1
|
Mohamed H, Child SA, Doherty DZ, Bruning JB, Bell SG. Structural determination and characterisation of the CYP105Q4 cytochrome P450 enzyme from Mycobacterium marinum. Arch Biochem Biophys 2024; 754:109950. [PMID: 38430969 DOI: 10.1016/j.abb.2024.109950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
The cytochrome P450 family of heme metalloenzymes (CYPs) catalyse important biological monooxygenation reactions. Mycobacterium marinum contains a gene encoding a CYP105Q4 enzyme of unknown function. Other members of the CYP105 CYP family have key roles in bacterial metabolism including the synthesis of secondary metabolites. We produced and purified the cytochrome P450 enzyme CYP105Q4 to enable its characterization. Several nitrogen-donor atom-containing ligands were found to bind to CYP105Q4 generating type II changes in the UV-vis absorbance spectrum. Based on the UV-vis absorbance spectra none of the potential substrate ligands we tested with CYP105Q4 were able to displace the sixth distal aqua ligand from the heme, though there was evidence for binding of oleic acid and amphotericin B. The crystal structure of CYP105Q4 in the substrate-free form was determined in an open conformation. A computational structural similarity search (Dali) was used to find the most closely related characterized relatives within the CYP105 family. The structure of CYP105Q4 enzyme was compared to the GfsF CYP enzyme from Streptomyces graminofaciens which is involved in the biosynthesis of a macrolide polyketide. This structural comparison to GfsF revealed conformational changes in the helices and loops near the entrance to the substrate access channel. A disordered B/C loop region, usually involved in substrate recognition, was also observed.
Collapse
Affiliation(s)
- Hebatalla Mohamed
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - Stella A Child
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - Daniel Z Doherty
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA, 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA, 5005, Australia.
| |
Collapse
|
2
|
Tüllinghoff A, Toepel J, Bühler B. Enlighting Electron Routes In Oxyfunctionalizing Synechocystis sp. PCC 6803. Chembiochem 2024; 25:e202300475. [PMID: 37994522 DOI: 10.1002/cbic.202300475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023]
Abstract
Phototrophic microorganisms, like cyanobacteria, are gaining attention as host organisms for biocatalytic processes with light as energy source and water as electron source. Redox enzymes, especially oxygenases, can profit from in-situ supply of co-substrates, i. e., reduction equivalents and O2 , by the photosynthetic light reaction. The electron transfer downstream of PS I to heterologous electron consuming enzymes in principle can involve NADPH, NADH, and/or ferredoxin, whereas most direct and efficient transfer is desirable. Here, we use the model organism Synechocystis sp. PCC 6803 to investigate, to what extent host and/or heterologous constituents are involved in electron transfer to a heterologous cytochrome P450 monooxygenase from Acidovorax sp. CHX100. Interestingly, in this highly active light-fueled cycloalkane hydroxylating biocatalyst, host-intrinsic enzymes were found capable of completely substituting the function of the Acidovorax ferredoxin reductase. To a certain extent (20 %), this also was true for the Acidovorax ferredoxin. These results indicate the presence of a versatile set of electron carriers in cyanobacteria, enabling efficient and direct coupling of electron consuming reactions to photosynthetic water oxidation. This will both simplify and promote the use of phototrophic microorganisms for sustainable production processes.
Collapse
Affiliation(s)
- Adrian Tüllinghoff
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Jörg Toepel
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Bruno Bühler
- Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| |
Collapse
|
3
|
Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
Collapse
Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| |
Collapse
|
4
|
Jordan S, Li B, Traore E, Wu Y, Usai R, Liu A, Xie ZR, Wang Y. Structural and spectroscopic characterization of RufO indicates a new biological role in rufomycin biosynthesis. J Biol Chem 2023; 299:105049. [PMID: 37451485 PMCID: PMC10424215 DOI: 10.1016/j.jbc.2023.105049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
Rufomycins constitute a class of cyclic heptapeptides isolated from actinomycetes. They are secondary metabolites that show promising treatment against Mycobacterium tuberculosis infections by inhibiting a novel drug target. Several nonproteinogenic amino acids are integrated into rufomycins, including a conserved 3-nitro-tyrosine. RufO, a cytochrome P450 (CYP)-like enzyme, was proposed to catalyze the formation of 3-nitro-tyrosine in the presence of O2 and NO. To define its biological function, the interaction between RufO and the proposed substrate tyrosine is investigated using various spectroscopic methods that are sensitive to the structural change of a heme center. However, a low- to high-spin state transition and a dramatic increase in the redox potential that are commonly found in CYPs upon ligand binding have not been observed. Furthermore, a 1.89-Å crystal structure of RufO shows that the enzyme has flexible surface regions, a wide-open substrate access tunnel, and the heme center is largely exposed to solvent. Comparison with a closely related nitrating CYP reveals a spacious and hydrophobic distal pocket in RufO, which is incapable of stabilizing a free amino acid. Molecular docking validates the experimental data and proposes a possible substrate. Collectively, our results disfavor tyrosine as the substrate of RufO and point to the possibility that the nitration occurs during or after the assembly of the peptides. This study indicates a new function of the unique nitrating enzyme and provides insights into the biosynthesis of nonribosomal peptides.
Collapse
Affiliation(s)
- Stephanie Jordan
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Bingnan Li
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Ephrahime Traore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Yifei Wu
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Remigio Usai
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Zhong-Ru Xie
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, Georgia, USA.
| |
Collapse
|
5
|
Hlavica P. Key regulators in the architecture of substrate access/egress channels in mammalian cytochromes P450 governing flexibility in substrate oxyfunctionalization. J Inorg Biochem 2023; 241:112150. [PMID: 36731371 DOI: 10.1016/j.jinorgbio.2023.112150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/21/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023]
Abstract
Cytochrome P450s (CYP) represent a superfamily of b-type hemoproteins catalyzing oxifunctionalization of a vast array of endogenous and exogenous compounds. The present review focuses on assessment of the topology of prospective determinants in substrate entry and product release channels of mammalian P450s, steering the conformational dynamics of substrate accessibility and productive ligand orientation toward the iron-oxene core. Based on a generalized, CYP3A4-related construct, the sum of critical elements from diverse target enzymes was found to cluster within the known substrate recognition sites. The majority of prevalent substrate access/egress tunnels revealed to be of fairly balanced functional importance. The hydrophobicity profile of the candidates revealed to be the most salient feature in functional interaction throughout the conduits, while bulkiness of the residues imposes steric restrictions on substrate traveling. Thus, small amino acids such as prolines and glycines serve as hinges, driving conformational flexibility in ligand passage. Similarly, bottlenecks in the tunnel architecture, being narrowest encounter points within the CYP3A4 model, have a vital function in substrate selectivity along with clusters of aromatic amino acids acting as gatekeepers. In addition, peripheral patches in conduits may house determinants modulating allosteric cooperativity between remote and central domains in the P450 structure. Remarkably, the bulk critical residues lining tunnels in the various isozymes reside in helices B'/C and F/G inclusive of their interhelical turns as well as in helix I. This suggests these regions to represent hotspots for targeted genetic engineering to tailor more sophisticated mammalian P450s exploitable in industrial, biotechnological and medicinal areas.
