redox partner genes are encoded in the same operon as CYP108N12 and here the isolation, expression, purification, and characterisation of its specific [2Fe-2S] ferredoxin redox partner, cymredoxin is presented. Reconstitution of CYP108N12 with cymredoxin in place of putidaredoxin, a [2Fe-2S] redox partner of another P450, improves both the rate of electron transfer (from 13 ± 2 to 70 ± 1 μM NADH/min/μM CYP108N12) and the efficiency of NADH utilisation (the so-called coupling efficiency increases from 13% to 90%). Cymredoxin improves the catalytic ability of CYP108N12 in vitro. Aldehyde oxidation products of the previously identified substrates p-cymene (4-isopropylbenzaldehyde) and limonene (perillaldehyde) were observed in addition to major hydroxylation products 4-isopropylbenzyl alcohol and perillyl alcohol respectively. These further oxidation products had not previously been seen with putidaredoxin supported oxidation. Furthermore, when supported by cymredoxin CYP108N12 is able to oxidise a wider range of substrates than previously reported. These include o-xylene, α-terpineol, (-)-carveol and thymol yielding o-tolylmethanol, 7-hydroxyterpineol, (4R)-7-hydroxycarveol and 5-hydroxymethyl-2-isopropylphenol, respectively. Cymredoxin is also capable of supporting CYP108A1 (P450terp) and CYP176A1 activity, allowing them to catalyse the hydroxylation of their native substrates α-terpineol to 7-hydroxyterpineol and 1,8-cineole to 6β-hydroxycineole respectively. These results indicate that cymredoxin not only improves the catalytic capability of CYP108N12 but can also support the activity of other P450s and prove useful for their characterisation.
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Affiliation(s)
- Peter D Giang
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4067, Australia.
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4
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Gable JA, Poulos TL, Follmer AH. Cooperative Substrate Binding Controls Catalysis in Bacterial Cytochrome P450terp (CYP108A1). J Am Chem Soc 2023; 145:10.1021/jacs.2c12388. [PMID: 36779970 PMCID: PMC10576961 DOI: 10.1021/jacs.2c12388] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Despite being one of the most well-studied aspects of cytochrome P450 chemistry, important questions remain regarding the nature and ubiquity of allosteric regulation of catalysis. The crystal structure of a bacterial P450, P450terp, in the presence of substrate reveals two binding sites, one above the heme in position for regioselective hydroxylation and another in the substrate access channel. Unlike many bacterial P450s, P450terp does not exhibit an open to closed conformational change when substrate binds; instead, P450terp uses the second substrate molecule to hold the first substrate molecule in position for catalysis. Spectral titrations clearly show that substrate binding to P450terp is cooperative with a Hill coefficient of 1.4 and is supported by isothermal titration calorimetry. The importance of the allosteric site was explored by a series of mutations that weaken the second site and that help hold the first substrate in position for proper catalysis. We further measured the coupling efficiency of both the wild-type (WT) enzyme and the mutant enzymes. While the WT enzyme exhibits 97% efficiency, each of the variants showed lower catalytic efficiency. Additionally, the variants show decreased spin shifts upon binding of substrate. These results are the first clear example of positive homotropic allostery in a class 1 bacterial P450 with its natural substrate. Combined with our recent results from P450cam showing complex substrate allostery and conformational dynamics, our present study with P450terp indicates that bacterial P450s may not be as simple as once thought and share complex substrate binding properties usually associated with only mammalian P450s.
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Affiliation(s)
- Jessica A Gable
- Departments of Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
- Departments of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3900, United States
- Departments of Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Alec H Follmer
- Departments of Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
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5
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CYP108N12 initiates p-cymene biodegradation in Rhodococcus globerulus. Arch Biochem Biophys 2022; 730:109410. [PMID: 36155781 DOI: 10.1016/j.abb.2022.109410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022]
Abstract
Rhodococcus globerulus (R. globerulus) isolated from soil beneath Eucalyptus sp. was found to live on the monoterpenes 1,8-cineole, p-cymene and (R)- and (S)-limonene as sole sources of carbon and energy. Previous metabolic studies revealed that R. globerulus is capable of living on 1,8-cineole, the main monoterpene component of eucalyptus essential oil through the activity of cytochrome P450cin (CYP176A1) [1]. Genomic sequencing of R. globerulus revealed a novel putative cytochrome P450 (CYP108N12) that shares 48% sequence identity with CYP108A1 (P450terp) from Pseudomonas sp., an α-terpineol hydroxylase. Given the sequence similarity between CYP108N12 and P450terp, it was hypothesised that CYP108N12 may be responsible for initiating the biodegradation of a monoterpene structurally similar to α-terpineol such as (R)-limonene, (S)-limonene or p-cymene. Encoded within the operon containing CYP108N12 were two putative bacterial P450 redox partners and putative alcohol and aldehyde dehydrogenases, suggesting a complete catalytic system for activating these monoterpenes. Binding studies revealed that p-cymene and (R)- and (S)-limonene all bound tightly to CYP108N12 but α-terpineol did not. A catalytically active system was reconstituted using the non-native redox partner putidaredoxin and putidaredoxin reductase that act with CYP101A1 (P450cam) from Pseudomonas. This reconstituted system catalysed the hydroxylation of p-cymene to 4-isopropylbenzyl alcohol, and (R)- and (S)-limonene to (R)- and (S)-perillyl alcohol, respectively. R. globerulus was successfully grown on solely p-cymene, (R)-limonene or (S)-limonene. CYP108N12 was detected when R. globerulus was grown on p-cymene, but not either limonene enantiomer. The native function of CYP108N12 is therefore proposed to be initiation of p-cymene biodegradation by methyl oxidation and is a potentially attractive biocatalyst capable of specific benzylic and allylic hydroxylation.
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Chen CC, Dai M, Zhang L, Zhao J, Zeng W, Shi M, Huang JW, Liu W, Guo RT, Li A. Molecular Basis for a Toluene Monooxygenase to Govern Substrate Selectivity. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Meng Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jing Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wei Zeng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Min Shi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin 300308, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Aitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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7
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Poulos TL, Follmer AH. Updating the Paradigm: Redox Partner Binding and Conformational Dynamics in Cytochromes P450. Acc Chem Res 2022; 55:373-380. [PMID: 34965086 PMCID: PMC8959394 DOI: 10.1021/acs.accounts.1c00632] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This Account summarizes recent findings centered on the role that redox partner binding, allostery, and conformational dynamics plays in cytochrome P450 proton coupled electron transfer. P450s are one of Nature's largest enzyme families and it is not uncommon to find a P450 wherever substrate oxidation is required in the formation of essential molecules critical to the life of the organism or in xenobiotic detoxification. P450s can operate on a remarkably large range of substrates from the very small to the very large, yet the overall P450 three-dimensional structure is conserved. Given this conservation of structure, it is generally assumed that the basic catalytic mechanism is conserved. In nearly all P450s, the O2 O-O bond must be cleaved heterolytically enabling one oxygen atom, the distal oxygen, to depart as water and leave behind a heme iron-linked O atom as the powerful oxidant that is used to activate the nearby substrate. For this process to proceed efficiently, externally supplied electrons and protons are required. Two protons must be added to the departing O atom while an electron is transferred from a redox partner that typically contains either a Fe2S2 or FMN redox center. The paradigm P450 used to unravel the details of these mechanisms has been the bacterial CYP101A1 or P450cam. P450cam is specific for its own Fe2S2 redox partner, putidaredoxin or Pdx, and it has long been postulated that Pdx plays an effector/allosteric role by possibly switching P450cam to an active conformation. Crystal structures, spectroscopic data, and direct binding experiments of the P450cam-Pdx complex provide some answers. Pdx shifts the conformation of P450cam to a more open state, a transition that is postulated to trigger the proton relay network required for O2 activation. An essential part of this proton relay network is a highly conserved Asp (sometimes Glu) that is known to be critical for activity in a number of P450s. How this Asp and proton delivery networks are connected to redox partner binding is quite simple. In the closed state, this Asp is tied down by salt bridges, but these salt bridges are ruptured when Pdx binds, leaving the Asp free to serve its role in proton transfer. An alternative hypothesis suggests that a specific proton relay network is not really necessary. In this scenario, the Asp plays a structural role in the open/close transition and merely opening the active site access channel is sufficient to enable solvent protons in for O2 protonation. Experiments designed to test these various hypotheses have revealed some surprises in both P450cam and other bacterial P450s. Molecular dynamics and crystallography show that P450cam can undergo rather significant conformational gymnastics that result in a large restructuring of the active site requiring multiple cis/trans proline isomerizations. It also has been found that X-ray driven substrate hydroxylation is a useful tool for better understanding the role that the essential Asp and surrounding residues play in catalysis. Here we summarize these recent results which provide a much more dynamic picture of P450 catalysis.
