1
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Gable JA, Poulos TL, Follmer AH. Redox partner recognition and selectivity of cytochrome P450lin (CYP111A1). J Inorg Biochem 2023; 244:112212. [PMID: 37058990 PMCID: PMC10519177 DOI: 10.1016/j.jinorgbio.2023.112212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 04/16/2023]
Abstract
The strict requirement of cytochrome P450cam for its native ferredoxin redox partner, putidaredoxin (Pdx), is not exhibited by any other known cytochrome P450 (CYP) system and the molecular details of redox partner selectivity are still not completely understood. We therefore examined the selectivity of a related Pseudomonas cytochrome P450, P450lin, by testing its activity with non-native redox partners. We found that P450lin could utilize Arx, the native redox partner of CYP101D1, to enable turnover of its substrate, linalool, while Pdx showed limited activity. Arx exhibited a higher sequence similarity to P450lins native redox partner, linredoxin (Ldx) than Pdx, including several residues that are believed to be at the interface of the two proteins, based on the P450cam-Pdx complex structure. We therefore mutated Pdx to resemble Ldx and Arx and found that a double mutant, D38L/∆106, displayed higher activity than Arx. In addition, Pdx D38L/∆106 does not induce a low-spin shift in linalool bound P450lin but does destabilize the P450lin-oxycomplex. Together our results suggest that P450lin and its redox partners may form a similar interface to P450cam-Pdx, but the interactions that allow for productive turnover are different.
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Affiliation(s)
- Jessica A Gable
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Thomas L Poulos
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Alec H Follmer
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.
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2
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Gable J, Tripathi S, Poulos TL. Structural Insights on the Conversion of Cytochrome P450 to P420. ACS OMEGA 2022; 7:18481-18485. [PMID: 35694512 PMCID: PMC9178766 DOI: 10.1021/acsomega.2c00960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
A characteristic feature of cytochromes P450* is that the complex formed between the ferrous heme iron and carbon monoxide generates an intense absorption band at 450 nm. This unique feature of P450s is due to the proximal thiolate Cys ligand coordinated to the heme iron. Various harsh treatments shift this band to 420 nm, thereby giving P420 which is most often associated with an inactive form of the enzyme. Various explanations have been put forward to explain the P450-to-P420 change ranging from protonation of the Cys heme ligand, displacement of the Cys ligand, or replacement of the Cys ligand with His. There are two crystal structures of the well-studied cytochrome P450cam that have a high fraction of P420. In one, P450cam is cross-linked to its redox partner, putidaredoxin (Pdx), and the second is P450cam crystallized in the absence of substrate. In both of these structures, a significant part of the substrate pocket is disordered and the poor quality of the electron density for the substrate indicates substantial disorder. However, in both structures there is no detectable change in the Cys-iron ligation or surrounding structure. These results indicate that the P450-to-P420 switch is due primarily to an opening and disordering around the substrate binding pocket and not ligand displacement or ligand swapping. Since it remains a possibility that ligand swapping could be responsible for P420 in some cases, we mutated to Gln the 3 His residues (352, 355, and 361) close enough to the proximal side of the heme that could possibly serve as heme ligands. The triple variant forms P420 which indicates that swapping Cys for His is not a requirement for the P450-to-P420 switch.
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Affiliation(s)
- Jessica
A. Gable
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Sarvind Tripathi
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, United States
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3
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Abstract
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Enzyme function requires that enzyme structures be dynamic. Substrate
binding, product release, and transition state stabilization typically
involve different enzyme conformers. Furthermore, in multistep enzyme-catalyzed
reactions, more than one enzyme conformation may be important for
stabilizing different transition states. While X-ray crystallography
provides the most detailed structural information of any current methodology,
X-ray crystal structures of enzymes capture only those conformations
that fit into the crystal lattice, which may or may not be relevant
to function. Solution nuclear magnetic resonance (NMR) methods can
provide an alternative approach to characterizing enzymes under nonperturbing
and controllable conditions, allowing one to identify and localize
dynamic processes that are important to function. However, many enzymes
are too large for standard approaches to making sequential resonance
assignments, a critical first step in analyzing and interpreting the
wealth of information inherent in NMR spectra. This Account
describes our long-standing NMR-based research into
structural and dynamic aspects of function in the cytochrome P450
monooxygenase superfamily. These heme-containing enzymes typically
catalyze the oxidation of unactivated C–H and C=C bonds
in a multitude of substrates, often with complete regio- and stereospecificity.
Over 600 000 genes in GenBank have been assigned to P450s,
yet all known P450 structures exhibit a highly conserved and unique
fold. This combination of functional and structural conservation with
a vast substrate clientele, each substrate having multiple possible
sites for oxidation, makes the P450s a unique target for understanding
the role of enzyme structure and dynamics in determining a particular
substrate–product combination. P450s are large by solution
NMR standards, requiring us to develop specialized approaches for
making sequential resonance assignments and interpreting the spectral
changes that occur as a function of changing conditions (e.g., oxidation
and spin state changes, ligand, substrate or effector binding). Solution
conformations are characterized by the fitting of residual dipolar
couplings (RDCs) measured for sequence-specifically assigned amide
N–H correlations to alignment tensors optimized in the course
of restrained molecular dynamics (MD) simulations. The conformational
ensembles obtained by such RDC-restrained simulations, which we call
“soft annealing”, are then tested by site-directed mutation
and spectroscopic and activity assays for relevance. These efforts
have gained us insights into cryptic conformational changes associated
with substrate and redox partner binding that were not suspected from
crystal structures, but were shown by subsequent work to be relevant
to function. Furthermore, it appears that many of these changes can
be generalized to P450s besides those that we have characterized,
providing guidance for enzyme engineering efforts. While past research
was primarily directed at the more tractable prokaryotic P450s, our
current efforts are aimed at medically relevant human enzymes, including
CYP17A1, CYP2D6, and CYP3A4.
