1
|
Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
Collapse
Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| |
Collapse
|
2
|
Bertelmann C, Mock M, Schmid A, Bühler B. Efficiency aspects of regioselective testosterone hydroxylation with highly active CYP450-based whole-cell biocatalysts. Microb Biotechnol 2024; 17:e14378. [PMID: 38018939 PMCID: PMC10832557 DOI: 10.1111/1751-7915.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023] Open
Abstract
Steroid hydroxylations belong to the industrially most relevant reactions catalysed by cytochrome P450 monooxygenases (CYP450s) due to the pharmacological relevance of hydroxylated derivatives. The implementation of respective bioprocesses at an industrial scale still suffers from several limitations commonly found in CYP450 catalysis, that is low turnover rates, enzyme instability, inhibition and toxicity related to the substrate(s) and/or product(s). Recently, we achieved a new level of steroid hydroxylation rates by introducing highly active testosterone-hydroxylating CYP450 BM3 variants together with the hydrophobic outer membrane protein AlkL into Escherichia coli-based whole-cell biocatalysts. However, the activity tended to decrease, which possibly impedes overall productivities and final product titres. In this study, a considerable instability was confirmed and subject to a systematic investigation regarding possible causes. In-depth evaluation of whole-cell biocatalyst kinetics and stability revealed a limitation in substrate availability due to poor testosterone solubility as well as inhibition by the main product 15β-hydroxytestosterone. Instability of CYP450 BM3 variants was disclosed as another critical factor, which is of general significance for CYP450-based biocatalysis. Presented results reveal biocatalyst, reaction and process engineering strategies auguring well for industrial implementation of the developed steroid hydroxylation platform.
Collapse
Affiliation(s)
| | - Magdalena Mock
- Department of Solar MaterialsLeipzigGermany
- Present address:
Department of Mechanical Engineering and Material SciencesGeorg Agricola University of Applied SciencesBochumGermany
| | | | - Bruno Bühler
- Department of Solar MaterialsLeipzigGermany
- Department of Microbial BiotechnologyHelmholtz Centre for Environmental Research GmbH–UFZLeipzigGermany
| |
Collapse
|
3
|
Yan Y, Wu J, Hu G, Gao C, Guo L, Chen X, Liu L, Song W. Current state and future perspectives of cytochrome P450 enzymes for C–H and C=C oxygenation. Synth Syst Biotechnol 2022; 7:887-899. [PMID: 35601824 PMCID: PMC9112060 DOI: 10.1016/j.synbio.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/11/2023] Open
Abstract
Cytochrome P450 enzymes (CYPs) catalyze a series of C–H and C=C oxygenation reactions, including hydroxylation, epoxidation, and ketonization. They are attractive biocatalysts because of their ability to selectively introduce oxygen into inert molecules under mild conditions. This review provides a comprehensive overview of the C–H and C=C oxygenation reactions catalyzed by CYPs and the various strategies for achieving higher selectivity and enzymatic activity. Furthermore, we discuss the application of C–H and C=C oxygenation catalyzed by CYPs to obtain the desired chemicals or pharmaceutical intermediates in practical production. The rapid development of protein engineering for CYPs provides excellent biocatalysts for selective C–H and C=C oxygenation reactions, thereby promoting the development of environmentally friendly and sustainable production processes.
Collapse
Affiliation(s)
- Yu Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- Corresponding author.
| |
Collapse
|
4
|
Wang L, Zhou Y, Wang X, Yuan G, Yuan C, Yang Y, Bian Q, Wang M, Zhong J. Asymmetric syntheses of four stereoisomers of 13-hydroxy-14-methylhexadecanoic acid as potential antibacterial agents. Chirality 2021; 33:797-809. [PMID: 34477253 DOI: 10.1002/chir.23352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/22/2021] [Accepted: 07/28/2021] [Indexed: 11/06/2022]
Abstract
The first total syntheses of four stereoisomers of 13-hydroxy-14-methylhexadecanoic acid have been accomplished. Central to this strategy are asymmetric alkynylation of aldehyde, acid-catalyzed lactonization, the selective protection of primary alcohol and Wittig reaction. The product 1a was obtained in 17 steps in 2% overall yield. Moreover, these synthetic chiral hydroxy fatty acids 1a-1d are valuable for the development of antibacterial agents.