Collapse
Affiliation(s)
- Peter Hlavica
- Walther-Straub Institut fuer Pharmakologie und Toxikologie, Goethestrasse 33, D80336 Muenchen, Germany.
| |
Collapse
|
6
|
Eltoukhy A, Jia Y, Lamraoui I, Abo-Kadoum MA, Atta OM, Nahurira R, Wang J, Yan Y. Transcriptome analysis and cytochrome P450 monooxygenase reveal the molecular mechanism of Bisphenol A degradation by Pseudomonas putida strain YC-AE1. BMC Microbiol 2022; 22:294. [PMID: 36482332 PMCID: PMC9733184 DOI: 10.1186/s12866-022-02689-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Bisphenol A (BPA) is a rapid spreading organic pollutant that widely used in many industries especially as a plasticizer in polycarbonate plastic and epoxy resins. BPA reported as a prominent endocrine disruptor compound that possesses estrogenic activity and fulminant toxicity. Pseudomonas putida YC-AE1 was isolated in our previous study and exerted a strong degradation capacity toward BPA at high concentrations; however, the molecular degradation mechanism is still enigmatic. RESULTS We employed RNA sequencing to analyze the differentially expressed genes (DEGs) in the YC-AE1 strain upon BPA induction. Out of 1229 differentially expressed genes, 725 genes were positively regulated, and 504 genes were down-regulated. The pathways of microbial metabolism in diverse environments were significantly enriched among DEGs based on KEGG enrichment analysis. qRT-PCR confirm the involvement of BPA degradation relevant genes in accordance with RNA Seq data. The degradation pathway of BPA in YC-AE1 was proposed with specific enzymes and encoded genes. The role of cytochrome P450 (CYP450) in BPA degradation was further verified. Sever decrease in BPA degradation was recorded by YC-AE1 in the presence of CYP450 inhibitor. Subsequently, CYP450bisdB deficient YC-AE1 strain △ bisdB lost its ability toward BPA transformation comparing with the wild type. Furthermore, Transformation of E. coli with pET-32a-bisdAB empowers it to degrade 66 mg l-1 of BPA after 24 h. Altogether, the results showed the role of CYP450 in biodegradation of BPA by YC-AE1. CONCLUSION In this study we propose the molecular basis and the potential role of YC-AE1cytochrome P450 monooxygenase in BPA catabolism.
Collapse
Affiliation(s)
- Adel Eltoukhy
- grid.411303.40000 0001 2155 6022Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, 71524 Egypt ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yang Jia
- grid.412899.f0000 0000 9117 1462National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, and Zhejiang Provincial Key Lab for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035 China
| | - Imane Lamraoui
- Higher National School of Biotechnology “Toufik Khaznadar” (ENSB), 25000 Constantine, Algeria
| | - M. A. Abo-Kadoum
- grid.411303.40000 0001 2155 6022Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, 71524 Egypt
| | - Omar Mohammad Atta
- grid.411303.40000 0001 2155 6022Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, 71524 Egypt
| | - Ruth Nahurira
- grid.449527.90000 0004 0534 1218Faculty of Science, Kabale University, Kabale, Uganda
| | - Junhuan Wang
- grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanchun Yan
- grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
7
|
Xie H, Song L, Katz S, Zhu J, Liu Y, Tang J, Cai L, Hildebrandt P, Han XX. Electron transfer between cytochrome c and microsomal monooxygenase generates reactive oxygen species that accelerates apoptosis. Redox Biol 2022; 53:102340. [PMID: 35609401 PMCID: PMC9130584 DOI: 10.1016/j.redox.2022.102340] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/20/2022] Open
Abstract
Generation of reactive oxygen species (ROS) are possibly induced by the crosstalk between mitochondria and endoplasmic reticula, which is physiologically important in apoptosis. Cytochrome c (Cyt c) is believed to play a crucial role in such signaling pathway by interrupting the coupling within microsomal monooxygenase (MMO). In this study, the correlation of ROS production with the electron transfer between Cyt c and the MMO system is investigated by resonance Raman (RR) spectroscopy. Binding of Cyt c to MMO is found to induce the production of ROS, which is quantitatively determined by the in-situ RR spectroscopy reflecting the interactions of Cyt c with generated ROS. The amount of ROS that is produced from isolated endoplasmic reticulum depends on the redox state of the Cyt c, indicating the important role of oxidized Cyt c in accelerating apoptosis. The role of electron transfer from MMO to Cyt c in the apoptotic mitochondria-endoplasmic reticulum pathway is accordingly proposed. This study is of significance for a deeper understanding of how Cyt c regulates apoptotic pathways through the endoplasmic reticulum, and thus may provide a rational basis for the design of antitumor drugs for cancer therapy.
Collapse
Affiliation(s)
- Han Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Li Song
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, 130012, PR China
| | - Sagie Katz
- Department of Chemistry, Technische Universität Berlin, 10623, Berlin, Germany
| | - Jinyu Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Yawen Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Jinping Tang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Linjun Cai
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun, 130012, PR China
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, 10623, Berlin, Germany.
| | - Xiao Xia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China.
| |
Collapse
|
8
|
Mohamed H, Child SA, Bruning JB, Bell SG. A comparison of the bacterial CYP51 cytochrome P450 enzymes from Mycobacterium marinum and Mycobacterium tuberculosis. J Steroid Biochem Mol Biol 2022; 221:106097. [PMID: 35346833 DOI: 10.1016/j.jsbmb.2022.106097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
Members of the CYP51 family of cytochrome P450 enzymes are classified as sterol demethylases involved in the metabolic formation of cholesterol and related derivatives. The CYP51 enzyme from Mycobacterium marinum was studied and compared to its counterpart from Mycobacterium tuberculosis to determine the degree of functional conservation between them. Spectroscopic analyses of substrate and inhibitor binding of the purified CYP51 enzymes from M. marinum and M. tuberculosis were performed. The catalytic oxidation of lanosterol and related steroids was investigated. M. marinum CYP51 was structurally characterized by X-ray crystallography. The CYP51 enzyme of M. marinum is sequentially closely related to CYP51B1 from M. tuberculosis. However, differences in the heme spin state of each enzyme were observed upon the addition of steroids and other ligands. Both enzymes displayed different binding properties to those reported for the CYP51-Fdx fusion protein from the bacterium Methylococcus capsulatus. The enzymes were able to oxidatively demethylate lanosterol to generate 14-demethylanosterol, but no products were detected for the related species dihydrolanosterol and eburicol. The crystal structure of CYP51 from M. marinum in the absence of added substrate but with a Bis-Tris molecule within the active site was resolved. The CYP51 enzyme of M. marinum displays differences in how steroids and other ligands bind compared to the M. tuberculosis enzyme. This was related to structural differences between the two enzymes. Overall, both of these CYP51 enzymes from mycobacterial species displayed significant differences to the CYP51 enzymes of eukaryotic species and the bacterial CYP51-Fdx enzyme of Me. capsulatus.