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4
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Erdogan H. One small step for cytochrome P450 in its catalytic cycle, one giant leap for enzymology. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The intermediates operating in the cytochrome P450 catalytic cycle have been investigated for more than half a century, fascinating many enzymologists. Each intermediate has its unique role to carry out diverse oxidations. Natural time course of the catalytic cycle is quite fast, hence, not all of the reactive intermediates could be isolated during physiological catalysis. Different high-valent iron intermediates have been proposed as primary oxidants: the candidates are compound 0 (Cpd 0, [FeOOH][Formula: see text]P450) and compound I (Cpd I, Fe(IV)[Formula: see text]O por[Formula: see text]P450). Among them, the role of Cpd I in hydroxylation is fairly well understood due the discovery of the peroxide shunt. This review endeavors to put the outstanding research efforts conducted to isolate and characterize the intermediates together. In addition to spectral features of each intermediate in the catalytic cycle, the oxidizing powers of Cpd 0 and Cpd I will be discussed along with most recent scientific findings.
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Affiliation(s)
- Huriye Erdogan
- Department of Chemistry, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
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5
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Follmer AH, Tripathi S, Poulos TL. Ligand and Redox Partner Binding Generates a New Conformational State in Cytochrome P450cam (CYP101A1). J Am Chem Soc 2019; 141:2678-2683. [PMID: 30672701 DOI: 10.1021/jacs.8b13079] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
It has become increasingly clear that cytochromes P450 can cycle back and forth between two extreme conformational states termed the closed and open states. In the well-studied cytochrome P450cam, the binding of its redox partner, putidaredoxin (Pdx), shifts P450cam toward the open state. Shifting to the open state is thought to be important in the formation of a proton relay network essential for O-O bond cleavage and formation of the active Fe(IV)═O intermediate. Another important intermediate is the oxy-P450cam complex when bound to Pdx. Trapping this intermediate in crystallo is challenging owing to its instability, but the CN- complex is both stable and an excellent mimic of the O2 complex. Here we present the P450cam-Pdx structure complexed with CN-. CN- results in large conformational changes including cis/trans isomerization of proline residues. Changes include large rearrangements of active-site residues and the formation of new active-site access channel that we have termed channel 2. The formation of channel 2 has also been observed in our previous molecular dynamics simulations wherein substrate binding to an allosteric site remote from the active site opens up channel 2. This new structure supports an extensive amount of previous work showing that distant regions of the structure are dynamically coupled and underscores the potentially important role that large conformational changes and dynamics play in P450 catalysis.
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Affiliation(s)
- Alec H Follmer
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California , Irvine , California 92697-3900 , United States
| | - Sarvind Tripathi
- Department of Chemistry & Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California , Irvine , California 92697-3900 , United States
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6
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Ramos S, Basom EJ, Thielges MC. Conformational Change Induced by Putidaredoxin Binding to Ferrous CO-ligated Cytochrome P450cam Characterized by 2D IR Spectroscopy. Front Mol Biosci 2018; 5:94. [PMID: 30483514 PMCID: PMC6243089 DOI: 10.3389/fmolb.2018.00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 11/16/2022] Open
Abstract
The importance of conformational dynamics to protein function is now well-appreciated. An outstanding question is whether they are involved in the effector role played by putidaredoxin (Pdx) in its reduction of the O2 complex of cytochrome P450cam (P450cam), an archetypical member of the cytochrome P450 superfamily. Recent studies have reported that binding of Pdx induces a conformational change from a closed to an open state of ferric P450cam, but a similar conformational change does not appear to occur for the ferrous, CO-ligated enzyme. To better understand the effector role of Pdx when binding the ferrous, CO-ligated P450cam, we applied 2D IR spectroscopy to compare the conformations and dynamics of the wild-type (wt) enzyme in the absence and presence of Pdx, as well as of L358P P450cam (L358P), which has served as a putative model for the Pdx complex. The CO vibrations of the Pdx complex and L358P report population of two conformational states in which the CO experiences distinct environments. The dynamics among the CO frequencies indicate that the energy landscape of substates within one conformation are reflective of the closed state of P450cam, and for the other conformation, differ from the free wt enzyme, but are equivalent between the Pdx complex and L358P. The two states co-populated by the Pdx complex are postulated to reflect a loosely bound encounter complex and a more tightly bound state, as is commonly observed for the dynamic complexes of redox partners. Significantly, this study shows that the binding of Pdx to ferrous, CO-ligated P450cam does perturb the conformational ensemble in a way that might underlie the effector role of Pdx.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Edward J Basom
- Department of Chemistry, Indiana University, Bloomington, IN, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, IN, United States
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7
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Ducharme J, Auclair K. Use of bioconjugation with cytochrome P450 enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28625736 DOI: 10.1016/j.bbapap.2017.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioconjugation, defined as chemical modification of biomolecules, is widely employed in biological and biophysical studies. It can expand functional diversity and enable applications ranging from biocatalysis, biosensing and even therapy. This review summarizes how chemical modifications of cytochrome P450 enzymes (P450s or CYPs) have contributed to improving our understanding of these enzymes. Genetic modifications of P450s have also proven very useful but are not covered in this review. Bioconjugation has served to gain structural information and investigate the mechanism of P450s via photoaffinity labeling, mechanism-based inhibition (MBI) and fluorescence studies. P450 surface acetylation and protein cross-linking have contributed to the investigation of protein complexes formation involving P450 and its redox partner or other P450 enzymes. Finally, covalent immobilization on polymer surfaces or electrodes has benefited the areas of biocatalysis and biosensor design. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Julie Ducharme