Collapse
Affiliation(s)
- Lifeng Wang
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Yun Zhou
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Xueyang Wang
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Gucheng Yuan
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Chaonan Yuan
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Yuxiong Yang
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Qinghua Bian
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Min Wang
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Jiangchun Zhong
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| |
Collapse
|
5
|
Negative catalysis / non-Bell-Evans-Polanyi reactivity by metalloenzymes: Examples from mononuclear heme and non-heme iron oxygenases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213914] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
6
|
Ma B, Wang Q, Han BN, Ikeda H, Zhang C, Xu LH. Hydroxylation, Epoxidation, and Dehydrogenation of Capsaicin by a Microbial Promiscuous Cytochrome P450 105D7. Chem Biodivers 2021; 18:e2000910. [PMID: 33656282 DOI: 10.1002/cbdv.202000910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/09/2021] [Indexed: 11/08/2022]
Abstract
Cytochrome P450 enzymes (P450s) are versatile biocatalysts, which insert a molecular oxygen into inactivated C-H bonds under mild conditions. CYP105D7 from Streptomyces avermitilis has been reported as a bacterial substrate-promiscuous P450 which catalyzes the hydroxylation of 1-deoxypentalenic acid, diclofenac, naringenin, compactin and steroids. In this study, CYP105D7 catalyzes hydroxylation, epoxidation and dehydrogenation of capsaicin, a pharmaceutical agent, revealing its functional diversity. The kinetic parameters of the CYP105D7 oxidation of capsaicin were determined as Km =311.60±87.30 μM and kcat =2.01±0.33 min-1 . In addition, we conducted molecular docking, mutagenesis and substrate binding analysis, indicating that Arg81 plays crucial role in the capsaicin binding and catalysis. To our best knowledge, this study presents the first report to illustrate that capsaicin can be catalyzed by prokaryotic P450s.
Collapse
Affiliation(s)
- Bingbing Ma
- Ocean College, Zhejiang University, Dinghai, Zhoushan, 316021, P. R. China
| | - Qianwen Wang
- Ocean College, Zhejiang University, Dinghai, Zhoushan, 316021, P. R. China
| | - Bing-Nan Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, P. R. China
| | - Haruo Ikeda
- Omura Satoshi Memorial Institute, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa, 252-0373, Japan
| | - Chunfang Zhang
- Ocean College, Zhejiang University, Dinghai, Zhoushan, 316021, P. R. China
| | - Lian-Hua Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, P. R. China
| |
Collapse
|
7
|
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: 140] [Impact Index Per Article: 28.0] [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.
Collapse
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.
| |
Collapse
|
8
|
Rimal H, Lee WH, Kim KH, Park H, Oh TJ. Characterization of Two Self-Sufficient Monooxygenases, CYP102A15 and CYP102A170, as Long-Chain Fatty Acid Hydroxylases. J Microbiol Biotechnol 2019; 30:777-784. [PMID: 32482945 PMCID: PMC9728198 DOI: 10.4014/jmb.1911.11048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/07/2020] [Indexed: 12/15/2022]
Abstract
Self-sufficient P450s, due to their fused nature, are the most effective tools for electron transfer to activate C-H bonds. They catalyze the oxygenation of fatty acids at different omega positions. Here, two new, self-sufficient cytochrome P450s, named CYP102A15 and CYP102A170, from polar Bacillus sp. PAMC 25034 and Paenibacillus sp. PAMC 22724, respectively, were cloned and expressed in E. coli. The genes are homologues of CYP102A1 from Bacillus megaterium. They catalyzed the hydroxylation of both saturated and unsaturated fatty acids ranging in length from C12-C20, with a moderately diverse profile compared to other members of the CYP102A subfamily. CYP102A15 exhibited the highest activity toward linoleic acid with Km 15.3 μM, and CYP102A170 showed higher activity toward myristic acid with Km 17.4 μM. CYP10A170 also hydroxylated the Eicosapentaenoic acid at ω-1 position only. Various kinetic parameters of both monooxygenases were also determined.
