1
|
Lee JHZ, Bruning JB, Bell SG. An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase. Chemistry 2024; 30:e202303335. [PMID: 37971151 DOI: 10.1002/chem.202303335] [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: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
The cytochrome P450 monooxygenases (CYPs) are a class of heme-thiolate enzymes that insert oxygen into unactivated C-H bonds. These enzymes can be converted into peroxygenases via protein engineering, which enables their activity to occur using hydrogen peroxide (H2 O2 ) without the requirement for additional nicotinamide co-factors or partner proteins. Here, we demonstrate that soaking crystals of an engineered P450 peroxygenase with H2 O2 enables the enzymatic reaction to occur within the crystal. Crystals of the designed P450 peroxygenase, the T252E mutant of CYP199A4, in complex with 4-methoxybenzoic acid were soaked with different concentrations of H2 O2 for varying times to initiate the in crystallo O-demethylation reaction. Crystal structures of T252E-CYP199A4 showed a distinct loss of electron density that was consistent with the O-demethylated metabolite, 4-hydroxybenzoic acid. A new X-ray crystal structure of this enzyme with the 4-hydroxybenzoic acid product was obtained to enable comparison alongside the existing substrate-bound structure. The visualisation of enzymatic catalysis in action is challenging in structural biology and the ability to initiate the reactions of P450 enzymes, in crystallo by simply soaking crystals with H2 O2 will enable new structural biology methods and techniques to be applied to study their mechanism of action.
Collapse
Affiliation(s)
- Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| |
Collapse
|
2
|
Churchman LR, Giang PD, Buczynski JB, Stok JE, Bell SG, De Voss JJ. Synthesis of substituted norcaranes for use as probes of enzyme mechanisms. Org Biomol Chem 2023; 21:9647-9658. [PMID: 38037692 DOI: 10.1039/d3ob01571h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Norcarane is a mechanistic probe of monooxygenase enzymes that is able to detect the presence of cationic or radical intermediates. The addition of substituents around the bicycloheptane ring of the norcarane scaffold can assist in improving enzyme binding affinity and thus improve the regioselectivity of oxidation. Here we prepare in three-step, diastereoselective syntheses, ten norcaranes monosubstituted α to the cyclopropane as advanced probes. Four of these compounds were examined in enzyme binding experiments to evaluate their potential as probe substrates. Additionally, 19 potential products of enzymatic oxidation were generated via two additional synthetic steps for use as product standards in future studies.
Collapse
Affiliation(s)
- Luke R Churchman
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
| | - Peter D Giang
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
| | - Julia B Buczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
| |
Collapse
|
3
|
Gable JA, Poulos TL, Follmer AH. Redox partner recognition and selectivity of cytochrome P450lin (CYP111A1). J Inorg Biochem 2023; 244:112212. [PMID: 37058990 PMCID: PMC10519177 DOI: 10.1016/j.jinorgbio.2023.112212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 04/16/2023]
Abstract
The strict requirement of cytochrome P450cam for its native ferredoxin redox partner, putidaredoxin (Pdx), is not exhibited by any other known cytochrome P450 (CYP) system and the molecular details of redox partner selectivity are still not completely understood. We therefore examined the selectivity of a related Pseudomonas cytochrome P450, P450lin, by testing its activity with non-native redox partners. We found that P450lin could utilize Arx, the native redox partner of CYP101D1, to enable turnover of its substrate, linalool, while Pdx showed limited activity. Arx exhibited a higher sequence similarity to P450lins native redox partner, linredoxin (Ldx) than Pdx, including several residues that are believed to be at the interface of the two proteins, based on the P450cam-Pdx complex structure. We therefore mutated Pdx to resemble Ldx and Arx and found that a double mutant, D38L/∆106, displayed higher activity than Arx. In addition, Pdx D38L/∆106 does not induce a low-spin shift in linalool bound P450lin but does destabilize the P450lin-oxycomplex. Together our results suggest that P450lin and its redox partners may form a similar interface to P450cam-Pdx, but the interactions that allow for productive turnover are different.