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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8
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Stok JE, Slessor KE, Farlow AJ, Hawkes DB, De Voss JJ. Cytochrome P450cin (CYP176A1). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:319-39. [PMID: 26002741 DOI: 10.1007/978-3-319-16009-2_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Cytochrome P450cin (P450cin) (CYP176A1) is a bacterial P450 enzyme that catalyses the enantiospecific hydroxylation of 1,8-cineole to (1R)-6β-hydroxycineole when reconstituted with its natural reduction-oxidation (redox) partner cindoxin, E. coli flavodoxin reductase, and NADPH as a source of electrons. This catalytic system has become a useful tool in the study of P450s as not only can large quantities of P450cin be prepared and rates of oxidation up to 1,500 min(-1) achieved, but it also displays a number of unusual characteristics. These include an asparagine residue in P450cin that has been found in place of the usual conserved threonine residue observed in most P450s. In general, this conserved threonine controls oxygen activation to create the potent ferryl (Fe(IV=O) porphyrin cation radical required for substrate oxidation. Another atypical characteristic of P450cin is that it utilises an FMN-containing redoxin (cindoxin) rather than a ferridoxin as is usually observed with other bacterial P450s (e.g. P450cam). This chapter will review what is currently known about P450cin and how this enzyme has provided a greater understanding of P450s in general.
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Affiliation(s)
- Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Brisbane, 4072, Australia
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9
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Hlavica P. Mechanistic basis of electron transfer to cytochromes p450 by natural redox partners and artificial donor constructs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 851:247-97. [PMID: 26002739 DOI: 10.1007/978-3-319-16009-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochromes P450 (P450s) are hemoproteins catalyzing oxidative biotransformation of a vast array of natural and xenobiotic compounds. Reducing equivalents required for dioxygen cleavage and substrate hydroxylation originate from different redox partners including diflavin reductases, flavodoxins, ferredoxins and phthalate dioxygenase reductase (PDR)-type proteins. Accordingly, circumstantial analysis of structural and physicochemical features governing donor-acceptor recognition and electron transfer poses an intriguing challenge. Thus, conformational flexibility reflected by togging between closed and open states of solvent exposed patches on the redox components was shown to be instrumental to steered electron transmission. Here, the membrane-interactive tails of the P450 enzymes and donor proteins were recognized to be crucial to proper orientation toward each other of surface sites on the redox modules steering functional coupling. Also, mobile electron shuttling may come into play. While charge-pairing mechanisms are of primary importance in attraction and complexation of the redox partners, hydrophobic and van der Waals cohesion forces play a minor role in docking events. Due to catalytic plasticity of P450 enzymes, there is considerable promise in biotechnological applications. Here, deeper insight into the mechanistic basis of the redox machinery will permit optimization of redox processes via directed evolution and DNA shuffling. Thus, creation of hybrid systems by fusion of the modified heme domain of P450s with proteinaceous electron carriers helps obviate the tedious reconstitution procedure and induces novel activities. Also, P450-based amperometric biosensors may open new vistas in pharmaceutical and clinical implementation and environmental monitoring.
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Affiliation(s)
- Peter Hlavica
- Walther-Straub-Institut für Pharmakologie und Toxikologie der LMU, Goethestrasse 33, 80336, München, Germany,
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10
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Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology & Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California Irvine, Irvine, California 92697-3900
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11
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Yasutake Y, Nishioka T, Imoto N, Tamura T. A Single Mutation at the Ferredoxin Binding Site of P450 Vdh Enables Efficient Biocatalytic Production of 25-Hydroxyvitamin D3. Chembiochem 2013; 14:2284-91. [DOI: 10.1002/cbic.201300386] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Indexed: 01/08/2023]
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12
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Myers WK, Lee YT, Britt RD, Goodin DB. The conformation of P450cam in complex with putidaredoxin is dependent on oxidation state. J Am Chem Soc 2013; 135:11732-5. [PMID: 23901883 DOI: 10.1021/ja405751z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Double electron-electron resonance (DEER) spectroscopy was used to determine the conformational state in solution for the heme monooxygenase P450cam when bound to its natural redox partner, putidaredoxin (Pdx). When oxidized Pdx was titrated into substrate-bound ferric P450cam, the enzyme shifted from the closed to the open conformation. In sharp contrast, however, the enzyme remained in the closed conformation when ferrous-CO P450cam was titrated with reduced Pdx. This result fully supports the proposal that binding of oxidized Pdx to P450cam opposes the open-to-closed transition induced by substrate binding. However, the data strongly suggest that in solution, binding of reduced Pdx to P450cam does not favor the open conformation. This supports a model in which substrate recognition is associated with the open-to-closed transition and electron transfer from Pdx occurs in the closed conformation. The opening of the enzyme in the ferric-hydroperoxo state following electron transfer from Pdx would provide for efficient O2 bond activation, substrate oxidation, and product release.