Collapse
Affiliation(s)
- Hemraj Rimal
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
| | - Woo-Haeng Lee
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 0841, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 3460, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asan 1460, Republic of Korea
- Genome-based BioIT Convergence Institute, Sunmoon University, Asan 3160, Republic of Korea
| |
Collapse
|
9
|
Child SA, Rossi VP, Bell SG. Selective ϖ-1 oxidation of fatty acids by CYP147G1 from Mycobacterium marinum. Biochim Biophys Acta Gen Subj 2019; 1863:408-417. [DOI: 10.1016/j.bbagen.2018.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/17/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
|
10
|
Tavanti M, Porter JL, Sabatini S, Turner NJ, Flitsch SL. Panel of New Thermostable CYP116B Self-Sufficient Cytochrome P450 Monooxygenases that Catalyze C−H Activation with a Diverse Substrate Scope. ChemCatChem 2018. [DOI: 10.1002/cctc.201701510] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michele Tavanti
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Joanne L. Porter
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Selina Sabatini
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Sabine L. Flitsch
- School of Chemistry, Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| |
Collapse
|
11
|
|
12
|
Kim J, Lee PG, Jung EO, Kim BG. In vitro characterization of CYP102G4 from Streptomyces cattleya: A self-sufficient P450 naturally producing indigo. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:60-67. [PMID: 28821467 DOI: 10.1016/j.bbapap.2017.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/22/2017] [Accepted: 08/04/2017] [Indexed: 02/01/2023]
Abstract
Self-sufficient CYP102As possess outstanding hydroxylating activity to fatty acids such as myristic acid. Other CYP102 subfamily members share substrate specificity of CYP102As, but, occasionally, unusual characteristics of its own subfamily have been found. In this study, only one self-sufficient cytochrome P450 from Streptomyces cattleya was renamed from CYP102A_scat to CYP102G4, purified and characterized. UV-Vis spectrometry pattern, FAD/FMN analysis, and protein sequence comparison among CYP102s have shown that CYP102 from Streptomyces cattleya belongs to CYP102G subfamily. It showed hydroxylation activity toward fatty acids generating ω-1, ω-2, and ω-3-hydroxyfatty acids, which is similar to the general substrate specificity of CYP102 family. Unexpectedly, however, expression of CYP102G4 showed indigo production in LB medium batch flask culture, and high catalytic activity (kcat/Km) for indole was measured as 6.14±0.10min-1mM-1. Besides indole, CYP102G4 was able to hydroxylate aromatic compounds such as flavone, benzophenone, and chloroindoles. Homology model has shown such ability to accept aromatic compounds is due to its bigger active site cavity. Unlike other CYP102s, CYP102G4 did not have biased cofactor dependency, which was possibly determined by difference in NAD(P)H binding residues (Ala984, Val990, and Tyr1064) compared to CYP102A1 (Arg966, Lys972 and Trp1046). Overall, a self-sufficient CYP within CYP102G subfamily was characterized using purified enzymes, which appears to possess unique properties such as an only prokaryotic CYP naturally producing indigo.