Collapse
Affiliation(s)
| | - Stella A Child
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
| |
Collapse
|
9
|
Davydov DR, Dangi B, Yue G, Ahire DS, Prasad B, Zgoda VG. Exploring the Interactome of Cytochrome P450 2E1 in Human Liver Microsomes with Chemical Crosslinking Mass Spectrometry. Biomolecules 2022; 12:biom12020185. [PMID: 35204686 PMCID: PMC8869672 DOI: 10.3390/biom12020185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/05/2022] Open
Abstract
Aiming to elucidate the system-wide effects of the alcohol-induced increase in the content of cytochrome P450 2E1 (CYP2E1) on drug metabolism, we explored the array of its protein-protein interactions (interactome) in human liver microsomes (HLM) with chemical crosslinking mass spectrometry (CXMS). Our strategy employs membrane incorporation of purified CYP2E1 modified with photoreactive crosslinkers benzophenone-4-maleimide and 4-(N-succinimidylcarboxy)benzophenone. Exposure of bait-incorporated HLM samples to light was followed by isolating the His-tagged bait protein and its crosslinked aggregates on Ni-NTA agarose. Analyzing the individual bands of SDS-PAGE slabs of thereby isolated protein with the toolset of untargeted proteomics, we detected the crosslinked dimeric and trimeric complexes of CYP2E1 with other drug-metabolizing enzymes. Among the most extensively crosslinked partners of CYP2E1 are the cytochromes P450 2A6, 2C8, 3A4, 4A11, and 4F2, UDP-glucuronosyltransferases (UGTs) 1A and 2B, fatty aldehyde dehydrogenase (ALDH3A2), epoxide hydrolase 1 (EPHX1), disulfide oxidase 1α (ERO1L), and ribophorin II (RPN2). These results demonstrate the exploratory power of the proposed CXMS strategy and corroborate the concept of tight functional integration in the human drug-metabolizing ensemble through protein-protein interactions of the constituting enzymes.
Collapse
Affiliation(s)
- Dmitri R. Davydov
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA;
- Correspondence:
| | - Bikash Dangi
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA;
| | - Guihua Yue
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (G.Y.); (D.S.A.); (B.P.)
| | - Deepak S. Ahire
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (G.Y.); (D.S.A.); (B.P.)
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (G.Y.); (D.S.A.); (B.P.)
| | - Victor G. Zgoda
- Orekhovich Institute of Biomedical Chemistry, Pogodinskaya 10, 119121 Moscow, Russia;
| |
Collapse
|
10
|
|
11
|
Dixit VA, Warwicker J, Visser SP. How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions? Chemistry 2020; 26:15270-15281. [DOI: 10.1002/chem.202003024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmacy Birla Institute of Technology and Sciences Pilani (BITS-Pilani) Vidya Vihar Campus 41 Pilani 333031 Rajasthan India
| | - Jim Warwicker
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemistry The University of Manchester Oxford Road Manchester M139PL United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemical Engineering and Analytical Science The University of Manchester Oxford Road Manchester M13 9PL United Kingdom
| |
Collapse
|
12
|
An overview of the factors playing a role in cytochrome P450 monooxygenase and ferredoxin interactions. Biophys Rev 2020; 12:1217-1222. [PMID: 32885385 DOI: 10.1007/s12551-020-00749-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/28/2020] [Indexed: 01/11/2023] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are heme-thiolate proteins that are ubiquitously present in organisms, including non-living entities such as viruses. With the exception of self-sufficient P450s, all other P450 enzymes need electrons to perform their enzymatic activity and these electrons are supplied by P450 redox proteins. Different types of P450 redox proteins can be found in organisms and are classified into different classes. Bacterial P450s (class I) receive electrons from ferredoxins which are iron-sulfur cluster proteins. The presence of more than one copy and different types of ferredoxins within a bacterial species poses fundamental questions about the selectivity of P450s and ferredoxins in relation to each other. Apart from transferring electrons, ferredoxins have also been found to modulate P450 functions. Achieving an understanding of the interaction between ferredoxins and P450s is required to harness their biotechnological potential for designing a universal electron transfer protein. A brief overview of factors playing a role in ferredoxin and P450 interactions is presented in this review article.
Collapse
|
13
|
Redox Partners: Function Modulators of Bacterial P450 Enzymes. Trends Microbiol 2020; 28:445-454. [DOI: 10.1016/j.tim.2020.02.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 01/25/2023]
|
14
|
Mie Y, Yasutake Y, Takayama H, Tamura T. Electrochemically boosted cytochrome P450 reaction that efficiently produces 25-hydroxyvitamin D3. J Catal 2020. [DOI: 10.1016/j.jcat.2020.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
15
|
A large-scale comparative analysis of affinity, thermodynamics and functional characteristics of interactions of twelve cytochrome P450 isoforms and their redox partners. Biochimie 2019; 162:156-166. [DOI: 10.1016/j.biochi.2019.04.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/24/2019] [Indexed: 12/16/2022]
|
16
|
Gnedenko O, Yablokov E, Ershov P, Svirid A, Shkel T, Haidukevich I, Strushkevich N, Gilep A, Usanov S, Ivanov A. Interaction of prostacyclin synthase with cytochromes P450. ACTA ACUST UNITED AC 2019; 65:63-66. [DOI: 10.18097/pbmc20196501063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Biosensor experiments on investigation of interaction between prostacyclin synthase (PGIS) and different proteins of the cytochrome P450 monooxygenase systems were perfomed. Interaction of PGIS with microsomal (CYP21A2, CYP2E1) and mitochondrial (CYP27A1, CYP11B1, CYP11B2, CYP11A1) cytochrome P450s was detected. Kinetic and equilibrium parameters of protein complexes formation were determined. Data obtained suggest an essential role of these hemoproteins interaction in regulation of prostacyclin and thromboxane A2 biosynthesis.
Collapse
Affiliation(s)
| | | | - P.V. Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A.V. Svirid
- Institute of Bioorganic Chemistry National Academy of Science of Belarus, Minsk, Belarus
| | - T.V. Shkel
- Institute of Bioorganic Chemistry National Academy of Science of Belarus, Minsk, Belarus
| | - I.V. Haidukevich
- Institute of Bioorganic Chemistry National Academy of Science of Belarus, Minsk, Belarus
| | - N.V. Strushkevich
- Institute of Bioorganic Chemistry National Academy of Science of Belarus, Minsk, Belarus
| | - A.A. Gilep
- Institute of Bioorganic Chemistry National Academy of Science of Belarus, Minsk, Belarus
| | - S.A. Usanov
- Institute of Bioorganic Chemistry National Academy of Science of Belarus, Minsk, Belarus
| | - A.S. Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| |
Collapse
|
17
|
Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
Collapse
Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| |
Collapse
|
18
|
Zhang W, Du L, Li F, Zhang X, Qu Z, Han L, Li Z, Sun J, Qi F, Yao Q, Sun Y, Geng C, Li S. Mechanistic Insights into Interactions between Bacterial Class I P450 Enzymes and Redox Partners. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02913] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Lei Du
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Fengwei Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Zepeng Qu
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Lei Han
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Jingran Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Fengxia Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Qiuping Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Yue Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| |
Collapse
|
19
|
Haga T, Hirakawa H, Nagamune T. Artificial Self‐Sufficient Cytochrome P450 Containing Multiple Auxiliary Proteins Demonstrates Improved Monooxygenase Activity. Biotechnol J 2018; 13:e1800088. [DOI: 10.1002/biot.201800088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Tomoaki Haga
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Teruyuki Nagamune
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| |
Collapse
|
20
|
Maugeri PT, Griese JJ, Branca RM, Miller EK, Smith ZR, Eirich J, Högbom M, Shafaat HS. Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase. J Am Chem Soc 2018; 140:1471-1480. [PMID: 29268610 DOI: 10.1021/jacs.7b11966] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The heterobimetallic R2lox protein binds both manganese and iron ions in a site-selective fashion and activates oxygen, ultimately performing C-H bond oxidation to generate a tyrosine-valine cross-link near the active site. In this work, we demonstrate that, following assembly, R2lox undergoes photoinduced changes to the active site geometry and metal coordination motif. Through spectroscopic, structural, and mass spectrometric characterization, the photoconverted species is found to consist of a tyrosinate-bound iron center following light-induced decarboxylation of a coordinating glutamate residue and cleavage of the tyrosine-valine cross-link. This process occurs with high quantum efficiencies (Φ = 3%) using violet and near-ultraviolet light, suggesting that the photodecarboxylation is initiated via ligand-to-metal charge transfer excitation. Site-directed mutagenesis and structural analysis suggest that the cross-linked tyrosine-162 is the coordinating residue. One primary product is observed following irradiation, indicating potential use of this class of proteins, which contains a putative substrate channel, for controlled photoinduced decarboxylation processes, with relevance for in vivo functionality of R2lox as well as application in environmental remediation.