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Affiliation(s)
- William K Myers
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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13
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Tripathi S, Li H, Poulos TL. Structural basis for effector control and redox partner recognition in cytochrome P450. Science 2013; 340:1227-30. [PMID: 23744947 DOI: 10.1126/science.1235797] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cytochromes P450 catalyze a variety of monooxygenase reactions that require electron transfer from redox partners. Although the structure of many P450s and a small handful of redox partners are known, there is very little structural information available on redox complexes, thus leaving a gap in our understanding on the control of P450-redox partner interactions. We have solved the crystal structure of oxidized and reduced P450cam complexed with its redox partner, putidaredoxin (Pdx), to 2.2 and 2.09 angstroms, respectively. It was anticipated that Pdx would favor closed substrate-bound P450cam, which differs substantially from the open conformer, but instead we found that Pdx favors the open state. These new structures indicate that the effector role of Pdx is to shift P450cam toward the open conformation, which enables the establishment of a water-mediated H-bonded network, which is required for proton-coupled electron transfer.
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Affiliation(s)
- Sarvind Tripathi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
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14
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Banerjee S. Induction of protein conformational change inside the charged electrospray droplet. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:193-204. [PMID: 23378092 DOI: 10.1002/jms.3148] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 11/25/2012] [Accepted: 11/26/2012] [Indexed: 06/01/2023]
Abstract
The behavior of the analyte molecules inside the neutral core of the charged electrospray (ES) droplet is not unambiguously known to date. The possibility of protein conformational change inside the charged ES droplet has been investigated. The ES droplets encapsulating the protein molecules were exposed to the acetic acid vapor in the ionization chamber to absorb the acetic acid vapor. Because of the faster evaporation of water than that of acetic acid, the droplets became enriched with acetic acid and thus altered the solvent environment (e.g. pH and polarity) of the final charged droplets from where the naked charged analytes (proteins) are formed. Thus, the perturbation of the ES droplet solvent environment resulted in the protein conformational change (unfolding) during the short lifespan of the ES droplet and that is reflected by the multimodal charge state distribution in the corresponding mass spectra. Further, the extent of this conformational change inside the ES droplet was found to be related to the structural flexibility of the protein. Although the protein conformational change inside the ES droplet has been driven by using acetic acid vapor in the present study, the results would help in the near future to understand the spontaneity of the conformational change of the analyte on the millisecond timescale of phase transition in the natural way of ES process.
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Affiliation(s)
- Shibdas Banerjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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15
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Poulos TL, Madrona Y. Oxygen activation and redox partner binding in cytochromes P450. Biotechnol Appl Biochem 2013; 60:128-33. [DOI: 10.1002/bab.1056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/25/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences; University of California; Irvine, Irvine; CA; USA
| | - Yarrow Madrona
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences; University of California; Irvine, Irvine; CA; USA
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16
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Bell SG, Yang W, Yorke JA, Zhou W, Wang H, Harmer J, Copley R, Zhang A, Zhou R, Bartlam M, Rao Z, Wong LL. Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:277-91. [PMID: 22349230 DOI: 10.1107/s090744491200145x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/12/2012] [Indexed: 11/11/2022]
Abstract
CYP108D1 from Novosphingobium aromaticivorans DSM12444 binds a range of aromatic hydrocarbons such as phenanthrene, biphenyl and phenylcyclohexane. Its structure, which is reported here at 2.2 Å resolution, is closely related to that of CYP108A1 (P450terp), an α-terpineol-oxidizing enzyme. The compositions and structures of the active sites of these two enzymes are very similar; the most significant changes are the replacement of Glu77 and Thr103 in CYP108A1 by Thr79 and Val105 in CYP108D1. Other residue differences lead to a larger and more hydrophobic access channel in CYP108D1. These structural features are likely to account for the weaker α-terpineol binding by CYP108D1 and, when combined with the presence of three hydrophobic phenylalanine residues in the active site, promote the binding of aromatic hydrocarbons. The haem-proximal surface of CYP108D1 shows a different charge distribution and topology to those of CYP101D1, CYP101A1 and CYP108A1, including a pronounced kink in the proximal loop of CYP108D1, which may result in poor complementarity with the [2Fe-2S] ferredoxins Arx, putidaredoxin and terpredoxin that are the respective redox partners of these three P450 enzymes. The unexpectedly low reduction potential of phenylcyclohexane-bound CYP108D1 (-401 mV) may also contribute to the low activity observed with these ferredoxins. CYP108D1 appears to function as an aromatic hydrocarbon hydroxylase that requires a different electron-transfer cofactor protein.
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Affiliation(s)
- Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford,South Parks Road, Oxford OX1 3QR, England.