Collapse
Affiliation(s)
- Joonwon Kim
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Pyung-Gang Lee
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun-Ok Jung
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byung-Gee Kim
- Department of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
13
|
Maddigan NK, Bell SG. The self-sufficient CYP102 family enzyme, Krac9955, from Ktedonobacter racemifer DSM44963 acts as an alkyl- and alkyloxy-benzoic acid hydroxylase. Arch Biochem Biophys 2016; 615:15-21. [PMID: 28048974 DOI: 10.1016/j.abb.2016.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 12/30/2016] [Accepted: 12/30/2016] [Indexed: 11/25/2022]
Abstract
A self-sufficient CYP102 family encoding gene (Krac_9955) has been identified from the bacterium Ktedonobacter racemifer DSM44963 which belongs to the Chloroflexi phylum. The characterisation of the substrate range of this enzyme was hampered by low levels of production using E. coli. The yield and purity of the Krac9555 enzyme was improved using a codon optimised gene, the introduction of a tag and modification of the purification protocol. The heme domain was isolated and in vitro analysis of substrate binding and turnover was performed. Krac9955 was found to preferentially bind alkyl- and alkyloxy-benzoic acids (≥95% high spin, Kd < 3 μM) over saturated and unsaturated fatty acids. Unusually for a self-sufficient CYP102 family member Krac9955 showed low levels of NAD(P)H oxidation activity for all the substrates tested though product formation was observed for many. For nearly all substrates the preferred site of hydroxylation of Krac9955 was eight carbons away from the carboxylate group with certain reactions proceeding at ≥ 90% selectivity. Krac9955 differs from CYP102A1 (P450Bm3), and is the first self-sufficient member of the CYP102 family of P450 enzymes which is not optimised for fast fatty acid hydroxylation close to the ω-terminus.
Collapse
Affiliation(s)
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
| |
Collapse
|
14
|
Li RJ, Xu JH, Yin YC, Wirth N, Ren JM, Zeng BB, Yu HL. Rapid probing of the reactivity of P450 monooxygenases from the CYP116B subfamily using a substrate-based method. NEW J CHEM 2016. [DOI: 10.1039/c6nj00809g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four types of O-methylated substrates were designed as probes for the detection of fingerprints of Type IV P450s.
Collapse
Affiliation(s)
- Ren-Jie Li
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Jian-He Xu
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Yue-Cai Yin
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Nicolas Wirth
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Jiang-Meng Ren
- Shanghai Key Laboratory of New Drug Design
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Bu-Bing Zeng
- Shanghai Key Laboratory of New Drug Design
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Hui-Lei Yu
- State Key of Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| |
Collapse
|
15
|
Bell SG, Zhou R, Yang W, Tan ABH, Gentleman AS, Wong LL, Zhou W. Investigation of the Substrate Range of CYP199A4: Modification of the Partition between Hydroxylation and Desaturation Activities by Substrate and Protein Engineering. Chemistry 2012; 18:16677-88. [DOI: 10.1002/chem.201202776] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Indexed: 11/08/2022]
|
16
|
Affiliation(s)
- Rudi Fasan
- Department of Chemistry,
Hutchison Hall, University of Rochester, Rochester, New York 14627,
United States
| |
Collapse
|
17
|
Abstract
P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.
Collapse
Affiliation(s)
- Christopher J C Whitehouse
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
| | | | | |
Collapse
|
18
|
Rowlatt B, Yorke JA, Strong AJ, Whitehouse CJC, Bell SG, Wong LL. Chain length-dependent cooperativity in fatty acid binding and oxidation by cytochrome P450BM3 (CYP102A1). Protein Cell 2011; 2:656-71. [PMID: 21904981 DOI: 10.1007/s13238-011-1082-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 08/02/2011] [Indexed: 11/25/2022] Open
Abstract
Fatty acid binding and oxidation kinetics for wild type P450(BM3) (CYP102A1) from Bacillus megaterium have been found to display chain length-dependent homotropic behavior. Laurate and 13-methyl-myristate display Michaelis-Menten behavior while there are slight deviations with myristate at low ionic strengths. Palmitate shows Michaelis-Menten kinetics and hyperbolic binding behavior in 100 mmol/L phosphate, pH 7.4, but sigmoidal kinetics (with an apparent intercept) in low ionic strength buffers and at physiological phosphate concentrations. In low ionic strength buffers both the heme domain and the full-length enzyme show complex palmitate binding behavior that indicates a minimum of four fatty acid binding sites, with high cooperativity for the binding of the fourth palmitate molecule, and the full-length enzyme showing tighter palmitate binding than the heme domain. The first flavin-to-heme electron transfer is faster for laurate, myristate and palmitate in 100 mmol/L phosphate than in 50 mmol/L Tris (pH 7.4), yet each substrate induces similar high-spin heme content. For palmitate in low phosphate buffer concentrations, the rate constant of the first electron transfer is much larger than k (cat). The results suggest that phosphate has a specific effect in promoting the first electron transfer step, and that P450(BM3) could modulate Bacillus membrane morphology and fluidity via palmitate oxidation in response to the external phosphate concentration.