Collapse
Affiliation(s)
- Jessica A Gable
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Thomas L Poulos
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Alec H Follmer
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.
| |
Collapse
|
4
|
Gable JA, Poulos TL, Follmer AH. Cooperative Substrate Binding Controls Catalysis in Bacterial Cytochrome P450terp (CYP108A1). J Am Chem Soc 2023; 145:10.1021/jacs.2c12388. [PMID: 36779970 PMCID: PMC10576961 DOI: 10.1021/jacs.2c12388] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Despite being one of the most well-studied aspects of cytochrome P450 chemistry, important questions remain regarding the nature and ubiquity of allosteric regulation of catalysis. The crystal structure of a bacterial P450, P450terp, in the presence of substrate reveals two binding sites, one above the heme in position for regioselective hydroxylation and another in the substrate access channel. Unlike many bacterial P450s, P450terp does not exhibit an open to closed conformational change when substrate binds; instead, P450terp uses the second substrate molecule to hold the first substrate molecule in position for catalysis. Spectral titrations clearly show that substrate binding to P450terp is cooperative with a Hill coefficient of 1.4 and is supported by isothermal titration calorimetry. The importance of the allosteric site was explored by a series of mutations that weaken the second site and that help hold the first substrate in position for proper catalysis. We further measured the coupling efficiency of both the wild-type (WT) enzyme and the mutant enzymes. While the WT enzyme exhibits 97% efficiency, each of the variants showed lower catalytic efficiency. Additionally, the variants show decreased spin shifts upon binding of substrate. These results are the first clear example of positive homotropic allostery in a class 1 bacterial P450 with its natural substrate. Combined with our recent results from P450cam showing complex substrate allostery and conformational dynamics, our present study with P450terp indicates that bacterial P450s may not be as simple as once thought and share complex substrate binding properties usually associated with only mammalian P450s.
Collapse
Affiliation(s)
- Jessica A Gable
- Departments of Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
- Departments of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3900, United States
- Departments of Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Alec H Follmer
- Departments of Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| |
Collapse
|
5
|
Bukhdruker S, Varaksa T, Orekhov P, Grabovec I, Marin E, Kapranov I, Kovalev K, Astashkin R, Kaluzhskiy L, Ivanov A, Mishin A, Rogachev A, Gordeliy V, Gilep A, Strushkevich N, Borshchevskiy V. Structural insights into the effects of glycerol on ligand binding to cytochrome P450. Acta Crystallogr D Struct Biol 2023; 79:66-77. [PMID: 36601808 DOI: 10.1107/s2059798322011019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/16/2022] [Indexed: 01/06/2023] Open
Abstract
New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124-CHImi complex reveals two glycerol molecules in the active site. A 1.15 Å resolution crystal structure of the glycerol-free CYP124-CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simulations show coherence of the ligand and enzyme conformations. Spectrophotometric titration confirmed the influence of glycerol on CHImi binding: the affinity decreases more than tenfold in glycerol-containing buffer. In addition, it also showed that glycerol has a similar effect on other azole and triazole CYP124 ligands. Together, these data show that glycerol may compromise structural-functional studies and impede rational drug-design campaigns.