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17
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Karunakaran V, Denisov I, Sligar SG, Champion PM. Investigation of the low frequency dynamics of heme proteins: native and mutant cytochrome P450(cam) and redox partner complexes. J Phys Chem B 2011; 115:5665-77. [PMID: 21391540 DOI: 10.1021/jp112298y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Vibrational coherence spectroscopy (VCS) is used to investigate the low-frequency dynamics of camphor-free and camphor-bound cytochrome P450(cam) (CYP 101) and its L358P mutant. The low-frequency heme vibrations are found to be perturbed upon binding to the electron transfer partner putidaredoxin (Pdx). A strong correlation between the "detuned" vibrational coherence spectrum, which monitors frequencies between 100 and 400 cm(-1), and the lower frequency part of the Raman spectrum is also demonstrated. The very low frequency region ≤200 cm(-1), uniquely accessed by open-band VCS measurements, reveals a mode near 103 cm(-1) in P450(cam) when camphor is not present in the distal pocket. This reflects the presence of a specific heme distortion, such as saddling or ruffling, in the substrate-free state where water is coordinated to the low-spin iron atom. Such distortions are likely to retard the rate of electron transfer to the substrate-free protein. The presence of strong mode near ∼33 cm(-1) in the camphor-bound form suggests a significant heme-doming distortion, which is supported by analysis using normal coordinate structural decomposition. Pdx also displays a strong coherent vibration near 30 cm(-1) that in principle could be involved in vibrational resonance with its electron transfer target. A splitting of the 33 cm(-1) feature and intensification of a mode near 78 cm(-1) appear when the P450(cam)/Pdx complex is formed. These observations are consistent with vibrational mixing and heme geometric distortions upon Pdx binding that are coincident with the increased thiolate electron donation to the heme. The appearance of a mode near 65 cm(-1) in the coherence spectra of the L358P mutant is comparable to the mode at 78 cm(-1) seen in the P450(cam)/Pdx complex and is consistent with the view that the heme and its environment in the L358P mutant are similar to the Pdx-bound native protein. Resonance Raman spectra are presented for both P450(cam) and the L358P mutant and the changes are correlated with an increased amount of thiolate electron donation to the heme in the mutant sample.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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18
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Lee YT, Glazer EC, Wilson RF, Stout CD, Goodin DB. Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel. Biochemistry 2011; 50:693-703. [PMID: 21171581 DOI: 10.1021/bi101726d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational changes in the substrate access channel have been observed for several forms of cytochrome P450, but the extent of conformational plasticity exhibited by a given isozyme has not been completely characterized. Here we present crystal structures of P450cam bound to a library of 12 active site probes containing a substrate analogue tethered to a variable linker. The structures provide a unique view of the range of protein conformations accessible during substrate binding. Principal component analysis of a total of 30 structures reveals three discrete clusters of conformations: closed (P450cam-C), intermediate (P450cam-I), and fully open (P450cam-O). Relative to P450cam-C, the P450cam-I state results predominantly from a retraction of helix F, while both helices F and G move in concert to reach the fully open P450cam-O state. Both P450cam-C and P450cam-I are well-defined states, while P450cam-O shows evidence of a somewhat broader distribution of conformations and includes the open form recently seen in the absence of substrate. The observed clustering of protein conformations over a wide range of ligand variants suggests a multistep closure of the enzyme around the substrate that begins by conformational selection from an ensemble of open conformations and proceeds through a well-defined intermediate, P450cam-I, before full closure to the P450cam-C state in the presence of small substrates. This multistep pathway may have significant implications for a full understanding of substrate specificity, kinetics, and coupling of substrate binding to P450 function.
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Affiliation(s)
- Young-Tae Lee
- Department of Molecular Biology, 10550 North Torrey Pines Road, The Scripps Research Institute, La Jolla, California 92037, United States
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19
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Covalent linkage of CYP101 with the electrode enhances the electrocatalytic activity of the enzyme: Vectorial electron transport from the electrode. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.03.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Pochapsky TC, Kazanis S, Dang M. Conformational plasticity and structure/function relationships in cytochromes P450. Antioxid Redox Signal 2010; 13:1273-96. [PMID: 20446763 PMCID: PMC2959183 DOI: 10.1089/ars.2010.3109] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The cytochrome P450s are a superfamily of enzymes that are found in all kingdoms of living organisms, and typically catalyze the oxidative addition of atomic oxygen to an unactivated C-C or C-H bond. Over 8000 nonredundant sequences of putative and confirmed P450 enzymes have been identified, but three-dimensional structures have been determined for only a small fraction of these. While all P450 enzymes for which structures have been determined share a common global fold, the flexibility and modularity of structure around the active site account for the ability of P450 enzymes to accommodate a vast number of structurally dissimilar substrates and support a wide range of selective oxidations. In this review, known P450 structures are compared, and some structural criteria for prediction of substrate selectivity and reaction type are suggested. The importance of dynamic processes such as redox-dependent and effector-induced conformational changes in determining catalytic competence and regio- and stereoselectivity is discussed, and noncrystallographic methods for characterizing P450 structures and dynamics, in particular, mass spectrometry and nuclear magnetic resonance spectroscopy are reviewed.