Collapse
Affiliation(s)
- Pearson T Maugeri
- Biophysics Graduate Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Rui M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet , SE-17165 Stockholm, Sweden
| | - Effie K Miller
- Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States
| | - Zachary R Smith
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Jürgen Eirich
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet , SE-17165 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Hannah S Shafaat
- Biophysics Graduate Program, The Ohio State University , Columbus, Ohio 43210, United States.,Ohio State Biochemistry Program, The Ohio State University , Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| |
Collapse
|
21
|
Lu Y, Qiao F, Li Y, Sang XH, Li CR, Jiang JD, Yang XY, You XF. Recombinant expression and biochemical characterization of Mycobacterium tuberculosis 3Fe-4S ferredoxin Rv1786. Appl Microbiol Biotechnol 2017; 101:7201-7212. [DOI: 10.1007/s00253-017-8454-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 11/25/2022]
|
22
|
Srivastava AP, Hardy EP, Allen JP, Vaccaro BJ, Johnson MK, Knaff DB. Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase. Biochemistry 2017; 56:5582-5592. [PMID: 28520412 DOI: 10.1021/acs.biochem.7b00025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An in silico model for the 1:1 ferredoxin (Fd)/nitrate reductase (NR) complex, using the known structure of Synechocystis sp. PCC 6803 Fd and the in silico model of Synechococcus sp. PCC 7942 NR, is used to map the interaction sites that define the interface between Fd and NR. To test the electrostatic interactions predicted by the model complex, five positively charged NR amino acids (Arg43, Arg46, Arg197, Lys201, and Lys614) and a negatively charged amino acid (Glu219) were altered using site-directed mutagenesis and characterized by activity measurements, metal analysis, and electron paramagnetic resonance (EPR) studies. All of the charge replacement variants retained wild-type levels of activity with reduced methyl viologen (MV), but a significant decrease in activity was observed for the R43Q, R46Q, K201Q, and K614Q variants when reduced Fd served as the electron donor. EPR analysis as well as the Fe and Mo analyses showed that loss of activity observed with these variants was not the consequence of perturbation of the Mo center or [4Fe-4S] cluster. Therefore, the loss of the Fd-linked specific activity observed with these variants can be explained only by invoking a role for Arg43, Arg46, Lys201, and Lys614 in Fd binding. The R43Q, R46Q, K201Q, and K614Q NR variants also showed a decreased binding affinity for Fd, compared to that of wild-type NR, supporting a key role of these four positively charged residues in the productive binding of Fd.
Collapse
Affiliation(s)
- Anurag P Srivastava
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
| | - Emily P Hardy
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
| | - James P Allen
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Brian J Vaccaro
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602-2556, United States
| | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602-2556, United States
| | - David B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States.,Center for Biotechnology and Genomics, Texas Tech University , Lubbock, Texas 79409-3132, United States
| |
Collapse
|
23
|
Challenges in assignment of allosteric effects in cytochrome P450-catalyzed substrate oxidations to structural dynamics in the hemoprotein architecture. J Inorg Biochem 2017; 167:100-115. [DOI: 10.1016/j.jinorgbio.2016.11.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/17/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
|
24
|
Batabyal D, Lewis-Ballester A, Yeh SR, Poulos TL. A Comparative Analysis of the Effector Role of Redox Partner Binding in Bacterial P450s. Biochemistry 2016; 55:6517-6523. [PMID: 27808504 DOI: 10.1021/acs.biochem.6b00913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The camphor monooxygenase, cytochrome P450cam, exhibits a strict requirement for its own redox partner, putidaredoxin (Pdx), a two-iron-sulfur ferredoxin. The closest homologue to P450cam, CYP101D1, is structurally very similar, uses a similar redox partner, and exhibits nearly identical enzymatic properties in the monooxygenation of camphor to give the same single 5-exo-hydroxy camphor product. However, CYP101D1 does not strictly require its own ferredoxin (Arx) for activity because Pdx can support CYP101D1 catalysis but Arx cannot support P450cam catalysis. We have further examined the differences between these two P450s by determining the effect of spin equilibrium, redox properties, and stability of oxygen complexes. We find that Arx shifts the spin state equilibrium toward high-spin, which is the opposite of the effect of Pdx on P450cam. In both P450s, redox partner binding destabilizes the oxy-P450 complex but this effect is much weaker with CYP101D1. In addition, resonance Raman data show that structural perturbations observed in P450cam upon addition of Pdx are absent in CYP101D1. These data indicate that Arx does not play the same effector role in catalysis as Pdx does with P450cam. The most relevant structural difference between these two P450s centers on a catalytically important Asp residue required for proton-coupled electron transfer. We postulate that with P450cam larger Pdx-assisted motions are required to free this Asp for catalysis while the smaller number of restrictions in CYP101D1 precludes the need for redox partner-assisted structural changes.
Collapse
Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| |
Collapse
|
25
|
Pearl NM, Wilcoxen J, Im S, Kunz R, Darty J, Britt RD, Ragsdale SW, Waskell L. Protonation of the Hydroperoxo Intermediate of Cytochrome P450 2B4 Is Slower in the Presence of Cytochrome P450 Reductase Than in the Presence of Cytochrome b5. Biochemistry 2016; 55:6558-6567. [PMID: 27797496 DOI: 10.1021/acs.biochem.6b00996] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microsomal cytochromes P450 (P450) require two electrons and two protons for the oxidation of substrates. Although the two electrons can be provided by cytochrome P450 reductase, the second electron can also be donated by cytochrome b5 (b5). The steady-state activity of P450 2B4 is increased up to 10-fold by b5. To improve our understanding of the molecular basis of the stimulatory effect of b5 and to test the hypothesis that b5 stimulates catalysis by more rapid protonation of the anionic ferric hydroperoxo heme intermediate of P450 (Fe3+OOH)- and subsequent formation of the active oxidizing species (Fe+4═O POR•+), we have freeze-quenched the reaction mixture during a single turnover following reduction of oxyferrous P450 2B4 by each of its redox partners, b5 and P450 reductase. The electron paramagnetic resonance spectra of the freeze-quenched reaction mixtures lacked evidence of a hydroperoxo intermediate when b5 was the reductant presumably because hydroperoxo protonation and catalysis occurred within the dead time of the instrument. However, when P450 reductase was the reductant, a hydroperoxo P450 intermediate was observed. The effect of b5 on the enzymatic efficiency in D2O and the kinetic solvent isotope effect under steady-state conditions are both consistent with the ability of b5 to promote rapid protonation of the hydroperoxo species and more efficient catalysis. In summary, by binding to the proximal surface of P450, b5 stimulates the activity of P450 2B4 by enhancing the rate of protonation of the hydroperoxo intermediate and formation of Compound I, the active oxidizing species, which allows less time for side product formation.