Collapse
Affiliation(s)
- Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Tatsiana Varaksa
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Kirill Kovalev
- EMBL Outstation Hamburg, c/o DESY, 22607 Hamburg, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Leonid Kaluzhskiy
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow 119121, Russian Federation
| | - Alexis Ivanov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow 119121, Russian Federation
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Andrey Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Valentin Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | | | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| |
Collapse
|
6
|
Poulos TL, Follmer AH. Updating the Paradigm: Redox Partner Binding and Conformational Dynamics in Cytochromes P450. Acc Chem Res 2022; 55:373-380. [PMID: 34965086 PMCID: PMC8959394 DOI: 10.1021/acs.accounts.1c00632] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This Account summarizes recent findings centered on the role that redox partner binding, allostery, and conformational dynamics plays in cytochrome P450 proton coupled electron transfer. P450s are one of Nature's largest enzyme families and it is not uncommon to find a P450 wherever substrate oxidation is required in the formation of essential molecules critical to the life of the organism or in xenobiotic detoxification. P450s can operate on a remarkably large range of substrates from the very small to the very large, yet the overall P450 three-dimensional structure is conserved. Given this conservation of structure, it is generally assumed that the basic catalytic mechanism is conserved. In nearly all P450s, the O2 O-O bond must be cleaved heterolytically enabling one oxygen atom, the distal oxygen, to depart as water and leave behind a heme iron-linked O atom as the powerful oxidant that is used to activate the nearby substrate. For this process to proceed efficiently, externally supplied electrons and protons are required. Two protons must be added to the departing O atom while an electron is transferred from a redox partner that typically contains either a Fe2S2 or FMN redox center. The paradigm P450 used to unravel the details of these mechanisms has been the bacterial CYP101A1 or P450cam. P450cam is specific for its own Fe2S2 redox partner, putidaredoxin or Pdx, and it has long been postulated that Pdx plays an effector/allosteric role by possibly switching P450cam to an active conformation. Crystal structures, spectroscopic data, and direct binding experiments of the P450cam-Pdx complex provide some answers. Pdx shifts the conformation of P450cam to a more open state, a transition that is postulated to trigger the proton relay network required for O2 activation. An essential part of this proton relay network is a highly conserved Asp (sometimes Glu) that is known to be critical for activity in a number of P450s. How this Asp and proton delivery networks are connected to redox partner binding is quite simple. In the closed state, this Asp is tied down by salt bridges, but these salt bridges are ruptured when Pdx binds, leaving the Asp free to serve its role in proton transfer. An alternative hypothesis suggests that a specific proton relay network is not really necessary. In this scenario, the Asp plays a structural role in the open/close transition and merely opening the active site access channel is sufficient to enable solvent protons in for O2 protonation. Experiments designed to test these various hypotheses have revealed some surprises in both P450cam and other bacterial P450s. Molecular dynamics and crystallography show that P450cam can undergo rather significant conformational gymnastics that result in a large restructuring of the active site requiring multiple cis/trans proline isomerizations. It also has been found that X-ray driven substrate hydroxylation is a useful tool for better understanding the role that the essential Asp and surrounding residues play in catalysis. Here we summarize these recent results which provide a much more dynamic picture of P450 catalysis.
Collapse
Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Alec H. Follmer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
7
|
Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species. Int J Mol Sci 2021; 22:ijms22115542. [PMID: 34073951 PMCID: PMC8197338 DOI: 10.3390/ijms22115542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins, are well-known players in the generation of chemicals valuable to humans and as a drug target against pathogens. Understanding the evolution of P450s in a bacterial population is gaining momentum. In this study, we report comprehensive analysis of P450s in the ancient group of the bacterial class Alphaproteobacteria. Genome data mining and annotation of P450s in 599 alphaproteobacterial species belonging to 164 genera revealed the presence of P450s in only 241 species belonging to 82 genera that are grouped into 143 P450 families and 214 P450 subfamilies, including 77 new P450 families. Alphaproteobacterial species have the highest average number of P450s compared to Firmicutes species and cyanobacterial species. The lowest percentage of alphaproteobacterial species P450s (2.4%) was found to be part of secondary metabolite biosynthetic gene clusters (BGCs), compared other bacterial species, indicating that during evolution large numbers of P450s became part of BGCs in other bacterial species. Our study identified that some of the P450 families found in alphaproteobacterial species were passed to other bacterial species. This is the first study to report on the identification of CYP125 P450, cholesterol and cholest-4-en-3-one hydroxylase in alphaproteobacterial species (Phenylobacterium zucineum) and to predict cholesterol side-chain oxidation capability (based on homolog proteins) by P. zucineum.