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Affiliation(s)
- Thomas C Pochapsky
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
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21
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Structural biology of redox partner interactions in P450cam monooxygenase: a fresh look at an old system. Arch Biochem Biophys 2010; 507:66-74. [PMID: 20816746 DOI: 10.1016/j.abb.2010.08.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 08/28/2010] [Accepted: 08/31/2010] [Indexed: 11/21/2022]
Abstract
The P450cam monooxygenase system consists of three separate proteins: the FAD-containing, NADH-dependent oxidoreductase (putidaredoxin reductase or Pdr), cytochrome P450cam and the 2Fe2S ferredoxin (putidaredoxin or Pdx), which transfers electrons from Pdr to P450cam. Over the past few years our lab has focused on the interaction between these redox components. It has been known for some time that Pdx can serve as an effector in addition to its electron shuttle role. The binding of Pdx to P450cam is thought to induce structural changes in the P450cam active site that couple electron transfer to substrate hydroxylation. The nature of these structural changes has remained unclear until a particular mutant of P450cam (Leu358Pro) was found to exhibit spectral perturbations similar to those observed in wild type P450cam bound to Pdx. The crystal structure of the L358P variant has provided some important insights on what might be happening when Pdx docks. In addition to these studies, many Pdx mutants have been analyzed to identify regions important for electron transfer. Somewhat surprisingly, we found that Pdx residues predicted to be at the P450cam-Pdx interface play different roles in the reduction of ferric P450cam and the ferrous P450-O(2) complex. More recently we have succeeded in obtaining the structure of a chemically cross-linked Pdr-Pdx complex. This fusion protein represents a valid model for the noncovalent Pdr-Pdx complex as it retains the redox activities of native Pdr and Pdx and supports monooxygenase reactions catalyzed by P450cam. The insights gained from these studies will be summarized in this review.
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22
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Cryle MJ, Bell SG, Schlichting I. Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase. Biochemistry 2010; 49:7282-96. [PMID: 20690619 DOI: 10.1021/bi100910y] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cytochrome P450 CypX (CYP134A1), isolated from Bacillus subtilis, has previously been implicated in the three-step oxidative transformation of the diketopiperazine cyclo-l-leucyl-l-leucyl into pulcherriminic acid, a precursor of the extracellular iron chelate pulcherrimin. In this study, we present the first experimental data relating to CYP134A1, where we show that CYP134A1 binds cyclo-l-leucyl-l-leucyl with an affinity of 24.5 +/- 0.5 muM. Structurally related diketopiperazines sharing similar alkyl side chains to cyclo-l-leucyl-l-leucyl also bind to CYP134A1 with comparable affinity. CYP134A1 is capable of catalyzing the in vitro oxidation of diketopiperazine substrates when supported with several alternate electron transfer partner systems. Products containing one additional oxygen atom and which are intermediate products of the expected pulcherriminic acid were identified by GCMS. The oxidation of related diketopiperazines reveals that different oxidative pathways exist for CYP134A1-catalyzed diketopiperazine oxidation. The crystal structure of CYP134A1 has been determined to 2.7 A resolution in the absence of substrate and in the presence of bound phenylimidazole ligands to 3.1 and 3.2 A resolution. The active site is dominated by hydrophobic residues and contains an unusual proline residue in place of the normally conserved alcohol residue that typically plays an important role in oxygen activation. The B-B(2) substrate recognition loop, which forms part of the active site, shows considerable flexibility and was found in both open and closed conformations in different structures. These results represent the first insights into the structural and biochemical basis underlying the multistep oxidation catalyzed by CYP134A1.
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Affiliation(s)
- Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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23
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Guallar V, Wallrapp FH. QM/MM methods: looking inside heme proteins biochemistry. Biophys Chem 2010; 149:1-11. [PMID: 20400222 DOI: 10.1016/j.bpc.2010.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 11/29/2022]
Abstract
Mixed quantum mechanics/molecular mechanics methods offer a valuable computational tool for understanding biochemical events. When combined with conformational sampling techniques, they allow for an exhaustive exploration of the enzymatic mechanism. Heme proteins are ubiquitous and essential for every organism. In this review we summarize our efforts towards the understanding of heme biochemistry. We present: 1) results on ligand migration on globins coupled to the ligand binding event, 2) results on the localization of the spin density in compound I of cytochromes and peroxidases, 3) novel methodologies for mapping the electron transfer pathways and 4) novel data on Tryptophan 2,3-dioxygenase. For this enzyme our results strongly indicate that the distal oxygen will end up on the C3 indole carbon, whereas the proximal oxygen will end up in the C2 position. Interestingly, the process involves the formation of an epoxide and a heme ferryl intermediate. The overall energy profile indicates an energy barrier of approximately 18 kcal/mol and an exothermic driving force of almost 80 kcal/mol.
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Affiliation(s)
- Victor Guallar
- Life Science Department, Barcelona Supercomputing Center, Jordi Girona, 29, 08034 Barcelona, Spain.
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24
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Protein recognition in ferredoxin–P450 electron transfer in the class I CYP199A2 system from Rhodopseudomonas palustris. J Biol Inorg Chem 2009; 15:315-28. [DOI: 10.1007/s00775-009-0604-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
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25
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Pochapsky SS, Dang M, OuYang B, Simorellis AK, Pochapsky TC. Redox-dependent dynamics in cytochrome P450cam. Biochemistry 2009; 48:4254-61. [PMID: 19366254 DOI: 10.1021/bi900002k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Local protein backbone dynamics of the camphor hydroxylase cytochrome P450(cam) (CYP101) depend upon the oxidation and ligation state of the heme iron. (1)H-(15)N correlation nuclear magnetic resonance experiments were used to compare backbone dynamics of oxidized and reduced forms of this 414-residue metalloenzyme via hydrogen-deuterium exchange kinetics (H-D exchange) and (15)N relaxation measurements, and these results are compared with previously published results obtained by H-D exchange mass spectrometry. In general, the reduced enzyme exhibits lower-amplitude motions of secondary structural features than the oxidized enzyme on all of the time scales accessible to these experiments, and these differences are more pronounced in regions of the enzyme involved in substrate access to the active site (B' helix and beta3 and beta5 sheets) and binding of putidaredoxin (C and L helices), the iron-sulfur protein that acts as the effector and reductant of CYP101 in vivo. These results are interpreted in terms of local structural effects of changes in the heme oxidation state, and the relevance of the observed effects to the enzyme mechanism is discussed.