Collapse
Affiliation(s)
- Naw May Pearl
- Department of Anesthesiology, University of Michigan Medical School , Ann Arbor, Michigan 48109-0112, United States
| | - Jarett Wilcoxen
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan Medical School , Ann Arbor, Michigan 48109-0112, United States
| | - Ryan Kunz
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109-0600, United States
| | - Joseph Darty
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109-0600, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109-0600, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan Medical School , Ann Arbor, Michigan 48109-0112, United States
| |
Collapse
|
26
|
Stiborová M, Indra R, Moserová M, Frei E, Schmeiser HH, Kopka K, Philips DH, Arlt V. NADH:Cytochrome b5 Reductase and Cytochrome b5 Can Act as Sole Electron Donors to Human Cytochrome P450 1A1-Mediated Oxidation and DNA Adduct Formation by Benzo[a]pyrene. Chem Res Toxicol 2016; 29:1325-34. [PMID: 27404282 PMCID: PMC4987862 DOI: 10.1021/acs.chemrestox.6b00143] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 11/29/2022]
Abstract
Benzo[a]pyrene (BaP) is a human carcinogen that covalently binds to DNA after activation by cytochrome P450 (P450). Here, we investigated whether NADH:cytochrome b5 reductase (CBR) in the presence of cytochrome b5 can act as sole electron donor to human P450 1A1 during BaP oxidation and replace the canonical NADPH:cytochrome P450 reductase (POR) system. We also studied the efficiencies of the coenzymes of these reductases, NADPH as a coenzyme of POR, and NADH as a coenzyme of CBR, to mediate BaP oxidation. Two systems containing human P450 1A1 were utilized: human recombinant P450 1A1 expressed with POR, CBR, epoxide hydrolase, and cytochrome b5 in Supersomes and human recombinant P450 1A1 reconstituted with POR and/or with CBR and cytochrome b5 in liposomes. BaP-9,10-dihydrodiol, BaP-7,8-dihydrodiol, BaP-1,6-dione, BaP-3,6-dione, BaP-9-ol, BaP-3-ol, a metabolite of unknown structure, and two BaP-DNA adducts were generated by the P450 1A1-Supersomes system, both in the presence of NADPH and in the presence of NADH. The major BaP-DNA adduct detected by (32)P-postlabeling was characterized as 10-(deoxyguanosin-N(2)-yl)-7,8,9-trihydroxy-7,8,9,10-tetrahydro-BaP (assigned adduct 1), while the minor adduct is probably a guanine adduct derived from 9-hydroxy-BaP-4,5-epoxide (assigned adduct 2). BaP-3-ol as the major metabolite, BaP-9-ol, BaP-1,6-dione, BaP-3,6-dione, an unknown metabolite, and adduct 2 were observed in the system using P450 1A1 reconstituted with POR plus NADPH. When P450 1A1 was reconstituted with CBR and cytochrome b5 plus NADH, BaP-3-ol was the predominant metabolite too, and an adduct 2 was also generated. Our results demonstrate that the NADH/cytochrome b5/CBR system can act as the sole electron donor both for the first and second reduction of P450 1A1 during the oxidation of BaP in vitro. They suggest that NADH-dependent CBR can replace NADPH-dependent POR in the P450 1A1-catalyzed metabolism of BaP.
Collapse
Affiliation(s)
- Marie Stiborová
- Department
of Biochemistry, Faculty of Science, Charles
University, Albertov
2030, 128 40, Prague 2, Czech
Republic
| | - Radek Indra
- Department
of Biochemistry, Faculty of Science, Charles
University, Albertov
2030, 128 40, Prague 2, Czech
Republic
| | - Michaela Moserová
- Department
of Biochemistry, Faculty of Science, Charles
University, Albertov
2030, 128 40, Prague 2, Czech
Republic
| | - Eva Frei
- Department
of Biochemistry, Faculty of Science, Charles
University, Albertov
2030, 128 40, Prague 2, Czech
Republic
| | - Heinz H. Schmeiser
- Division
of Radiopharmaceutical Chemistry, German
Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Klaus Kopka
- Department
of Biochemistry, Faculty of Science, Charles
University, Albertov
2030, 128 40, Prague 2, Czech
Republic
| | - David H. Philips
- Analytical
and Environmental Sciences Division, MRC-PHE Centre for Environment
and Health, King’s College London, Franklin-Wilkins Building, 150 Stamford
Street, London SE1 9NH, United Kingdom
- NIHR
Health Protection Research Unit in Health Impact of Environmental
Hazards at King’s College London in Partnership with Public
Health England, Franklin-Wilkins
Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Volker
M. Arlt
- Analytical
and Environmental Sciences Division, MRC-PHE Centre for Environment
and Health, King’s College London, Franklin-Wilkins Building, 150 Stamford
Street, London SE1 9NH, United Kingdom
- NIHR
Health Protection Research Unit in Health Impact of Environmental
Hazards at King’s College London in Partnership with Public
Health England, Franklin-Wilkins
Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| |
Collapse
|
27
|
Gricman Ł, Weissenborn MJ, Hoffmann SM, Borlinghaus N, Hauer B, Pleiss J. Redox Partner Interaction Sites in Cytochrome P450 Monooxygenases:In SilicoAnalysis and Experimental Validation. ChemistrySelect 2016. [DOI: 10.1002/slct.201600369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sara M. Hoffmann
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Niels Borlinghaus
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
28
|
Gricman Ł, Vogel C, Pleiss J. Identification of universal selectivity-determining positions in cytochrome P450 monooxygenases by systematic sequence-based literature mining. Proteins 2015; 83:1593-603. [DOI: 10.1002/prot.24840] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry, University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry, University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
29
|
Hlavica P. Mechanistic basis of electron transfer to cytochromes p450 by natural redox partners and artificial donor constructs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:247-97. [PMID: 26002739 DOI: 10.1007/978-3-319-16009-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochromes P450 (P450s) are hemoproteins catalyzing oxidative biotransformation of a vast array of natural and xenobiotic compounds. Reducing equivalents required for dioxygen cleavage and substrate hydroxylation originate from different redox partners including diflavin reductases, flavodoxins, ferredoxins and phthalate dioxygenase reductase (PDR)-type proteins. Accordingly, circumstantial analysis of structural and physicochemical features governing donor-acceptor recognition and electron transfer poses an intriguing challenge. Thus, conformational flexibility reflected by togging between closed and open states of solvent exposed patches on the redox components was shown to be instrumental to steered electron transmission. Here, the membrane-interactive tails of the P450 enzymes and donor proteins were recognized to be crucial to proper orientation toward each other of surface sites on the redox modules steering functional coupling. Also, mobile electron shuttling may come into play. While charge-pairing mechanisms are of primary importance in attraction and complexation of the redox partners, hydrophobic and van der Waals cohesion forces play a minor role in docking events. Due to catalytic plasticity of P450 enzymes, there is considerable promise in biotechnological applications. Here, deeper insight into the mechanistic basis of the redox machinery will permit optimization of redox processes via directed evolution and DNA shuffling. Thus, creation of hybrid systems by fusion of the modified heme domain of P450s with proteinaceous electron carriers helps obviate the tedious reconstitution procedure and induces novel activities. Also, P450-based amperometric biosensors may open new vistas in pharmaceutical and clinical implementation and environmental monitoring.