Collapse
|
8
|
Petrik ID, Davydov R, Kahle M, Sandoval B, Dwaraknath S, Ädelroth P, Hoffman B, Lu Y. An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network. Biochemistry 2021; 60:346-355. [PMID: 33464878 PMCID: PMC7888536 DOI: 10.1021/acs.biochem.0c00852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Efficiently carrying out the oxygen reduction reaction (ORR) is critical for many applications in biology and chemistry, such as bioenergetics and fuel cells, respectively. In biology, this reaction is carried out by large, transmembrane oxidases such as heme-copper oxidases (HCOs) and cytochrome bd oxidases. Common to these oxidases is the presence of a glutamate residue next to the active site, but its precise role in regulating the oxidase activity remains unclear. To gain insight into its role, we herein report that incorporation of glutamate next to a designed heme-copper center in two biosynthetic models of HCOs improves O2 binding affinity, facilitates protonation of reaction intermediates, and eliminates release of reactive oxygen species. High-resolution crystal structures of the models revealed extended, water-mediated hydrogen-bonding networks involving the glutamate. Electron paramagnetic resonance of the cryoreduced oxy-ferrous centers at cryogenic temperature followed by thermal annealing allowed observation of the key hydroperoxo intermediate that can be attributed to the hydrogen-bonding network. By demonstrating these important roles of glutamate in oxygen reduction biochemistry, this work offers deeper insights into its role in native oxidases, which may guide the design of more efficient artificial ORR enzymes or catalysts for applications such as fuel cells.
Collapse
Affiliation(s)
- Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Roman Davydov
- The Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Braddock Sandoval
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sudharsan Dwaraknath
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brian Hoffman
- The Department of Chemistry, Northwestern University, Evanston, Illinois 60201
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
9
|
Finnigan JD, Young C, Cook DJ, Charnock SJ, Black GW. Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:289-320. [PMID: 32951814 DOI: 10.1016/bs.apcsb.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).
Collapse
Affiliation(s)
| | - Carl Young
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | - Darren J Cook
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | | | - Gary W Black
- Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
10
|
Murarka VC, Batabyal D, Amaya JA, Sevrioukova IF, Poulos TL. Unexpected Differences between Two Closely Related Bacterial P450 Camphor Monooxygenases. Biochemistry 2020; 59:2743-2750. [PMID: 32551522 DOI: 10.1021/acs.biochem.0c00366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The bacterial cytochrome P450cam catalyzes the oxidation of camphor to 5-exo-hydroxycamphor as the first step in the oxidative assimilation of camphor as a carbon/energy source. CYP101D1 is another bacterial P450 that catalyzes the same reaction. A third P450 (P450tcu) has recently been discovered that has ≈86% sequence identity to P450cam as well as very similar enzymatic properties. P450tcu, however, exhibits three unusual features not found in P450cam. First, we observe product in at least two orientations in the X-ray structure that indicates that, unlike the case for P450cam, X-ray-generated reducing equivalents can drive substrate hydroxylation in crystallo. We postulate, on the basis of molecular dynamics simulations, that greater flexibility in P450tcu enables easier access of protons to the active site and, together with X-ray driven reduction, results in O2 activation and substrate hydroxylation. Second, the characteristic low-spin to high-spin transition when camphor binds occurs immediately with P450cam but is very slow in P450tcu. Third, isothermal titration calorimetry shows that in P450cam substrate binding is entropically driven with a ΔH of >0 while in P450tcu with a ΔH of <0 with a more modest change in -TΔS. These results indicate that despite nearly identical structures and enzymatic properties, these two P450s exhibit quite different properties most likely related to differences in conformational dynamics.