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Affiliation(s)
- Susan Sondej Pochapsky
- Department of Chemistry, Brandeis University, 415 South Street, MS 015, Waltham, Massachusetts 02454-9110, USA
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26
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Asciutto EK, Madura JD, Pochapsky SS, OuYang B, Pochapsky TC. Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam. J Mol Biol 2009; 388:801-14. [PMID: 19327368 DOI: 10.1016/j.jmb.2009.03.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/06/2009] [Accepted: 03/13/2009] [Indexed: 11/18/2022]
Abstract
Experimental evidence has been provided for a functionally relevant cis-trans isomerization of the Ile88-Pro89 peptide bond in cytochrome P450(cam) (CYP101). The isomerization is proposed to be a key element of the structural reorganization leading to the catalytically competent form of CYP101 upon binding of the effector protein putidaredoxin (Pdx). A detailed comparison of the results of molecular dynamics simulations on the cis and trans conformations of substrate- and carbonmonoxy-bound ferrous CYP101 with sequence-specific Pdx-induced structural perturbations identified by nuclear magnetic resonance is presented, providing insight into the structural and dynamic consequences of the isomerization. The mechanical coupling between the Pdx binding site on the proximal face of CYP101 and the site of isomerization is described.
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Affiliation(s)
- Eliana K Asciutto
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282-1530, USA
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27
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Virus C, Bernhardt R. Molecular evolution of a steroid hydroxylating cytochrome P450 using a versatile steroid detection system for screening. Lipids 2008; 43:1133-41. [PMID: 18830657 DOI: 10.1007/s11745-008-3236-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 08/30/2008] [Indexed: 11/26/2022]
Abstract
Molecular evolution is a powerful tool for improving or changing activities of enzymes for their use in biotechnological processes. Cytochromes P450 are highly interesting enzymes for biotechnological purposes because they are able to hydroxylate a broad variety of substrates with high regio- and stereoselectivity. One promising steroid hydroxylating cytochrome P450 for biotechnological applications is CYP106A2 from Bacillus megaterium ATCC 13368. It is one of a few known bacterial cytochromes P450 able to transform steroids such as progesterone and 11-deoxycortisol. CYP106A2 can be easily expressed in Escherichia coli with a high yield and can be reconstituted using the adrenal redox proteins, adrenodoxin and adrenodoxin reductase. We developed a simple screening assay for this system and performed random mutagenesis of CYP106A2, yielding variants with improved 11-deoxycortisol and progesterone hydroxylation activity. After two generations of directed evolution, we were able to improve the k (cat)/K (m) of the 11-deoxycortisol hydroxylation by a factor of more than four. At the same time progesterone conversion was improved about 1.4-fold. Mapping the mutations identified in catalytically improved CYP106A2 variants into the structure of a CYP106A2 model suggests that these mutations influence the mobility of the F/G loop, and the interaction with the redox partner adrenodoxin. The results show the evolution of a soluble steroid hydroxylase as a potential new catalyst for the production of steroidogenic compounds.
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Affiliation(s)
- Cornelia Virus
- Naturwissenschaftlich-Technische Fakultät III, Institut für Biochemie, Universität des Saarlandes, Postfach 151150, 66041, Saarbrücken, Germany.
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28
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Wallrapp F, Masone D, Guallar V. Electron Transfer in the P450cam/PDX Complex. The QM/MM e-Pathway. J Phys Chem A 2008; 112:12989-94. [DOI: 10.1021/jp803538u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank Wallrapp
- ICREA Research Professor, Life Science Department, Barcelona Supercomputing Center, Jordi Girona, 29, 08034 Barcelona, Spain
| | - Diego Masone
- ICREA Research Professor, Life Science Department, Barcelona Supercomputing Center, Jordi Girona, 29, 08034 Barcelona, Spain
| | - Victor Guallar
- ICREA Research Professor, Life Science Department, Barcelona Supercomputing Center, Jordi Girona, 29, 08034 Barcelona, Spain
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29
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Zhang W, Pochapsky SS, Pochapsky TC, Jain NU. Solution NMR structure of putidaredoxin-cytochrome P450cam complex via a combined residual dipolar coupling-spin labeling approach suggests a role for Trp106 of putidaredoxin in complex formation. J Mol Biol 2008; 384:349-63. [PMID: 18835276 DOI: 10.1016/j.jmb.2008.09.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 09/01/2008] [Accepted: 09/03/2008] [Indexed: 11/30/2022]
Abstract
The 58-kDa complex formed between the [2Fe-2S] ferredoxin, putidaredoxin (Pdx), and cytochrome P450cam (CYP101) from the bacterium Pseudomonas putida has been investigated by high-resolution solution NMR spectroscopy. Pdx serves as both the physiological reductant and effector for CYP101 in the enzymatic reaction involving conversion of substrate camphor to 5-exo-hydroxycamphor. In order to obtain an experimental structure for the oxidized Pdx-CYP101 complex, a combined approach using orientational data on the two proteins derived from residual dipolar couplings and distance restraints from site-specific spin labeling of Pdx has been applied. Spectral changes for residues in and near the paramagnetic metal cluster region of Pdx in complex with CYP101 have also been mapped for the first time using (15)N and (13)C NMR spectroscopy, leading to direct identification of the residues strongly affected by CYP101 binding. The new NMR structure of the Pdx-CYP101 complex agrees well with results from previous mutagenesis and biophysical studies involving residues at the binding interface such as formation of a salt bridge between Asp38 of Pdx and Arg112 of CYP101, while at the same time identifying key features different from those of earlier modeling studies. Analysis of the binding interface of the complex reveals that the side chain of Trp106, the C-terminal residue of Pdx and critical for binding to CYP101, is located across from the heme-binding loop of CYP101 and forms non-polar contacts with several residues in the vicinity of the heme group on CYP101, pointing to a potentially important role in complex formation.