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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, United States
| | - Alec H. Follmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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8
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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9
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Chao RR, Lau ICK, Coleman T, Churchman LR, Child SA, Lee JHZ, Bruning JB, De Voss JJ, Bell SG. The stereoselective oxidation of para-substituted benzenes by a cytochrome P450 biocatalyst. Chemistry 2021; 27:14765-14777. [PMID: 34350662 DOI: 10.1002/chem.202102757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Indexed: 11/10/2022]
Abstract
The serine 244 to aspartate (S244D) variant of the cytochrome P450 enzyme CYP199A4 was used to expand its substrate range beyond benzoic acids. Substrates, in which the carboxylate group of the benzoic acid moiety is replaced, were oxidised with high activity by the S244D mutant (product formation rates > 60 nmol.(nmol-CYP) -1 .min -1 ) and with total turnover numbers of up to 20,000. Ethyl α-hydroxylation was more rapid than methyl oxidation, styrene epoxidation and S -oxidation. The S244D mutant catalysed the ethyl hydroxylation, epoxidation and sulfoxidation reactions with an excess of one stereoisomer (in some instances up to >98%). The crystal structure of 4-methoxybenzoic acid-bound CYP199A4 S244D showed that the active site architecture and the substrate orientation were similar to that of the WT enzyme. Overall, this work demonstrates that CYP199A4 can catalyse the stereospecific hydroxylation, epoxidation or sulfoxidation of substituted benzene substrates under mild conditions resulting in more sustainable transformations using this heme monooxygenase enzyme.
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Affiliation(s)
- Rebecca R Chao
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Ian C-K Lau
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Tom Coleman
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Luke R Churchman
- The University of Queensland, School of Chemistry and Molecular Biosciences, AUSTRALIA
| | - Stella A Child
- The University of Adelaide, Department of Chemistry, AUSTRALIA
| | - Joel H Z Lee
- The University of Adelaide, The Department of Chemistry, AUSTRALIA
| | - John B Bruning
- The University of Adelaide, School of Biological Sciences, AUSTRALIA
| | - James J De Voss
- The University of Queensland, School of Chemistry and Molecular Biosciences, AUSTRALIA
| | - Stephen Graham Bell
- University of Adelaide, School of Chemistry & Physics, North Terrace, 5005, Adelaide, AUSTRALIA
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10
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Midlik A, Navrátilová V, Moturu TR, Koča J, Svobodová R, Berka K. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Sci Rep 2021; 11:12345. [PMID: 34117311 PMCID: PMC8196199 DOI: 10.1038/s41598-021-91494-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/21/2021] [Indexed: 12/25/2022] Open
Abstract
Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)-a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz .
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Affiliation(s)
- Adam Midlik
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Veronika Navrátilová
- Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, 771 46, Czech Republic
| | - Taraka Ramji Moturu
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Radka Svobodová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, 771 46, Czech Republic.
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11
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Soares-Castro P, Soares F, Santos PM. Current Advances in the Bacterial Toolbox for the Biotechnological Production of Monoterpene-Based Aroma Compounds. Molecules 2020; 26:molecules26010091. [PMID: 33379215 PMCID: PMC7794910 DOI: 10.3390/molecules26010091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Monoterpenes are plant secondary metabolites, widely used in industrial processes as precursors of important aroma compounds, such as vanillin and (-)-menthol. However, the physicochemical properties of monoterpenes make difficult their conventional conversion into value-added aromas. Biocatalysis, either by using whole cells or enzymes, may overcome such drawbacks in terms of purity of the final product, ecological and economic constraints of the current catalysis processes or extraction from plant material. In particular, the ability of oxidative enzymes (e.g., oxygenases) to modify the monoterpene backbone, with high regio- and stereo-selectivity, is attractive for the production of "natural" aromas for the flavor and fragrances industries. We review the research efforts carried out in the molecular analysis of bacterial monoterpene catabolic pathways and biochemical characterization of the respective key oxidative enzymes, with particular focus on the most relevant precursors, β-pinene, limonene and β-myrcene. The presented overview of the current state of art demonstrates that the specialized enzymatic repertoires of monoterpene-catabolizing bacteria are expanding the toolbox towards the tailored and sustainable biotechnological production of values-added aroma compounds (e.g., isonovalal, α-terpineol, and carvone isomers) whose implementation must be supported by the current advances in systems biology and metabolic engineering approaches.
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12
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Finnigan JD, Young C, Cook DJ, Charnock SJ, Black GW. Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:289-320. [PMID: 32951814 DOI: 10.1016/bs.apcsb.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).
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Affiliation(s)
| | - Carl Young
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | - Darren J Cook
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | | | - Gary W Black
- Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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13
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Lv G, Liu X, Zeng B, He B. Genome-Wide Analysis of the Cytochromes P450 Gene Family in Cordyceps militaris. JOURNAL OF PHYSICS: CONFERENCE SERIES 2020; 1549:032069. [DOI: 10.1088/1742-6596/1549/3/032069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Abstract
Cytochromes P450 (CYP450) gene family has been shown to play significant roles in various physiological processes of some species, including participate in the metabolism of various exogenous substances, synthesis of endogenous substances, abiotic and biotic stress responses and stress signaling. In this study, the members of CYP450 gene family in Cordyceps militaris (C.militaris) were identified and analyzed on the whole genome level using bioinformatics-based methods. The phylogenetic tree, gene structure, motifs and gene expression level under pH stress were analyzed. In total, 54 putative CYP450 gene family members were identified in C.militaris. The phylogenetic analysis indicated that all of the C.militaris CYP450 (CmCYP) genes, except CmCYP19, were grouped into 3 groups. The 54 CmCYP genes were randomly distributed on 7 chromosomes. The expression analysis of CmCYP under different pH environments showed the mechanism of CmCYP genes family involved in stress resistance regulation is complex and diversified. Systematic investigation of a gene family, would provide important insights into gene function and application. The results of this study will provide reference information for studying other abiotic and biotic stress response regulation mechanism of C.militaris.