Collapse
Affiliation(s)
- Peter Hlavica
- Walther-Straub-Institut für Pharmakologie und Toxikologie der LMU, Goethestrasse 33, 80336, München, Germany,
| |
Collapse
|
30
|
Badiefar L, Yakhchali B, Rodriguez-Couto S, Veloso A, García-Arenzana JM, Matsumura Y, Khodabandeh M. Biodegradation of bisphenol A by the newly-isolated Enterobacter gergoviae strain BYK-7 enhanced using genetic manipulation. RSC Adv 2015. [DOI: 10.1039/c5ra01818h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Endogenous bacterial strains possessing a high bisphenol A (BPA)-tolerance/degradation activity were isolated from different outlets of petrochemical wastewater in Iran using the enrichment cultivation approach.
Collapse
Affiliation(s)
- Leila Badiefar
- National Institute of Genetic Engineering and Biotechnology (NIGEB)
- Institute of Industrial and Environmental Biotechnology (IIEB)
- Tehran
- Iran
| | - Bagher Yakhchali
- National Institute of Genetic Engineering and Biotechnology (NIGEB)
- Institute of Industrial and Environmental Biotechnology (IIEB)
- Tehran
- Iran
| | | | - Antonio Veloso
- POLYMAT
- University of the Basque Country UPV/EHU
- Joxe Mari Korta R&D Ctr
- Donostia-San Sebastian 20018
- Spain
| | | | | | - Mahvash Khodabandeh
- National Institute of Genetic Engineering and Biotechnology (NIGEB)
- Institute of Industrial and Environmental Biotechnology (IIEB)
- Tehran
- Iran
| |
Collapse
|
31
|
Reid GGJ, Bin Yameen TA, Parker JL. Impact of biomarkers on clinical trial risk. Pharmacogenomics 2014; 14:1645-58. [PMID: 24088135 DOI: 10.2217/pgs.13.167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The last decade has witnessed the cost of drug development rise dramatically; concurrently, the number of new drug approvals has declined. Clinical trial failure rates have contributed significantly to this 'innovation' crisis and are directly related to clinical trial risk. One strategy that is often touted to resolve this challenge depends on embracing a personalized medicine approach where treatment is tailored to a patient's unique genetic background. We highlight a new risk-based paradigm of clinical trial risk that evaluates the utility of biomarkers in drug development and their risk mitigation benefits. Furthermore, examples elucidating the current state of biomarker integration during clinical trials and the potential risks posed by doing so will be discussed.
Collapse
|
32
|
Pandey BP, Lee N, Choi KY, Kim JN, Kim EJ, Kim BG. Identification of the specific electron transfer proteins, ferredoxin, and ferredoxin reductase, for CYP105D7 in Streptomyces avermitilis MA4680. Appl Microbiol Biotechnol 2014; 98:5009-17. [PMID: 24549766 DOI: 10.1007/s00253-014-5525-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 12/22/2013] [Accepted: 01/07/2014] [Indexed: 01/29/2023]
Abstract
It was previously proposed that regiospecific hydroxylation of daidzein at 3'-position is mediated by cytochrome P450 hydroxylase (CYP105D7) in the presence of putidaredoxin (CamB) and putidaredoxin reductase (CamA) as electron transfer proteins from Pseudomonas putida. The genome sequence of Streptomyces avermitilis MA4680 revealed 33 P450 (CYPs) with 6 ferredoxin reductases (Fprs) and 9 ferredoxins (Fdxs) as their putative electron transfer partner proteins. To identify right endogenous electron transfer proteins for CYP105D7 activity, in vitro reconstitution, gene disruption, and quantitative reverse transcription polymerase chain reaction (qRT-PCR) mRNA expression profile analysis were examined. The most effective electron transfer proteins for CYP105D7 appear to be FdxH (SAV7470), which is located downstream to CYP105D7 as a cluster, and FprD (SAV5675). Throughout our overall analysis, we proposed that the primary electron transfer pathway for CYP105D7 follows as such NAD(P)H→FdxH→FprD→CYP105D7.
Collapse
Affiliation(s)
- Bishnu Prasad Pandey
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, Institute of Bioengineering, Seoul National University, Seoul, South Korea
| | | | | | | | | | | |
Collapse
|
33
|
Gricman Ł, Vogel C, Pleiss J. Conservation analysis of class-specific positions in cytochrome P450 monooxygenases: Functional and structural relevance. Proteins 2013; 82:491-504. [DOI: 10.1002/prot.24415] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/23/2013] [Accepted: 09/02/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry, University of Stuttgart; 70569 Stuttgart Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry, University of Stuttgart; 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart; 70569 Stuttgart Germany
| |
Collapse
|
34
|
Han D, Sadowsky MJ, Chong Y, Hur HG. Characterization of a self-sufficient trans-anethole oxygenase from Pseudomonas putida JYR-1. PLoS One 2013; 8:e73350. [PMID: 24066043 PMCID: PMC3774712 DOI: 10.1371/journal.pone.0073350] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/18/2013] [Indexed: 11/18/2022] Open
Abstract
A novel flavoprotein monooxygenase, trans-anethole oxygenase (TAO), from Pseudomonas putida JYR-1, which is capable of catalyzing the oxidation of trans-anethole to p-anisaldehyde, was heterologously expressed in E. coli and purified. Enzymatic kinetics of diverse substrates and cofactors revealed that TAO is likely to be a novel self-sufficient flavoprotein monooxygenase. Enzyme assays of GST-TAO demonstrated that TAO catalyzed a trans-anethole oxidation reaction without auxiliary component enzyme-like electron-transfer flavin reductases. The single component TAO had the ability to reduce flavin cofactors and simultaneously oxidize trans-anthole to p-anisaldehyde. In the processes of reduction of flavin and oxidation of trans-anethole, TAO accepted various flavin and NAD(P)H cofactors. TAO also catalyzed oxidation of isoeugenol, O-methyl isoeugenol, and isosafrole, all of which contain the 2-propenyl functional group on the aromatic ring structure with different catalytic efficiency. TAO had the greatest catalytic efficiency (kcat/Km) with the original substrate, trans-anethole. Investigation about partially deleted mutants of TAO indicated that reductase active sites appeared to be located near the N terminal. Site directed mutagenesis studies also proved that the proposed flavin binding sites, Trp-38, Thr-43, Tyr-55, were critical for flavin reduction. However, disruption of any portion of TAO eliminated the oxygenase activity.