Collapse
Affiliation(s)
- Vidhi C Murarka
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Jose A Amaya
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Irina F Sevrioukova
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| |
Collapse
|
11
|
Amaya JA, Batabyal D, Poulos TL. Proton Relay Network in the Bacterial P450s: CYP101A1 and CYP101D1. Biochemistry 2020; 59:2896-2902. [DOI: 10.1021/acs.biochem.0c00329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- José A. Amaya
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| |
Collapse
|
12
|
Coleman T, Stok JE, Podgorski MN, Bruning JB, De Voss JJ, Bell SG. Structural insights into the role of the acid-alcohol pair of residues required for dioxygen activation in cytochrome P450 enzymes. J Biol Inorg Chem 2020; 25:583-596. [PMID: 32248305 DOI: 10.1007/s00775-020-01781-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/22/2020] [Indexed: 10/24/2022]
Abstract
The cytochrome P450 heme monooxygenases commonly use an acid-alcohol pair of residues, within the I-helix, to activate iron-bound dioxygen. This work aims to clarify conflicting reports on the importance of the alcohol functionality in this process. Mutants of the P450, CYP199A4 (CYP199A4D251N and CYP199A4T252A), were prepared, characterised and their crystal structures were solved. The acid residue of CYP199A4 is not part of a salt bridge network, a key feature of paradigmatic model system P450cam. Instead, there is a direct proton delivery network, via a chain of water molecules, extending to the surface. Nevertheless, CYP199A4D251N dramatically reduced the activity of the enzyme consistent with a role in proton delivery. CYP199A4T252A decreased the coupling efficiency of the enzyme with a concomitant increase in the hydrogen peroxide uncoupling pathway. However, the effect of this mutation was much less pronounced than reported with P450cam. Its crystal structures revealed fewer changes at the I-helix, compared to the P450cam system. The structural changes observed within the I-helix of P450cam during oxygen activation do not seem to be required in this P450. These differences are due to the presence of a second threonine residue at position 253, which is absent in P450cam. This threonine forms part of the hydrogen bonding network, resulting in subtle structural changes and is also present across the majority of the P450 superfamily. Overall, the results suggest that while the acid-alcohol pair is important for dioxygen activation this process and the method of proton delivery can differ across P450s.Graphic abstract.
Collapse
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia.
| |
Collapse
|
13
|
Child SA, Flint KL, Bruning JB, Bell SG. The characterisation of two members of the cytochrome P450 CYP150 family: CYP150A5 and CYP150A6 from Mycobacterium marinum. Biochim Biophys Acta Gen Subj 2019; 1863:925-934. [PMID: 30826435 DOI: 10.1016/j.bbagen.2019.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Actinobacteria, including the Mycobacteria, have a large component of cytochrome P450 family monooxygenases. This includes Mycobacterium tuberculosis, M. ulcerans and M. marinum, and M. vanbaalenii. These enzymes can abstract CH bonds and have important roles in natural product biosynthesis. METHODS Two members of the bacterial CYP150 family, CYP150A5 and CYP150A6 from M. marinum, were produced, purified and characterised. The potential substrate ranges of both enzymes were analysed and the monooxygenase activity of CYP150A5 was reconstituted using a physiological electron transfer partner system. CYP150A6 was structurally characterised by X-ray crystallography. RESULTS CYP150A5 was shown to bind various norisoprenoids and terpenoids. It could regioselectively hydroxylate β-ionol. The X-ray crystal structure of substrate-free CYP150A6 was solved to 1.5 Å. This displayed an open conformation with short F and G helices, an unresolved F-G loop region and exposed active site pocket. The active site residues could be identified and important variations were found among the CYP150A enzymes. Haem-binding azole inhibitors were identified for both enzymes. CONCLUSIONS The structure of CYP150A6 will facilitate the identification of physiological substrates and the design of better inhibitors for members of this P450 family. Based on the observed differences in substrate binding preference and sequence variations among the active site residues, their roles are predicted to be different. GENERAL SIGNIFICANCE Multiple CYP150 family members were found in many bacteria and are prevalent in the Mycobacteria including several human pathogens. Inhibition and structural data are reported here for these enzymes for the first time.
Collapse
Affiliation(s)
- Stella A Child
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - Kate L Flint
- 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
|
14
|
Batabyal D, Poulos TL. Effect of redox partner binding on CYP101D1 conformational dynamics. J Inorg Biochem 2018; 183:179-183. [PMID: 29550100 PMCID: PMC5976445 DOI: 10.1016/j.jinorgbio.2018.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/13/2018] [Accepted: 02/18/2018] [Indexed: 11/27/2022]
Abstract
We have compared the thermodynamics of substrate and redox partner binding of P450cam to its close homologue, CYP101D1, using isothermal titration calorimetry (ITC). CYP101D1 binds camphor about 10-fold more weakly than P450cam which is consistent with the inability of camphor to cause a complete low- to high-spin shift in CYP101D1. Even so molecular dynamics simulations show that camphor is very stable in the CYP101D1 active site similar to P450cam. ITC data on the binding of the CYP101D1 ferredoxin redox partner (abbreviated Arx) shows that the substrate-bound closed state of CYP101D1 binds Arx more tightly than the substrate-free open form. This is just the opposite to P450cam where Pdx (ferredoxin redox partner of P450cam) favors binding to the P450cam open state. In addition, CYP101D1-Arx binding has a large negative ΔS while the P450cam-Pdx has a much smaller ΔS indicating that interactions at the docking interface are different. The most obvious difference is that PDXD38 which forms an important ion pair with P450camR112 at the center of the interface is ArxL39 in Arx. This suggests that Arx may adopt a different orientation than Pdx in order to optimize nonpolar interactions with ArxL39.