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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15
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Wong NR, Liu X, Lloyd H, Colthart AM, Ferrazzoli AE, Cooper DL, Zhuang Y, Esquea P, Futcher J, Pochapsky TM, Matthews JM, Pochapsky TC. A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild. J Inorg Biochem 2018; 188:96-101. [PMID: 30170307 DOI: 10.1016/j.jinorgbio.2018.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/24/2018] [Accepted: 08/03/2018] [Indexed: 01/30/2023]
Abstract
A strategy for elucidating sequence determinants of function in the class of cytochrome P450 (CYP) enzymes that catalyze the first steps of terpene metabolism in wild microbiomes is described. Wild organisms that can use camphor, terpineol, pinene and limonene were isolated from soils rich in coniferous waste. Cell free extracts and growth beers were analyzed by gas chromatography/mass spectrometry to identify primary oxidative metabolites. For one organism, Pseudomonas nitroreducens TPJM, a cytochrome P450 (CYP108B1) isolated from cell free extracts was demonstrated to catalyze the oxidation of α-terpineol in assays combining the native ferredoxin and putidaredoxin reductase, and the resulting oxidation products identified by gas chromatography/mass spectrometry. Shotgun sequencing of PnTPJM identified four candidate P450 genes, including an apparently fragmentary gene with a high degree of homology with the known enzyme CYP108 (P450terp).
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Affiliation(s)
- Nathan R Wong
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Xinyue Liu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Hannah Lloyd
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Allison M Colthart
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Alexander E Ferrazzoli
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Deani L Cooper
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Yihao Zhuang
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Phillix Esquea
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Jeffrey Futcher
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Theodore M Pochapsky
- Malden Catholic High School, 90 Crystal St., Malden, MA 02148, United States of America
| | - Jeffrey M Matthews
- Malden Catholic High School, 90 Crystal St., Malden, MA 02148, United States of America
| | - Thomas C Pochapsky
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America; Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America.
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Dubey KD, Wang B, Vajpai M, Shaik S. MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450 BM3 alter the active site's complexity and the chemoselectivity of oxidation without changing the active species. Chem Sci 2017; 8:5335-5344. [PMID: 29568477 PMCID: PMC5851339 DOI: 10.1039/c7sc01932g] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/11/2017] [Indexed: 12/28/2022] Open
Abstract
A new water channel appears in the T268A mutant of P450BM3 and plays a role in the enzyme’s chemoselectivity.
It is a long-standing mechanistic consensus that the mutation of the proton-shuttle mediator Threonine (T) in Cytochrome P450 enzymes severs the water channel and thereby quenches the formation of the active species: the high-valent iron(iv)-oxo porphyrin π-cation radical species, compound I (Cpd I). Using MD simulations and hybrid QM/MM calculations of P450BM3 we demonstrate that this is not the case. Thus, while the original water channel is disrupted in the T268A mutant of the enzyme, a new channel is formed that generates Cpd I. With this new understanding, we address the puzzling regiochemical and kinetic-isotope effect (KIE) results (Volz et al., J. Am. Chem. Soc., 2002, 124, 9724–9725) on the sulfoxidation and N-dealkylation of dimethyl-(4-methylsulfanyl-phenyl)-amine by wild type (WT) P450BM3 and its T268A vs. F87A mutants. We show that the observed variable ratio of S/Me oxidation for these enzymes, vis-à-vis the constant KIE, originates from Cpd I being the sole oxidant. Thus, while the conserved KIE probes the conserved nature of the transition state, the variable regiochemical S/Me ratio reflects the active-site reorganization in the mutants: the shifted location of the new water channel in T268A tightens the binding of the S-end by Cpd I and increases the S/Me ratio, whereas the absence of π-interaction with the S-end in F87A creates a looser binding that lowers the S/Me ratio. Our results match the experimental findings. As such, this study sheds light on puzzling experimental results, and may shift a central paradigm in P450 research. The broader implication on enzymatic research is that a single-site mutation is not a localised alteration but one that may lead to a profound change in the active site, sufficiently so as to change the chemoselectivity of catalyzed reactions.
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Affiliation(s)
- Kshatresh Dutta Dubey
- Institute of Chemistry , The Lise Meitner-Minerva Center for Computational Quantum Chemistry , The Hebrew University of Jerusalem , 91904 , Jerusalem , Israel .
| | - Binju Wang
- Institute of Chemistry , The Lise Meitner-Minerva Center for Computational Quantum Chemistry , The Hebrew University of Jerusalem , 91904 , Jerusalem , Israel .
| | - Manu Vajpai
- Department of Biological Sciences and Bioengineering , Indian Institute of Technology-Kanpur , Kanpur-208016 , UP , India
| | - Sason Shaik
- Institute of Chemistry , The Lise Meitner-Minerva Center for Computational Quantum Chemistry , The Hebrew University of Jerusalem , 91904 , Jerusalem , Israel .
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Lee CW, Yu SC, Lee JH, Park SH, Park H, Oh TJ, Lee JH. Crystal Structure of a Putative Cytochrome P450 Alkane Hydroxylase (CYP153D17) from Sphingomonas sp. PAMC 26605 and Its Conformational Substrate Binding. Int J Mol Sci 2016; 17:ijms17122067. [PMID: 27941697 PMCID: PMC5187867 DOI: 10.3390/ijms17122067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/29/2016] [Accepted: 12/06/2016] [Indexed: 01/07/2023] Open
Abstract
Enzymatic alkane hydroxylation reactions are useful for producing pharmaceutical and agricultural chemical intermediates from hydrocarbons. Several cytochrome P450 enzymes catalyze the regio- and stereo-specific hydroxylation of alkanes. We evaluated the substrate binding of a putative CYP alkane hydroxylase (CYP153D17) from the bacterium Sphingomonas sp. PAMC 26605. Substrate affinities to C10-C12 n-alkanes and C10-C14 fatty acids with Kd values varied from 0.42 to 0.59 μM. A longer alkane (C12) bound more strongly than a shorter alkane (C10), while shorter fatty acids (C10, capric acid; C12, lauric acid) bound more strongly than a longer fatty acid (C14, myristic acid). These data displayed a broad substrate specificity of CYP153D17, hence it was named as a putative CYP alkane hydroxylase. Moreover, the crystal structure of CYP153D17 was determined at 3.1 Å resolution. This is the first study to provide structural information for the CYP153D family. Structural analysis showed that a co-purified alkane-like compound bound near the active-site heme group. The alkane-like substrate is in the hydrophobic pocket containing Thr74, Met90, Ala175, Ile240, Leu241, Val244, Leu292, Met295, and Phe393. Comparison with other CYP structures suggested that conformational changes in the β1-β2, α3-α4, and α6-α7 connecting loop are important for incorporating the long hydrophobic alkane-like substrate. These results improve the understanding of the catalytic mechanism of CYP153D17 and provide valuable information for future protein engineering studies.
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Affiliation(s)
- Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea.
| | - Sang-Cheol Yu
- Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea.
| | - Joo-Ho Lee
- Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea.
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea.
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea.
| | - Tae-Jin Oh
- Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea.
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea.