Collapse
Affiliation(s)
- Dongfei Han
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Michael J. Sadowsky
- Department of Soil, Water, and Climate; and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Youhoon Chong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Hor-Gil Hur
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
- * E-mail:
| |
Collapse
|
35
|
Evaluation of structural features in fungal cytochromes P450 predicted to rule catalytic diversification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:205-20. [DOI: 10.1016/j.bbapap.2012.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/17/2012] [Accepted: 09/18/2012] [Indexed: 01/11/2023]
|
36
|
Schneider E, Clark DS. Cytochrome P450 (CYP) enzymes and the development of CYP biosensors. Biosens Bioelectron 2013; 39:1-13. [DOI: 10.1016/j.bios.2012.05.043] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/29/2012] [Accepted: 05/30/2012] [Indexed: 11/29/2022]
|
37
|
Bezirtzoglou EEV. Intestinal cytochromes P450 regulating the intestinal microbiota and its probiotic profile. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2012; 23:18370. [PMID: 23990816 PMCID: PMC3747728 DOI: 10.3402/mehd.v23i0.18370] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 08/06/2012] [Accepted: 08/17/2012] [Indexed: 12/29/2022]
Abstract
Cytochromes P450 (CYPs) enzymes metabolize a large variety of xenobiotic substances. In this vein, a plethora of studies were conducted to investigate their role, as cytochromes are located in both liver and intestinal tissues. The P450 profile of the human intestine has not been fully characterized. Human intestine serves primarily as an absorptive organ for nutrients, although it has also the ability to metabolize drugs. CYPs are responsible for the majority of phase I drug metabolism reactions. CYP3A represents the major intestinal CYP (80%) followed by CYP2C9. CYP1A is expressed at high level in the duodenum, together with less abundant levels of CYP2C8-10 and CYP2D6. Cytochromes present a genetic polymorphism intra- or interindividual and intra- or interethnic. Changes in the pharmacokinetic profile of the drug are associated with increased toxicity due to reduced metabolism, altered efficacy of the drug, increased production of toxic metabolites, and adverse drug interaction. The high metabolic capacity of the intestinal flora is due to its enormous pool of enzymes, which catalyzes reactions in phase I and phase II drug metabolism. Compromised intestinal barrier conditions, when rupture of the intestinal integrity occurs, could increase passive paracellular absorption. It is clear that high microbial intestinal charge following intestinal disturbances, ageing, environment, or food-associated ailments leads to the microbial metabolism of a drug before absorption. The effect of certain bacteria having a benefic action on the intestinal ecosystem has been largely discussed during the past few years by many authors. The aim of the probiotic approach is to repair the deficiencies in the gut flora and establish a protective effect. There is a tentative multifactorial association of the CYP (P450) cytochrome role in the different diseases states, environmental toxic effects or chemical exposures and nutritional status.
Collapse
Affiliation(s)
- Eugenia Elefterios Venizelos Bezirtzoglou
- Laboratory of Microbiology, Biotechnology and Hygiene, Department of Food Science, Faculty of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| |
Collapse
|
38
|
Insect cytochromes P450: Topology of structural elements predicted to govern catalytic versatility. J Inorg Biochem 2011; 105:1354-64. [DOI: 10.1016/j.jinorgbio.2011.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 04/26/2011] [Accepted: 05/02/2011] [Indexed: 01/30/2023]
|
39
|
Miao Y, Baudry J. Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process. Biophys J 2011; 101:1493-503. [PMID: 21943431 DOI: 10.1016/j.bpj.2011.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 07/28/2011] [Accepted: 08/11/2011] [Indexed: 11/15/2022] Open
Abstract
Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.
Collapse
Affiliation(s)
- Yinglong Miao
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | | |
Collapse
|
40
|
Shrestha P, Oh TJ, Niraula NP, Liou K, Yoo JC, Sohng JK. Characterization of CYP166B1 and its electron transfer system in Streptomyces peucetius var. caesius ATCC 27952. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
41
|
Hlavica P. Assembly of non-natural electron transfer conduits in the cytochrome P450 system: A critical assessment and update of artificial redox constructs amenable to exploitation in biotechnological areas. Biotechnol Adv 2009; 27:103-21. [DOI: 10.1016/j.biotechadv.2008.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 09/29/2008] [Accepted: 10/04/2008] [Indexed: 10/21/2022]
|
42
|
Shumyantseva VV, Bulko TV, Rudakov YO, Kuznetsova GP, Samenkova NF, Lisitsa AV, Karuzina II, Archakov AI. Nanoelectrochemistry of cytochrome P450s: Direct electron transfer and electrocatalysis. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2007. [DOI: 10.1134/s1990750807040075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
43
|
Li S, Podust LM, Sherman DH. Engineering and analysis of a self-sufficient biosynthetic cytochrome P450 PikC fused to the RhFRED reductase domain. J Am Chem Soc 2007; 129:12940-1. [PMID: 17915876 DOI: 10.1021/ja075842d] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shengying Li
- Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | |
Collapse
|
44
|
Iyanagi T. Molecular mechanism of phase I and phase II drug-metabolizing enzymes: implications for detoxification. ACTA ACUST UNITED AC 2007; 260:35-112. [PMID: 17482904 DOI: 10.1016/s0074-7696(06)60002-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes that catalyze the biotransformation of drugs and xenobiotics are generally referred to as drug-metabolizing enzymes (DMEs). DMEs can be classified into two main groups: oxidative or conjugative. The NADPH-cytochrome P450 reductase (P450R)/cytochrome P450 (P450) electron transfer systems are oxidative enzymes that mediate phase I reactions, whereas the UDP-glucuronosyltransferases (UGTs) are conjugative enzymes that mediate phase II enzymes. Both enzyme systems are localized to the endoplasmic reticulum (ER) where a number of drugs are sequentially metabolized. DMEs, including P450s and UGTs, generally have a highly plastic active site that can accommodate a wide variety of substrates. The P450 and UGT genes constitute a supergene family, in which UGT proteins are encoded by distinct genes and a complex gene. Both the P450 and UGT genes have evolved to diversify their functions. This chapter reviews advances in understanding the structure and function of the P450R/P450 and UGT enzyme systems. In particular, the coordinate biotransformation of xenobiotics by phase I and II enzymes in the ER membrane is examined.
Collapse
Affiliation(s)
- Takashi Iyanagi
- Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| |
Collapse
|
45
|
Shumyantseva VV, Bulko TV, Rudakov YO, Kuznetsova GP, Samenkova NF, Lisitsa AV, Karuzina II, Archakov AI. Electrochemical properties of cytochroms P450 using nanostructured electrodes: Direct electron transfer and electro catalysis. J Inorg Biochem 2007; 101:859-65. [PMID: 17376532 DOI: 10.1016/j.jinorgbio.2007.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/31/2007] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
The present study demonstrates direct electron transfer between cytochromes P450 2B4 (CYP2B4), P450 1A2 (CYP1A2), sterol 14alpha-demethylase (CYP51b1) on the one hand and screen-printed graphite electrodes, modified with gold nanoparticles and didodecyldimethylammonium bromide (DDAB) on the other. Electro detection of heme proteins was possible when 2-200 pmol P450/electrode were adsorbed on the surface of nanostructured electrochemical interfaces. Electron transfer, direct electrochemical reduction and interaction with P450 substrates (oxygen, benzphetamine, and lanosterol) and with P450 inhibitor (ketoconazole) were analyzed using cyclic voltammetry (CV), square wave voltammetry (SWV) differential pulse voltammetry (DPV), and amperometry.