Collapse
Affiliation(s)
- Benjamin Rowlatt
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
| | | | | | | | | | | |
Collapse
|
19
|
Van Bogaert INA, Groeneboer S, Saerens K, Soetaert W. The role of cytochrome P450 monooxygenases in microbial fatty acid metabolism. FEBS J 2010; 278:206-21. [DOI: 10.1111/j.1742-4658.2010.07949.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
20
|
Abstract
The cytochromes P450 (P450s) are a superfamily of oxidative haemoproteins that are capable of catalysing a vast range of oxidative transformations, including the oxidation of unactivated alkanes, often with high stereo- and regio-selectivity. Fatty acid hydroxylation by P450s is widespread across both bacteria and higher organisms, with the sites of oxidation and specificity of oxidation varying from system to system. Several key examples are discussed in the present article, with the focus on P450(BioI) (CYP107H1), a biosynthetic P450 found in the biotin operon of Bacillus subtilis. The biosynthetic function of P450(BioI) is the formation of pimelic acid, a biotin precursor, via a multiple-step oxidative cleavage of long-chain fatty acids. P450(BioI) is a member of an important subgroup of P450s that accept their substrates not free in solution, but rather presented by a separate carrier protein. Structural characterization of the P450(BioI)-ACP (acyl-carrier protein) complex has recently been performed, which has revealed the basis for the oxidation of the centre of the fatty acid chain. The P450(BioI)-ACP structure is the first such P450-carrier protein complex to be characterized structurally, with important implications for other biosynthetically intriguing P450-carrier protein complexes.
Collapse
|
21
|
Shul'pin GB. Selectivity enhancement in functionalization of C–H bonds: A review. Org Biomol Chem 2010; 8:4217-28. [DOI: 10.1039/c004223d] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
22
|
Whitehouse C, Bell S, Wong LL. Desaturation of Alkylbenzenes by Cytochrome P450BM3(CYP102A1). Chemistry 2008; 14:10905-8. [DOI: 10.1002/chem.200801927] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
23
|
Cryle MJ, De Voss JJ. The Role of the Conserved Threonine in P450BM3 Oxygen Activation: Substrate-Determined Hydroxylation Activity of the Thr268Ala Mutant. Chembiochem 2008; 9:261-6. [DOI: 10.1002/cbic.200700537] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
24
|
Fasan R, Chen MM, Crook NC, Arnold FH. Engineered alkane-hydroxylating cytochrome P450(BM3) exhibiting nativelike catalytic properties. Angew Chem Int Ed Engl 2008; 46:8414-8. [PMID: 17886313 DOI: 10.1002/anie.200702616] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rudi Fasan
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 California Blvd. MC 210-41, Pasadena, CA 91125, USA
| | | | | | | |
Collapse
|
25
|
Whitehouse CJC, Bell SG, Tufton HG, Kenny RJP, Ogilvie LCI, Wong LL. Evolved CYP102A1 (P450BM3) variants oxidise a range of non-natural substrates and offer new selectivity options. Chem Commun (Camb) 2008:966-8. [DOI: 10.1039/b718124h] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
26
|
Chowdhary PK, Alemseghed M, Haines DC. Cloning, expression and characterization of a fast self-sufficient P450: CYP102A5 from Bacillus cereus. Arch Biochem Biophys 2007; 468:32-43. [DOI: 10.1016/j.abb.2007.09.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 09/10/2007] [Accepted: 09/13/2007] [Indexed: 11/27/2022]
|
27
|
Fasan R, Chen M, Crook N, Arnold F. Engineered Alkane-Hydroxylating Cytochrome P450BM3 Exhibiting Nativelike Catalytic Properties. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702616] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
28
|
Watanabe Y, Laschat S, Budde M, Affolter O, Shimada Y, Urlacher VB. Oxidation of acyclic monoterpenes by P450 BM-3 monooxygenase: influence of the substrate E/Z-isomerism on enzyme chemo- and regioselectivity. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.06.104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
29
|
Bloom JD, Romero PA, Lu Z, Arnold FH. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct 2007; 2:17. [PMID: 17598905 PMCID: PMC1914045 DOI: 10.1186/1745-6150-2-17] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 06/28/2007] [Indexed: 11/10/2022] Open
Abstract