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Luo A, Wu YR, Xu Y, Kan J, Qiao J, Liang L, Huang T, Hu Z. Characterization of a cytochrome P450 monooxygenase capable of high molecular weight PAHs oxidization from Rhodococcus sp. P14. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.07.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Olatunji-Ojo OA, Cundari TR. C–H Activation by Multiply Bonded Complexes with Potentially Noninnocent Ligands: A Computational Study. Inorg Chem 2013; 52:8106-13. [DOI: 10.1021/ic400804x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Olayinka A. Olatunji-Ojo
- Department of Chemistry
and Center for Advanced Scientific
Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle, #305070 Denton, Texas 76203-5070,
United States
| | - Thomas R. Cundari
- Department of Chemistry
and Center for Advanced Scientific
Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle, #305070 Denton, Texas 76203-5070,
United States
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20
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Zhang M, Liu Y, Sun S, Zhang H, Wang W, Ning G, Li X. A prevalent and three novel mutations in CYP11B1 gene identified in Chinese patients with 11-beta hydroxylase deficiency. J Steroid Biochem Mol Biol 2013; 133:25-9. [PMID: 22964742 DOI: 10.1016/j.jsbmb.2012.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/25/2012] [Accepted: 08/28/2012] [Indexed: 01/28/2023]
Abstract
UNLABELLED 11β-Hydroxylase deficiency (11β-OHD), caused by CYP11B1 mutations, is characterized by hyporeninemic, hypokalemic hypertension and hyperandrogenism. We identified a prevalent and three novel mutations of CYP11B1 gene in nine patients with classic 11β-OHD. SUBJECTS AND METHODS Nine patients with 11β-OHD from unrelated families were recruited. The complications of 11β-OHD occurred in three patients who never received glucocorticoid treatment. CYP11B1 gene was sequenced and 11β-hydroxylase enzymatic activities were assessed in vitro. A haplotype analysis was performed to determine a common ancestor for those subjects who carried the same p.R454C mutation. RESULTS CYP11B1 gene mutations were identified in all patients, with a prevalent (p.R454C) and three novel mutations (p.V148G, IVS7-9C>A, c.1359_1360insG). The p.R141X, p.V148G, c.1359_1360insG and p.R454C mutations retained 4.9%, 3.9%, 3.7%, 4.5% of residual enzymatic activity, respectively. Five of nine patients carried p.R454C mutation, which was only reported in Chinese 11OHD patients. Haplotype analysis showed that this mutation might be inherited from a common ancestor. CONCLUSION The enzymatic activities for p.R141X, p.V148G, c.1359_1360insG and p.R454C mutants were almost completely abolished, which corresponds to classic form of 11β-OHD. The observations of a prevalent mutation and three novel mutations might have potential clinical utility for genetic counseling and prenatal diagnosis in Chinese 11β-OHD patients.
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Affiliation(s)
- Manna Zhang
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory of Endocrine Tumor, Shanghai Institute of Endocrinology and Metabolism, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 RuiJin 2nd Road, Shanghai 200025, China
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21
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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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23
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Zhou R, Huang C, Zhang A, Bell SG, Zhou W, Wong LL. Crystallization and preliminary X-ray analysis of CYP153C1 from Novosphingobium aromaticivorans DSM12444. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:964-7. [PMID: 21821906 PMCID: PMC3151139 DOI: 10.1107/s174430911102464x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 06/22/2011] [Indexed: 11/10/2022]
Abstract
Cytochrome P450 (CYP) enzymes constitute a large family of haemoproteins that catalyze the monooxygenation of a great variety of endogenous and exogenous organic compounds. In common with other members of the CYP153 family of alkane hydroxylases, CYP153C1 from the oligotrophic bacterium Novosphingobium aromaticivorans DSM 12444 can bind linear alkanes such as heptane, octane and nonane. Here, the production, purification and crystallization of CYP153C1 and the collection of high-resolution diffraction data to 1.77 Å resolution are reported. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 61.0, b = 96.3, c = 149.8 Å, α = β = γ = 90.0°. Preliminary X-ray diffraction data analysis revealed that the asymmetric unit is most likely to contain two protein molecules.
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Affiliation(s)
- Ruimin Zhou
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Cong Huang
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Aili Zhang
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Stephen G. Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, England
| | - Weihong Zhou
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Luet-Lok Wong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, England
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Fujishiro T, Shoji O, Nagano S, Sugimoto H, Shiro Y, Watanabe Y. Crystal structure of H2O2-dependent cytochrome P450SPalpha with its bound fatty acid substrate: insight into the regioselective hydroxylation of fatty acids at the alpha position. J Biol Chem 2011; 286:29941-50. [PMID: 21719702 DOI: 10.1074/jbc.m111.245225] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cytochrome P450(SPα) (CYP152B1) isolated from Sphingomonas paucimobilis is the first P450 to be classified as a H(2)O(2)-dependent P450. P450(SPα) hydroxylates fatty acids with high α-regioselectivity. Herein we report the crystal structure of P450(SPα) with palmitic acid as a substrate at a resolution of 1.65 Å. The structure revealed that the C(α) of the bound palmitic acid in one of the alternative conformations is 4.5 Å from the heme iron. This conformation explains the highly selective α-hydroxylation of fatty acid observed in P450(SPα). Mutations at the active site and the F-G loop of P450(SPα) did not impair its regioselectivity. The crystal structures of mutants (L78F and F288G) revealed that the location of the bound palmitic acid was essentially the same as that in the WT, although amino acids at the active site were replaced with the corresponding amino acids of cytochrome P450(BSβ) (CYP152A1), which shows β-regioselectivity. This implies that the high regioselectivity of P450(SPα) is caused by the orientation of the hydrophobic channel, which is more perpendicular to the heme plane than that of P450(BSβ).
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Affiliation(s)
- Takashi Fujishiro
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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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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Abstract
A hydrogen bond network has been identified that adjusts protein-substrate contacts in cytochrome P450(cam) (CYP101A1). Replacing the native substrate camphor with adamantanone or norcamphor causes perturbations in NMR-detected NH correlations assigned to the network, which includes portions of a β sheet and an adjacent helix that is remote from the active site. A mutation in this helix reduces enzyme efficiency and perturbs the extent of substrate-induced spin state changes at the haem iron that accompany substrate binding. In turn, the magnitude of the spin state changes induced by alternate substrate binding parallel the NMR-detected perturbations observed near the haem in the enzyme active site.
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Affiliation(s)
- Marina Dang
- Dept. of Chemistry, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110 USA
| | - Susan Sondej Pochapsky
- Dept. of Chemistry, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110 USA
| | - Thomas C. Pochapsky
- Dept. of Chemistry, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110 USA
- Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, MA 02454-9110 USA
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Whitehouse CJC, Yang W, Yorke JA, Rowlatt BC, Strong AJF, Blanford CF, Bell SG, Bartlam M, Wong LL, Rao Z. Structural Basis for the Properties of Two Single-Site Proline Mutants of CYP102A1 (P450BM3). Chembiochem 2010; 11:2549-56. [DOI: 10.1002/cbic.201000421] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pochapsky TC, Kazanis S, Dang M. Conformational plasticity and structure/function relationships in cytochromes P450. Antioxid Redox Signal 2010; 13:1273-96. [PMID: 20446763 PMCID: PMC2959183 DOI: 10.1089/ars.2010.3109] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The cytochrome P450s are a superfamily of enzymes that are found in all kingdoms of living organisms, and typically catalyze the oxidative addition of atomic oxygen to an unactivated C-C or C-H bond. Over 8000 nonredundant sequences of putative and confirmed P450 enzymes have been identified, but three-dimensional structures have been determined for only a small fraction of these. While all P450 enzymes for which structures have been determined share a common global fold, the flexibility and modularity of structure around the active site account for the ability of P450 enzymes to accommodate a vast number of structurally dissimilar substrates and support a wide range of selective oxidations. In this review, known P450 structures are compared, and some structural criteria for prediction of substrate selectivity and reaction type are suggested. The importance of dynamic processes such as redox-dependent and effector-induced conformational changes in determining catalytic competence and regio- and stereoselectivity is discussed, and noncrystallographic methods for characterizing P450 structures and dynamics, in particular, mass spectrometry and nuclear magnetic resonance spectroscopy are reviewed.