Collapse
Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900, USA
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, CA 92697-3900, USA.
| |
Collapse
|
15
|
Batabyal D, Richards LS, Poulos TL. Effect of Redox Partner Binding on Cytochrome P450 Conformational Dynamics. J Am Chem Soc 2017; 139:13193-13199. [PMID: 28823160 DOI: 10.1021/jacs.7b07656] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Previous crystal structures of cytochrome P450cam complexed with its redox partner, putidaredoxin (Pdx), shows that P450cam adopts the open conformation. It has been hypothesized that the Pdx-induced shift toward the open state frees the essential Asp251 from salt bridges with Arg186 and Lys178 so that Asp251 can participate in a proton relay network required for O2 activation. This in part explains why P450cam has such a strict requirement for Pdx. One problem with this view is that looser substrate-protein interactions in the open state may not be compatible with the observed regio- and stereoselective hydroxylation. In the present study, molecular dynamics simulations show that Pdx binding favors a conformation that stabilizes the active site and decreases camphor mobility yet retains a partially open conformation compatible with the required proton relay network. The R186A mutant which frees Asp251 in the absence of Pdx retains good enzyme activity, and the crystal structure shows that product, 5-exo-hydroxycamphor, is bound. This indicates that rupture of the Asp251-Arg186 relaxes selectivity with respect to source of electrons and enables X-ray generated reducing equivalents to support substrate hydroxylation. These combined computational and experimental results are consistent with the proposed role of Pdx in assisting the release of Asp251 from ion pairs so that it can participate in proton-coupled electron transfer.
Collapse
Affiliation(s)
- Dipanwita Batabyal
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Logan S Richards
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States
| |
Collapse
|
16
|
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
|
17
|
Abstract
The heme iron of cytochromes P450 must be reduced to bind and activate molecular oxygen for substrate oxidation. Reducing equivalents are derived from a redox partner, which requires the formation of a protein-protein complex. A subject of increasing discussion is the role that redox partner binding plays, if any, in favoring significant structural changes in the P450s that are required for activity. Many P450s now have been shown to experience large open and closed motions. Several structural and spectral studies indicate that the well-studied P450cam adopts the open conformation when its redox partner, putidaredoxin (Pdx), binds, whereas recent NMR studies indicate that this view is incorrect. Given the relevance of this discrepancy to P450 chemistry, it is important to determine whether Pdx favors the open or closed form of P450cam. Here, we have used both computational and experimental isothermal titration calorimetry studies that unequivocally show Pdx favors binding to the open form of P450cam. Analyses of molecular-dynamic trajectories also provide insights into intermediate conformational states that could be relevant to catalysis.