Background Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve when selection begins to favor other, "promiscuous" functions that are incidental to a protein's original biological role. If mutations that are neutral with respect to a protein's primary biological function cause substantial changes in promiscuous functions, these mutations could enable future functional evolution. Results Here we investigate this possibility experimentally by examining how cytochrome P450 enzymes that have evolved neutrally with respect to activity on a single substrate have changed in their abilities to catalyze reactions on five other substrates. We find that the enzymes have sometimes changed as much as four-fold in the promiscuous activities. The changes in promiscuous activities tend to increase with the number of mutations, and can be largely rationalized in terms of the chemical structures of the substrates. The activities on chemically similar substrates tend to change in a coordinated fashion, potentially providing a route for systematically predicting the change in one activity based on the measurement of several others. Conclusion Our work suggests that initially neutral genetic drift can lead to substantial changes in protein functions that are not currently under selection, in effect poising the proteins to more readily undergo functional evolution should selection favor new functions in the future. Reviewers This article was reviewed by Martijn Huynen, Fyodor Kondrashov, and Dan Tawfik (nominated by Christoph Adami).
Collapse
Affiliation(s)
- Jesse D Bloom
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Philip A Romero
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Zhongyi Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| |
Collapse
|
30
|
Cryle MJ, De Voss JJ. Is the ferric hydroperoxy species responsible for sulfur oxidation in cytochrome p450s? Angew Chem Int Ed Engl 2007; 45:8221-3. [PMID: 17111450 DOI: 10.1002/anie.200603411] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Max J Cryle
- Department of Chemistry, School of Molecular and Microbial Sciences, University of Queensland, St. Lucia Brisbane 4072, Australia
| | | |
Collapse
|
31
|
Facile determination of the absolute stereochemistry of hydroxy fatty acids by GC: application to the analysis of fatty acid oxidation by a P450BM3 mutant. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.01.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
32
|
Cryle MJ, Matovic NJ, De Voss JJ. The stereochemistry of fatty acid hydroxylation by cytochrome P450BM3. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2006.10.136] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
33
|
Is the Ferric Hydroperoxy Species Responsible for Sulfur Oxidation in Cytochrome P450s? Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200603411] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
34
|
Girvan HM, Waltham TN, Neeli R, Collins HF, McLean KJ, Scrutton NS, Leys D, Munro AW. Flavocytochrome P450 BM3 and the origin of CYP102 fusion species. Biochem Soc Trans 2006; 34:1173-7. [PMID: 17073779 DOI: 10.1042/bst0341173] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Flavocytochrome P450 (cytochrome P450) BM3 is an intensively studied model system within the P450 enzyme superfamily, and is a natural fusion of a P450 to its P450 reductase redox partner. The fusion arrangement enables efficient electron transfer within the enzyme and a catalytic efficiency that cannot be matched in P450 systems from higher organisms. P450 BM3's potential for industrially relevant chemical transformations is now recognized, and variants with biotechnological applications have been constructed. Simultaneously, structural and mechanistic studies continue to reveal the intricate mechanistic details of this enzyme, including its dimeric organization and the relevance of this quaternary structure to catalysis. Homologues of BM3 have been found in several bacteria and fungi, indicating important physiological functions in these microbes and enabling first insights into evolution of the enzyme family. This short paper deals with recent developments in our understanding of structure, function, evolution and biotechnological applications of this important P450 system.
Collapse
Affiliation(s)
- H M Girvan
- Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester M1 7ND, UK
| | | | | | | | | | | | | | | |
Collapse
|