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Affiliation(s)
- Thomas C Pochapsky
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
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29
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Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R. How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel? J Phys Chem B 2010; 114:5964-70. [PMID: 20387782 PMCID: PMC2861407 DOI: 10.1021/jp101894k] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 03/27/2010] [Indexed: 11/28/2022]
Abstract
Water molecules play a major role in the P450 catalytic cycle. Here, we locate the preferred water pathways and their gating mechanisms for the human cytochrome P450 3A4 (CYP3A4) and elucidate the role of the cytochrome P450 reductase (CPR) in turning on and activating these water channels. We perform explicit solvent molecular dynamic simulations of CYP3A4, unbound and bound to two substrates, and with and without the flavin mononucleotide (FMN)-binding domain of CPR. We observe in/out passage of water molecules via a water-specific and conserved channel (aqueduct) located between the active site and the heme proximal side. We find that the aqueduct gating mechanism is mediated by R375, the conserved arginine that salt bridges with the heme 7-propionate. When R375 rotates, it opens the aqueduct and establishes a connection between a cluster of active site water molecules network and the bulk solvent. The aqueduct region overlaps with the CPR binding-site to CYP3A4. Indeed, we find that when the FMN domain of CPR binds to CYP3A4, the aqueduct fully opens up, thereby allowing a flow of water molecules. The aqueduct's opening can permit proton transfer, shuttling the protons to the active site through ordered water molecules. In addition, the expulsion of water molecules via the aqueduct contributes to substrate binding. As such, the CPR binding has a function: it triggers the aqueduct's opening and thereby enables a proton shuttle pathway, which is needed for the dioxygen activation. This mechanism could be a general paradigm in P450s.
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Affiliation(s)
| | | | | | - Ruth Nussinov
- Corresponding author. Phone: 301-846-5579. Fax: 301-846-5598. E-mail:
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30
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Swart AC, Storbeck KH, Swart P. A single amino acid residue, Ala 105, confers 16alpha-hydroxylase activity to human cytochrome P450 17alpha-hydroxylase/17,20 lyase. J Steroid Biochem Mol Biol 2010; 119:112-20. [PMID: 20043997 DOI: 10.1016/j.jsbmb.2009.12.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 11/19/2022]
Abstract
In adrenal steroidogenesis, CYP17 catalyses the 17alpha-hydroxylation of pregnenolone and progesterone and the subsequent 17,20-lyase reaction, yielding adrenal androgens. The enzyme exhibits distinctly different selectivities towards these substrates in various species. CYP17 has also been shown to exhibit 16alpha-hydroxylase activity towards progesterone in some species, with only human and chimp CYP17 catalysing the biosynthesis of substantial amounts of 16-OHprogesterone. The 16alpha-hydroxylase activity was investigated by introducing an Ala105Leu substitution into human CYP17. The converse mutation, Leu105Ala was introduced into the baboon, goat and pig enzymes. Wt human CYP17 converted approximately 30% progesterone to 16-OHprogesterone while the Ala105Leu mutant converted negligible amounts to 16-OHprogesterone ( approximately 9%), comparable to wt CYP17 of the other three species when expressed in COS-1 cells. The ratio of 17-hydroxylated products to 16-OHprogesterone of human CYP17 was 2.7 and that of the mutant human construct 10.5. Similar ratios were observed for human and goat CYP17 with the corresponding Ala or Leu residues. Although the Leu105Ala mutation of both baboon and pig CYP17 exhibited the same trend regarding the ratios, the rate of progesterone conversion was reduced. Coexpression with cytochrome b(5) significantly decreased the ratio of 17-hydroxylated products to 16-OHprogesterone in the Leu105 constructs, while effects were negligible with Ala at this position. Homology models show that Ala105 faces towards the active pocket in the predicted B'-C domain of CYP17. The smaller residue allows more flexibility of movement in the active pocket than Leu, presenting both the C16 and C17 of progesterone to the iron-oxy complex.
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Affiliation(s)
- Amanda C Swart
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7600, South Africa.
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31
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Ghosh D, Griswold J, Erman M, Pangborn W. X-ray structure of human aromatase reveals an androgen-specific active site. J Steroid Biochem Mol Biol 2010; 118:197-202. [PMID: 19808095 PMCID: PMC2826573 DOI: 10.1016/j.jsbmb.2009.09.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 09/13/2009] [Accepted: 09/24/2009] [Indexed: 11/30/2022]
Abstract
Aromatase is a unique cytochrome P450 that catalyzes the removal of the 19-methyl group and aromatization of the A-ring of androgens for the synthesis of estrogens. All human estrogens are synthesized via this enzymatic aromatization pathway. Aromatase inhibitors thus constitute a frontline therapy for estrogen-dependent breast cancer. Despite decades of intense investigation, this enzyme of the endoplasmic reticulum membrane has eluded all structure determination efforts. We have determined the crystal structure of the highly active aromatase purified from human placenta, in complex with its natural substrate androstenedione. The structure shows the binding mode of androstenedione in the catalytically active oxidized high-spin ferric state of the enzyme. Hydrogen bond-forming interactions and tight packing hydrophobic side chains that complement the puckering of the steroid backbone provide the molecular basis for the exclusive androgenic specificity of aromatase. Locations of catalytic residues and water molecules shed new light on the mechanism of the aromatization step. The structure also suggests a membrane integration model indicative of the passage of steroids through the lipid bilayer.
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Affiliation(s)
- Debashis Ghosh
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA.
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32
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McLean KJ, Lafite P, Levy C, Cheesman MR, Mast N, Pikuleva IA, Leys D, Munro AW. The Structure of Mycobacterium tuberculosis CYP125: molecular basis for cholesterol binding in a P450 needed for host infection. J Biol Chem 2010; 284:35524-33. [PMID: 19846552 DOI: 10.1074/jbc.m109.032706] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report characterization and the crystal structure of the Mycobacterium tuberculosis cytochrome P450 CYP125, a P450 implicated in metabolism of host cholesterol and essential for establishing infection in mice. CYP125 is purified in a high spin form and undergoes both type I and II spectral shifts with various azole drugs. The 1.4-A structure of ligand-free CYP125 reveals a "letterbox" active site cavity of dimensions appropriate for entry of a polycyclic sterol. A mixture of hexa-coordinate and penta-coordinate states could be discerned, with water binding as the 6th heme-ligand linked to conformation of the I-helix Val(267) residue. Structures in complex with androstenedione and the antitubercular drug econazole reveal that binding of hydrophobic ligands occurs within the active site cavity. Due to the funnel shape of the active site near the heme, neither approaches the heme iron. A model of the cholesterol CYP125 complex shows that the alkyl side chain extends toward the heme iron, predicting hydroxylation of cholesterol C27. The alkyl chain is in close contact to Val(267), suggesting a substrate binding-induced low- to high-spin transition coupled to reorientation of the latter residue. Reconstitution of CYP125 activity with a redox partner system revealed exclusively cholesterol 27-hydroxylation, consistent with structure and modeling. This activity may enable catabolism of host cholesterol or generation of immunomodulatory compounds that enable persistence in the host. This study reveals structural and catalytic properties of a potential M. tuberculosis drug target enzyme, and the likely mode by which the host-derived substrate is bound and hydroxylated.
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Affiliation(s)
- Kirsty J McLean
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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33
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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34
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Saberi MR, Shah K, Simons C. Benzofuran- and furan-2-yl-(phenyl)-3-pyridylmethanols: Synthesis and inhibition of P450 aromatase. J Enzyme Inhib Med Chem 2008; 20:135-41. [PMID: 15968818 DOI: 10.1080/14756360400015256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
A series of benzofuran-2-yl-(phenyl)-3-pyridylmethanol derivatives were prepared using an efficient 1-step procedure in good yields. In addition furan-2-yl-(phenyl)-3-pyridylmethanol derivatives were also prepared to determine the effect of the benzene ring in benzofuran with respect to inhibitory activity. The pyridylmethanol derivatives were all evaluated in vitro for inhibitory activity against aromatase (P450(AROM), CYP19), using human placental microsomes. The benzofuran-2-yl-(phenyl)-3-pyridylmethanol derivatives showed good to moderate activity (IC50 = 1.3-25.1 microM), which was either better than or comparable with aminoglutethimide (IC50 = 18.5 microM) but lower than arimidex (IC50 = 0.6 microM), with the 4-methoxyphenyl substituted derivative displaying optimum activity. Molecular modelling of the benzofuran-2-yl-(4-fluorophenyl)-3-pyridylmethanol derivative suggested activity to reside with the (S)-enantiomer. The furan-2-yl-(phenyl)-3-pyridylmethanol derivatives were devoid of activity indicating the essential role of the benzene ring of the benzofuran component for enzyme binding.