Collapse
|
18
|
Quesne MG, Senthilnathan D, Singh D, Kumar D, Maldivi P, Sorokin AB, de Visser SP. Origin of the Enhanced Reactivity of μ-Nitrido-Bridged Diiron(IV)-Oxo Porphyrinoid Complexes over Cytochrome P450 Compound I. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02720] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matthew G. Quesne
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Dhurairajan Senthilnathan
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- Center for
Computational Chemistry, CRD, PRIST University, Vallam, Thanjavur, Tamilnadu 613403, India
| | - Devendra Singh
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Devesh Kumar
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Pascale Maldivi
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- CEA, INAC-SCIB, F-38000 Grenoble, France
| | - Alexander B. Sorokin
- Institut
de Recherches sur la Catalyse et l’Environnement de Lyon (IRCELYON),
UMR 5256, CNRS-Université Lyon 1, 2, av. A. Einstein, 69626 Villeurbanne, France
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
19
|
Boaz NC, Bell SR, Groves JT. Ferryl protonation in oxoiron(IV) porphyrins and its role in oxygen transfer. J Am Chem Soc 2015; 137:2875-85. [PMID: 25651467 PMCID: PMC4363944 DOI: 10.1021/ja508759t] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ferryl porphyrins, P-Fe(IV)═O, are central reactive intermediates in the catalytic cycles of numerous heme proteins and a variety of model systems. There has been considerable interest in elucidating factors, such as terminal oxo basicity, that may control ferryl reactivity. Here, the sulfonated, water-soluble ferryl porphyrin complexes tetramesitylporphyrin, oxoFe(IV)TMPS (FeTMPS-II), its 2,6-dichlorophenyl analogue, oxoFe(IV)TDClPS (FeTDClPS-II), and two other analogues are shown to be protonated under turnover conditions to produce the corresponding bis-aqua-iron(III) porphyrin cation radicals. The results reveal a novel internal electromeric equilibrium, P-Fe(IV)═O ⇆ P(+)-Fe(III)(OH2)2. Reversible pKa values in the range of 4-6.3 have been measured for this process by pH-jump, UV-vis spectroscopy. Ferryl protonation has important ramifications for C-H bond cleavage reactions mediated by oxoiron(IV) porphyrin cation radicals in protic media. Both solvent O-H and substrate C-H deuterium kinetic isotope effects are observed for these reactions, indicating that hydrocarbon oxidation by these oxoiron(IV) porphyrin cation radicals occurs via a solvent proton-coupled hydrogen atom transfer from the substrate that has not been previously described. The effective FeO-H bond dissociation energies for FeTMPS-II and FeTDClPS-II were estimated from similar kinetic reactivities of the corresponding oxoFe(IV)TMPS(+) and oxoFe(IV)TDClPS(+) species to be ∼92-94 kcal/mol. Similar values were calculated from the two-proton P(+)-Fe(III)(OH2)2 pKa(obs) and the porphyrin oxidation potentials, despite a 230 mV range for the iron porphyrins examined. Thus, the iron porphyrin with the lower ring oxidation potential has a compensating higher basicity of the ferryl oxygen. The solvent-derived proton adds significantly to the driving force for C-H bond scission.
Collapse
Affiliation(s)
- Nicholas C. Boaz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Seth R. Bell
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - John T. Groves
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
20
|
Hollingsworth SA, Poulos TL. Molecular dynamics of the P450cam-Pdx complex reveals complex stability and novel interface contacts. Protein Sci 2014; 24:49-57. [PMID: 25307478 DOI: 10.1002/pro.2583] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/02/2014] [Accepted: 10/05/2014] [Indexed: 11/07/2022]
Abstract
Cytochrome P450cam catalyzes the stereo and regiospecific hydroxylation of camphor to 5-exo-hydroxylcamphor. The two electrons for the oxidation of camphor are provided by putidaredoxin (Pdx), a Fe2 S2 containing protein. Two recent crystal structures of the P450cam-Pdx complex, one solved with the aid of covalent cross-linking and one without, have provided a structural picture of the redox partner interaction. To study the stability of the complex structure and the minor differences between the recent crystal structures, a 100 nanosecond molecular dynamics (MD) simulation of the cross-linked structure, mutated in silico to wild type and the linker molecule removed, was performed. The complex was stable over the course of the simulation though conformational changes including the movement of the C helix of P450cam further toward Pdx allowed for the formation of a number of new contacts at the complex interface that remained stable throughout the simulation. While several minor crystal contacts were lost in the simulation, all major contacts that had been experimentally studied previously were maintained. The equilibrated MD structure contained a mixture of contacts resembling both the cross-linked and noncovalent structures and the newly identified interactions. Finally, the reformation of the P450cam Asp251-Arg186 ion pair in the MD simulation mirrors the ion pair observed in the more promiscuous CYP101D1 and suggests that the Asp251-Arg186 ion pair may be important.
Collapse
Affiliation(s)
- Scott A Hollingsworth
- Departments of Chemistry, Pharmaceutical Sciences, and Molecular Biology and Biochemistry, University of California, Irvine, California, 92697
| | | |
Collapse
|