Collapse
Affiliation(s)
- V V Shumyantseva
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Street, 10, Moscow 119121, Russia.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Dai YJ, Chen T, Ge F, Huan Y, Yuan S, Zhu FF. Enhanced hydroxylation of imidacloprid by Stenotrophomonas maltophilia upon addition of sucrose. Appl Microbiol Biotechnol 2007; 74:995-1000. [PMID: 17216456 DOI: 10.1007/s00253-006-0762-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 11/12/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
Sucrose's ability to promote the hydroxylation of imidacloprid (IMI) by bacterium Stenotrophomonas maltophilia strain CGMCC 1.1788 was examined. Both growing culture and resting cells could transform IMI into 5-hydroxy IMI. Adding 2% sucrose to the growing culture transformation broth and 5% sucrose to the resting cell transformation broth resulted in biotransformation yields, respectively, 2.5 and 9 times greater than without sucrose. In the growing culture transformation, sucrose increased biomass, which led to enhance hydroxylation of IMI. In the resting cell transformation, sucrose was used not as a carbon source but as an energy source for cofactor regeneration for hydroxylation of IMI. The hydroxylation activity of IMI was promoted eightfold by adding reduced nicotinamide adenine dinucleotide (NADH) to the cell-free extract. The hydroxylation of IMI was significantly inhibited by P450 inhibitor piperonyl butoxide. It seems that the hydroxylation of IMI by S. maltophilia CGMCC 1.1788 might proceed through a system by cooperating with P450 enzyme.
Collapse
Affiliation(s)
- Yi-Jun Dai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, NNU Key Laboratory for Microbial Technology, College of Life Science, Nanjing Normal University, Nanjing 210097, China
| | | | | | | | | | | |
Collapse
|
47
|
Shumyantseva VV, Bulko TV, Samenkova NF, Kuznetsova GP, Usanov SA, Schulze H, Bachmann TT, Schmid RD, Archakov AI. A new format of electrodes for the electrochemical reduction of cytochromes P450. J Inorg Biochem 2006; 100:1353-7. [PMID: 16697466 DOI: 10.1016/j.jinorgbio.2006.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Revised: 03/20/2006] [Accepted: 03/21/2006] [Indexed: 01/25/2023]
Abstract
New approach to the electrochemical reduction of cytochromes P450 (P450s, CYPs) at electrodes chemically modified with appropriate substrates for P450s ("reverse" electrodes) was proposed. The method is based on the analysis of cyclic voltammograms, square-wave voltammograms and amperograms with subsequent determination of electrochemical characteristics such as catalytic current and redox potential. The sensitivity of proposed method is 0.2-1 nmol P450/electrode. The changes of maximal current and of redox potentials in square-wave voltammograms as well as the changes of catalytic current in amperometric experiments proved to be informative and reliable. Planar regime of screen-printed electrodes (strip-type sensors) enabled to utilise 20-60 microl of electrolyte volume. The enzyme-substrate pairs P450 2B4/benzphetamine and P450scc/cholesterol were investigated. Electrochemical parameters of electrodes with unspecific P450 substrates differed considerably from electrodes with appropriate substrates.
Collapse
Affiliation(s)
- Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Street, 10, Moscow 119121, Russia.
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Sasaki M, Akahira A, Oshiman KI, Tsuchido T, Matsumura Y. Purification of cytochrome P450 and ferredoxin, involved in bisphenol A degradation, from Sphingomonas sp. strain AO1. Appl Environ Microbiol 2006; 71:8024-30. [PMID: 16332782 PMCID: PMC1317416 DOI: 10.1128/aem.71.12.8024-8030.2005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous study (M. Sasaki, J. Maki, K. Oshiman, Y. Matsumura, and T. Tsuchido, Biodegradation 16:449-459, 2005), the cytochrome P450 monooxygenase system was shown to be involved in bisphenol A (BPA) degradation by Sphingomonas sp. strain AO1. In the present investigation, we purified the components of this monooxygenase, cytochrome P450 (P450bisd), ferredoxin (Fd(bisd)), and ferredoxin reductase (Red(bisd)). We demonstrated that P450bisd and Fd(bisd) are homodimeric proteins with molecular masses of 102.3 and 19.1 kDa, respectively, by gel filtration chromatography analysis. Spectroscopic analysis of Fd(bisd) revealed the presence of a putidaredoxin-type [2Fe-2S] cluster. P450(bisd), in the presence of Fd(bisd), Red(bisd), and NADH, was able to convert BPA. The K(m) and kcat values for BPA degradation were 85 +/- 4.7 microM and 3.9 +/- 0.04 min(-1), respectively. NADPH, spinach ferredoxin, and spinach ferredoxin reductase resulted in weak monooxygenase activity. These results indicated that the electron transport system of P450bisd might exhibit strict specificity. Two BPA degradation products of the P450(bisd) system were detected by high-performance liquid chromatography analysis and were thought to be 1,2-bis(4-hydroxyphenyl)-2-propanol and 2,2-bis(4-hydroxyphenyl)-1-propanol based on mass spectrometry-mass spectrometry analysis. This is the first report demonstrating that the cytochrome P450 monooxygenase system in bacteria is involved in BPA degradation.
Collapse
Affiliation(s)
- Miho Sasaki
- Department of Biotechnology, Faculty of Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | | | | | | | | |
Collapse
|
49
|
Lewis DF, Ito Y, Goldfarb PS. Cytochrome P450 structures and their substrate interactions. Drug Dev Res 2006. [DOI: 10.1002/ddr.20040] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
50
|
Todorovic S, Jung C, Hildebrandt P, Murgida DH. Conformational transitions and redox potential shifts of cytochrome P450 induced by immobilization. J Biol Inorg Chem 2005; 11:119-27. [PMID: 16328458 DOI: 10.1007/s00775-005-0054-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 10/26/2005] [Indexed: 11/26/2022]
Abstract
Cytochrome P450 (P450) from Pseudomonas putida was immobilized on Ag electrodes coated with self-assembled monolayers (SAMs) via electrostatic and hydrophobic interactions as well as by covalent cross-linking. The redox and conformational equilibria of the immobilized protein were studied by potential-dependent surface-enhanced resonance Raman spectroscopy. All immobilization conditions lead to the formation of the cytochrome P420 (P420) form of the enzyme. The redox potential of the electrostatically adsorbed P420 is significantly more positive than in solution and shows a steady downshift upon shortening of the length of the carboxyl-terminated SAMs, i.e., upon increasing the strength of the local electric field. Thus, two opposing effects modulate the redox potential of the adsorbed enzyme. First, the increased hydrophobicity of the heme environment brought about by immobilization on the SAM tends to upshift the redox potential by stabilizing the formally neutral ferrous form. Second, increasing electric fields tend to stabilize the positively charged ferric form, producing the opposite effect. The results provide insight into the parameters that control the structure and redox properties of heme proteins and contribute to the understanding of the apparently anomalous behavior of P450 enzymes in bioelectronic devices.
Collapse
Affiliation(s)
- Smilja Todorovic
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | | | | | | |
Collapse
|