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Affiliation(s)
- Mohammed R Saberi
- Medicinal Chemistry Division, Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3XF, UK
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35
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Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase. Proc Natl Acad Sci U S A 2008; 105:13883-8. [PMID: 18787124 DOI: 10.1073/pnas.0804099105] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome P450s exist ubiquitously in all organisms and are involved in many biological processes. Allene oxide synthase (AOS) is a P450 enzyme that plays a key role in the biosynthesis of oxylipin jasmonates, which are involved in signal and defense reactions in higher plants. The crystal structures of guayule (Parthenium argentatum) AOS (CYP74A2) and its complex with the substrate analog 13(S)-hydroxyoctadeca-9Z,11E-dienoic acid have been determined. The structures exhibit a classic P450 fold but possess a heme-binding mode with an unusually long heme binding loop and a unique I-helix. The structures also reveal two channels through which substrate and product may access and leave the active site. The entrances are defined by a loop between beta3-2 and beta3-3. Asn-276 in the substrate binding site may interact with the substrate's hydroperoxy group and play an important role in catalysis, and Lys-282 at the entrance may control substrate access and binding. These studies provide both structural insights into AOS and related P450s and a structural basis to understand the distinct reaction mechanism.
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36
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Bell SG, Xu F, Forward I, Bartlam M, Rao Z, Wong LL. Crystal structure of CYP199A2, a para-substituted benzoic acid oxidizing cytochrome P450 from Rhodopseudomonas palustris. J Mol Biol 2008; 383:561-74. [PMID: 18762195 DOI: 10.1016/j.jmb.2008.08.033] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 08/13/2008] [Accepted: 08/14/2008] [Indexed: 11/17/2022]
Abstract
CYP199A2, a cytochrome P450 enzyme from Rhodopseudomonas palustris, oxidatively demethylates 4-methoxybenzoic acid to 4-hydroxybenzoic acid. 4-Ethylbenzoic acid is converted to a mixture of predominantly 4-(1-hydroxyethyl)-benzoic acid and 4-vinylbenzoic acid, the latter being a rare example of CC bond dehydrogenation of an unbranched alkyl group. The crystal structure of CYP199A2 has been determined at 2.0-A resolution. The enzyme has the common P450 fold, but the B' helix is missing and the G helix is broken into two (G and G') by a kink at Pro204. Helices G and G' are bent back from the extended BC loop and the I helix to open up a clearly defined substrate access channel. Channel openings in this region of the P450 fold are rare in bacterial P450 enzymes but more common in eukaryotic P450 enzymes. The channel is hydrophobic except for the basic residue Arg246 at the entrance, which probably plays a role in the specificity of this enzyme for charged benzoates over neutral phenols and benzenes. The substrate binding pocket is hydrophobic, with Ser97 and Ser247 being the only polar residues. Computer docking of 4-ethylbenzoic acid into the active site suggests that the substrate carboxylate oxygens interact with Ser97 and Ser247, and the beta-methyl group is located over the heme iron by Phe185, the side chain of which is only 6.35 A above the iron in the native structure. This binding orientation is consistent with the observed product profile of exclusive attack at the para substituent. Putidaredoxin of the CYP101A1 system from Pseudomonas putida supports substrate oxidation by CYP199A2 at approximately 6% of the activity of the physiological ferredoxin. Comparison of the heme proximal faces of CYP199A2 and CYP101A1 suggests that charge reversal surrounding the surface residue Leu369 in CYP199A2 may be a significant factor in this low cross-activity.
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Affiliation(s)
- Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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37
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Lisurek M, Simgen B, Antes I, Bernhardt R. Theoretical and Experimental Evaluation of a CYP106A2 Low Homology Model and Production of Mutants with Changed Activity and Selectivity of Hydroxylation. Chembiochem 2008; 9:1439-49. [DOI: 10.1002/cbic.200700670] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Zhao LQ, Han S, Tian HM. Progress in molecular-genetic studies on congenital adrenal hyperplasia due to 11beta-hydroxylase deficiency. World J Pediatr 2008; 4:85-90. [PMID: 18661760 DOI: 10.1007/s12519-008-0016-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND 11beta-hydroxylase deficiency is one of the main causes of congenital adrenal hyperplasia (CAH). It is caused by the mutation of the CYP11B1 gene that encodes the enzyme. Researches have shown that mutations of the CYP11B1 gene would result in activity decrease or inactivation of the enzyme in classical 11beta-hydroxylase deficiency. DATA SOURCES Articles on CAH and CYP11B1 gene mutation were retrieved from PubMed and MEDLINE published after 1991. RESULTS The prevalence, pathophysiology, and molecular-genetic mechanisms were summarized. CONCLUSIONS The disease is caused by genetic mutations of CYP11B1, and types of the mutations are varied. In classical 11beta-hydroxylase deficiency, genetic mutations of CYP11B1 lead to activity decrease or loss; mutations in unclassical 11beta-hydroxylase deficiency are not definite. And the relationship between genotype and phenotype is not established.
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Affiliation(s)
- Li-Qiang Zhao
- Department of Endocrinology, West China Hospital of Sichuan University, Chengdu 610000, China
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39
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Hata M, Tanaka Y, Kyoda N, Osakabe T, Yuki H, Ishii I, Kitada M, Neya S, Hoshino T. An epoxidation mechanism of carbamazepine by CYP3A4. Bioorg Med Chem 2008; 16:5134-48. [DOI: 10.1016/j.bmc.2008.03.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 03/05/2008] [Accepted: 03/06/2008] [Indexed: 11/25/2022]
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40
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Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions. Br J Pharmacol 2007; 153 Suppl 1:S82-9. [PMID: 18026129 DOI: 10.1038/sj.bjp.0707570] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The cytochromes P450 (CYPs) comprise a vast superfamily of enzymes found in virtually all life forms. In mammals, xenobiotic metabolizing CYPs provide crucial protection from the effects of exposure to a wide variety of chemicals, including environmental toxins and therapeutic drugs. Ideally, the information on the possible metabolism by CYPs required during drug development would be obtained from crystal structures of all the CYPs of interest. For some years only crystal structures of distantly related bacterial CYPs were available and homology modelling techniques were used to bridge the gap and produce structural models of human CYPs, and thereby obtain useful functional information. A significant step forward in the reliability of these models came seven years ago with the first crystal structure of a mammalian CYP, rabbit CYP2C5, followed by the structures of six human enzymes, CYP1A2, CYP2A6, CYP2C8, CYP2C9, CYP2D6 and CYP3A4, and a second rabbit enzyme, CYP2B4. In this review we describe as a case study the evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism. This work has led directly to the successful design of CYP2D6 mutants with novel activity-including creating a testosterone hydroxylase, converting quinidine from inhibitor to substrate, creating a diclofenac hydroxylase and creating a dextromethorphan O-demethylase. Our modelling-derived hypothesis-driven integrated interdisciplinary studies have given key insight into the molecular determinants of CYP2D6 and other important drug metabolizing enzymes.
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41
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Berne C, Pignol D, Lavergne J, Garcia D. CYP201A2, a cytochrome P450 from Rhodopseudomonas palustris, plays a key role in the biodegradation of tributyl phosphate. Appl Microbiol Biotechnol 2007; 77:135-44. [PMID: 17786430 DOI: 10.1007/s00253-007-1140-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 07/26/2007] [Accepted: 07/31/2007] [Indexed: 10/22/2022]
Abstract
Tributyl phosphate (TBP) is a toxic organophosphorous compound widely used in nuclear fuel processing and chemical industries. Rhodopseudomonas palustris, one of the most metabolically versatile photosynthetic bacteria, is shown here to degrade TBP efficiently under photosynthetic conditions. This study shows that this O(2)- and NADPH/FMNH(2)-dependent process was also catalyzed when TBP was incubated with membrane-associated proteins extracted from this strain. The effects of several regulators of cytochrome P450 activity on the TBP consumption suggest a key role for a cytochrome P450 in this process. Disruption of the rpa0241 gene encoding a putative cytochrome P450 led to a 60% decrease of the TBP catabolism, whereas reintroducing the gene in the mutant restored the wild-type phenotype. The rpa0241 gene was expressed and purified in Escherichia coli. Characterization by UV-visible spectroscopy of the purified recombinant membrane-bound protein (CYP201A2) encoded by the rpa0241 gene revealed typical spectral characteristics of cytochrome P450 with a large spin state change of the heme iron associated with binding of TBP (K (d) approximately 65 microM). It is proposed that CYP201A2 catalyzes the initial step of the biodegradation process of TBP.
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Affiliation(s)
- Cécile Berne
- DSV/IBEB/SBVME/LBC, Unité Mixte de Recherche 6191, Centre National de la Recherche Scientifique/CEA/Univ. Aix-Marseille, CEA Cadarache, Saint Paul lez Durance, France
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42
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Li L, Cheng H, Gai J, Yu D. Genome-wide identification and characterization of putative cytochrome P450 genes in the model legume Medicago truncatula. PLANTA 2007; 226:109-23. [PMID: 17273868 DOI: 10.1007/s00425-006-0473-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 12/20/2006] [Indexed: 05/13/2023]
Abstract
In plants, cytochrome P450 is a group of monooxygenases existing as a gene superfamily and plays important roles in metabolizing physiologically important compounds. However, to date only a limited number of P450s have been identified and characterized in legumes. In this study, data mining methods were used, and 151 putative P450 genes in the model legume Medicago truncatula were identified, including 135 novel sequences. These genes were classified into 9 clans and 44 families by sequence similarity, and among those 4 new clans and 21 new families not reported previously in legumes. By comparison of these genes with P450 genes in Arabidopsis and rice, it was found that most of the known P450 families in dicot species exist in M. truncatula. The representative protein sequences of putative P450s were aligned, and the secondary elements were assigned based on the known structure P450BM3. Putative substrate recognition sites (SRSs) and substrate binding sites were also identified in these sequences. In addition, the ESTs-derived expression profiles (digital Northern) of the putative P450 genes were analyzed, which was confirmed by semi-quantitative RT-PCR analyses of several selected P450 genes. These results will provide a base for catalogue information on P450 genes in M. truncatula and for further functional analysis of P450 superfamily genes in legumes.
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Affiliation(s)
- Lingyong Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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43
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Hudecek J, Hodek P, Anzenbacherová E, Anzenbacher P. Structural analysis of cytochromes P450 shows differences in flexibility of heme 2- and 4-vinyls. Biochim Biophys Acta Gen Subj 2007; 1770:413-9. [PMID: 17123739 DOI: 10.1016/j.bbagen.2006.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/11/2006] [Accepted: 10/13/2006] [Indexed: 11/29/2022]
Abstract
Structural analysis of the orientations of heme vinyl side chains was carried out using the published crystallographic data for different cytochromes P450. Torsional angles (tau, C(alpha)C(beta)-C(a)C(b)) show different distributions for the vinyls in positions 2 and 4. Whereas the orientation of 2-vinyls is rather restricted (tau between -120 degrees and -180 degrees ), the 4-vinyls have a much higher mobility over almost the entire conformational space. On the basis of the empirical correlation recently reported for peroxidases (M.P. Marzocchi, G. Smulevich, Relationship between heme vinyl conformation and the protein matrix in peroxidases, J. Raman Spectrosc. 34 (2003), 725-736), an attempt has been made to compare the observed vinyl orientations with the experimental frequencies of the vinyl stretching vibrational modes. The data for P450 proteins do not exactly match the peroxidase-derived function, although a qualitatively similar relationship is likely to exist. Differences between P450 forms suggest a variability in heme-region flexibility and in communication with the rest of enzyme.
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Affiliation(s)
- Jirí Hudecek
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12840 Prague 2, Czech Republic.
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44
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Bonifacio A, Groenhof AR, Keizers PHJ, de Graaf C, Commandeur JNM, Vermeulen NPE, Ehlers AW, Lammertsma K, Gooijer C, van der Zwan G. Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study. J Biol Inorg Chem 2007; 12:645-54. [PMID: 17318599 PMCID: PMC1915625 DOI: 10.1007/s00775-007-0210-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 01/23/2007] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) is one of the most important cytochromes P450 in humans. Resonance Raman data from the T309V mutant of CYP2D6 show that the substitution of the conserved I-helix threonine situated in the enzyme's active site perturbs the heme spin equilibrium in favor of the six-coordinated low-spin species. A mechanistic hypothesis is introduced to explain the experimental observations, and its compatibility with the available structural and spectroscopic data is tested using quantum-mechanical density functional theory calculations on active-site models for both the CYP2D6 wild type and the T309V mutant.
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Affiliation(s)
- Alois Bonifacio
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - André R. Groenhof
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Peter H. J. Keizers
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jan N. M. Commandeur
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Andreas W. Ehlers
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Koop Lammertsma
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Cees Gooijer
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Gert van der Zwan
- Department of Chemistry and Pharmaceutical Sciences, Sections of Analytical Chemistry and Applied Spectroscopy (ACAS), Organic and Inorganic Chemistry and Molecular Toxicology, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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45
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Munro AW, Girvan HM, McLean KJ. Variations on a (t)heme—novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily. Nat Prod Rep 2007; 24:585-609. [PMID: 17534532 DOI: 10.1039/b604190f] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Andrew W Munro
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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46
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Storbeck KH, Swart P, Graham S, Swart AC. Evidence for the functional role of residues in the B'-C loop of baboon cytochrome P450 side-chain cleavage (CYP11A1) obtained by site-directed mutagenesis, kinetic analysis and homology modelling. J Steroid Biochem Mol Biol 2007; 103:65-75. [PMID: 17081746 DOI: 10.1016/j.jsbmb.2006.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 07/12/2006] [Indexed: 10/24/2022]
Abstract
To gain further insight into the structure/function relationship of cytochrome P450 side-chain cleavage (CYP11A1), this enzyme was investigated in the Cape baboon (Papio ursinus). Four constructs were cloned and characterised in non-steroidogenic mammalian COS-1 cells. Wild type recombinant baboon CYP11A1 cDNA yielded a K(m) value of 1.6 microM for 25-hydroxycholesterol. The single amino acid substitutions, I98Q and I98K resulted in a 1.7- and 2.8-fold increases in K(m) values, respectively. Conversely, the introduction of the mutation, K103A, resulted in a 1.8-fold decrease in K(m). A homology model of CYP11A1, based on the crystal structures of CYP102 and CYP2C5, revealed that residues 98 and 103 lie within the B'-C loop and contribute to the spatial orientation and structural integrity of this domain. Based on these results we propose a topological model of the CYP11A1 active pocket, which is supported by substrate docking analysis and kinetic studies.
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Affiliation(s)
- Karl-Heinz Storbeck
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa
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47
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Chiang CW, Yeh HC, Wang LH, Chan NL. Crystal structure of the human prostacyclin synthase. J Mol Biol 2006; 364:266-74. [PMID: 17020766 PMCID: PMC1995163 DOI: 10.1016/j.jmb.2006.09.039] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 09/13/2006] [Accepted: 09/14/2006] [Indexed: 11/25/2022]
Abstract
Prostacyclin synthase (PGIS) catalyzes an isomerization of prostaglandin H(2) to prostacyclin, a potent mediator of vasodilation and anti-platelet aggregation. Here, we report the crystal structure of human PGIS at 2.15 A resolution, which represents the first three-dimensional structure of a class III cytochrome P450. While notable sequence divergence has been recognized between PGIS and other P450s, PGIS exhibits the typical triangular prism-shaped P450 fold with only moderate structural differences. The conserved acid-alcohol pair in the I helix of P450s is replaced by residues G286 and N287 in PGIS, but the distinctive disruption of the I helix and the presence of a nearby water channel remain conserved. The side-chain of N287 appears to be positioned to facilitate the endoperoxide bond cleavage, suggesting a functional conservation of this residue in O-O bond cleavage. A combination of bent I helix and tilted B' helix creates a channel extending from the heme distal pocket, which seemingly allows binding of various ligands; however, residue W282, placed in this channel at a distance of 8.4 A from the iron with its indole side-chain lying parallel with the porphyrin plane, may serve as a threshold to exclude most ligands from binding. Additionally, a long "meander" region protruding from the protein surface may impede electron transfer. Although the primary sequence of the PGIS cysteine ligand loop diverges significantly from the consensus, conserved tertiary structure and hydrogen bonding pattern are observed for this region. The substrate-binding model was constructed and the structural basis for prostacyclin biosynthesis is discussed.
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Affiliation(s)
- Chia-Wang Chiang
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung City 402, Taiwan
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48
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de Groot MJ. Designing better drugs: predicting cytochrome P450 metabolism. Drug Discov Today 2006; 11:601-6. [PMID: 16793528 DOI: 10.1016/j.drudis.2006.05.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 04/21/2006] [Accepted: 05/10/2006] [Indexed: 10/24/2022]
Abstract
Many 3D ligand-based and structure-based computational approaches have been used to predict, and thus help explain, the metabolism catalyzed by the enzymes of the cytochrome P450 superfamily (P450s). P450s are responsible for >90% of the metabolism of all drugs, so the computational prediction of metabolism can help to design out drug-drug interactions in the early phases of the drug discovery process. Computational methodologies have focused on a few P450s that are directly involved in drug metabolism. The recently derived crystal structures for human P450s enable better 3D modelling of these important metabolizing enzymes. Models derived for P450s have evolved from simple comparisons of known substrates to more-elaborate experiments that require considerable computer power involving 3D overlaps and docking experiments. These models help to explain and, more importantly, predict the involvement of P450s in the metabolism of specific compounds and guide the drug-design process.
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Affiliation(s)
- Marcel J de Groot
- Sandwich Chemistry, Pfizer Global Research & Development, Sandwich Laboratories, Kent CT13 9NJ, UK.
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49
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Yu J, Paine MJI, Maréchal JD, Kemp CA, Ward CJ, Brown S, Sutcliffe MJ, Roberts GCK, Rankin EM, Wolf CR. IN SILICO PREDICTION OF DRUG BINDING TO CYP2D6: IDENTIFICATION OF A NEW METABOLITE OF METOCLOPRAMIDE. Drug Metab Dispos 2006; 34:1386-92. [PMID: 16698891 DOI: 10.1124/dmd.106.009852] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Patients with cancer often take many different classes of drugs to treat the effects of their malignancy and the side effects of treatment, as well as their comorbidities. The potential for drug-drug interactions that may affect the efficacy of anticancer treatment is high, and a major source of such interactions is competition for the drug-metabolizing enzymes, cytochromes P450 (P450s). We have examined a series of 20 drugs commonly prescribed to cancer patients to look for potential interactions via CYP2D6. We used a homology model of CYP2D6, together with molecular docking techniques, to perform an in silico screen for binding to CYP2D6. Experimental IC50 values were determined for these compounds and compared with the model predictions to reveal a correlation with a regression coefficient of r2= 0.61. Importantly, the docked conformation of the commonly prescribed antiemetic metoclopramide predicted a new site of metabolism that was further investigated through in vitro analysis with recombinant CYP2D6. An aromatic N-hydroxy metabolite of metoclopramide, consistent with predictions from our modeling studies, was identified by high-performance liquid chromatography/mass spectrometry. This metabolite was found to represent a major product of metabolism in human liver microsomes, and CYP2D6 was identified as the main P450 isoform responsible for catalyzing its formation. In view of the prevalence of interindividual variation in the CYP2D6 genotype and phenotype, we suggest that those experiencing adverse reactions with metoclopramide, e.g., extrapyramidal syndrome, are likely to have a particular CYP2D6 genotype/phenotype. This warrants further investigation.
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Affiliation(s)
- Jinglei Yu
- Division of Cancer Medicine, Biomedical Research Centre, University of Dundee, Ninewells Hospital & Medical School, Dundee, DD1 9SY, UK
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50
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Adris P, Chung KT. Metabolic activation of bladder procarcinogens, 2-aminofluorene, 4-aminobiphenyl, and benzidine by Pseudomonas aeruginosa and other human endogenous bacteria. Toxicol In Vitro 2006; 20:367-74. [PMID: 16203120 DOI: 10.1016/j.tiv.2005.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 07/28/2005] [Accepted: 08/17/2005] [Indexed: 11/20/2022]
Abstract
Pseudomonas aeruginosa, an opportunistic pathogen of the human urinary tract, and other selected human endogenous bacteria were investigated for metabolic activation of the bladder procarcinogens, 2-aminofluorene (2-AF), 4-aminobiphenyl (4-AB), and benzidine (Bz). The cell-free extracts of Pseudomonas aeruginosa, Escherichia coli, Enterobacter aerogenes, Proteus mirabilis, Proteus vulgaris, Staphylococcus epidermidis, Staphylococcus saprophyticus, Klebsiella pneumoniae, and intestinal anaerobes, Bacteroides fragilis, Clostridium perfringens, and Eubacterium aerofaciens produced increased histidine revertant frequencies with the tester strain Salmonella typhimurium TA98 in the Ames Salmonella mutagenicity assay. In addition, the cell-free extracts of Pseudomonas aeruginosa, Bacteroides fragilis, and Eubacterium aerofaciens each showed the presence of a cytochrome P450 absorption peak in the carbon monoxide (CO) difference spectrum. This was not demonstratable for the other bacteria. Our findings indicate that human endogenous bacteria, which are opportunistic pathogens of the urinary bladder, can metabolically activate the bladder procarcinogens 2-AF, 4-AB, and Bz into mutagens. The metabolic activation by Pseudomonas aeruginosa, Bacteroides fragilis, and Eubacterium aerofaciens is mediated by a cytochrome P450 enzyme. For those organisms that induced metabolic activation but did not show a P450 absorption peak with the cell-free extracts, other oxidative enzymes may be involved.
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Affiliation(s)
- Piyatilake Adris
- Department of Biology, The University of Memphis, 3774 Walker Street, Memphis, TN 38152, USA
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