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Affiliation(s)
- Wei Zhang
- Biochemistry, Cellular and Molecular Biology Department, M407 Walters Life Sciences, University of Tennessee, Knoxville, TN 37996-0840, USA
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30
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Bell SG, Xu F, Forward I, Bartlam M, Rao Z, Wong LL. Crystal structure of CYP199A2, a para-substituted benzoic acid oxidizing cytochrome P450 from Rhodopseudomonas palustris. J Mol Biol 2008; 383:561-74. [PMID: 18762195 DOI: 10.1016/j.jmb.2008.08.033] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 08/13/2008] [Accepted: 08/14/2008] [Indexed: 11/17/2022]
Abstract
CYP199A2, a cytochrome P450 enzyme from Rhodopseudomonas palustris, oxidatively demethylates 4-methoxybenzoic acid to 4-hydroxybenzoic acid. 4-Ethylbenzoic acid is converted to a mixture of predominantly 4-(1-hydroxyethyl)-benzoic acid and 4-vinylbenzoic acid, the latter being a rare example of CC bond dehydrogenation of an unbranched alkyl group. The crystal structure of CYP199A2 has been determined at 2.0-A resolution. The enzyme has the common P450 fold, but the B' helix is missing and the G helix is broken into two (G and G') by a kink at Pro204. Helices G and G' are bent back from the extended BC loop and the I helix to open up a clearly defined substrate access channel. Channel openings in this region of the P450 fold are rare in bacterial P450 enzymes but more common in eukaryotic P450 enzymes. The channel is hydrophobic except for the basic residue Arg246 at the entrance, which probably plays a role in the specificity of this enzyme for charged benzoates over neutral phenols and benzenes. The substrate binding pocket is hydrophobic, with Ser97 and Ser247 being the only polar residues. Computer docking of 4-ethylbenzoic acid into the active site suggests that the substrate carboxylate oxygens interact with Ser97 and Ser247, and the beta-methyl group is located over the heme iron by Phe185, the side chain of which is only 6.35 A above the iron in the native structure. This binding orientation is consistent with the observed product profile of exclusive attack at the para substituent. Putidaredoxin of the CYP101A1 system from Pseudomonas putida supports substrate oxidation by CYP199A2 at approximately 6% of the activity of the physiological ferredoxin. Comparison of the heme proximal faces of CYP199A2 and CYP101A1 suggests that charge reversal surrounding the surface residue Leu369 in CYP199A2 may be a significant factor in this low cross-activity.
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Affiliation(s)
- Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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31
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Lisurek M, Simgen B, Antes I, Bernhardt R. Theoretical and Experimental Evaluation of a CYP106A2 Low Homology Model and Production of Mutants with Changed Activity and Selectivity of Hydroxylation. Chembiochem 2008; 9:1439-49. [DOI: 10.1002/cbic.200700670] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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Freindorf M, Shao Y, Kong J, Furlani TR. Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin. J Inorg Biochem 2007; 102:427-32. [PMID: 18180042 DOI: 10.1016/j.jinorgbio.2007.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 11/11/2007] [Accepted: 11/13/2007] [Indexed: 10/22/2022]
Abstract
Combined QM/MM calculations of the active-site of cytochrome P450cam have been performed before and after the binding of P450cam to putidaredoxin. The calculations were carried out for both a 5-coordinated and a 6-coordinated active-site of cytochrome P450cam, with either a water molecule or a carbon monoxide molecule as a 6th distal ligand. An experimentally observed increase in the Fe-S stretching frequency that occurs after cytochrome P450cam binds to putidaredoxin, has been reproduced in our study. Experimentally observed changes in the Fe-C and C-O vibration frequencies that occur after binding of both proteins, have also been reproduced in our study. The computed increase of the Fe-S and Fe-C stretching frequencies is correlated with a corresponding decrease of the Fe-S and Fe-C interatomic distances. According to our calculations, for the active-site with carbon monoxide in the triplet electronic state, the binding process increases the spin densities on the iron and sulfur atoms, which changes the Fe-C and C-O stretching frequencies in opposite directions, in agreement with experimental data.
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Affiliation(s)
- Marek Freindorf
- Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14260, United States.
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33
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Affiliation(s)
- Thomas L Poulos
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, USA
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34
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Karyakin A, Motiejunas D, Wade RC, Jung C. FTIR studies of the redox partner interaction in cytochrome P450: The Pdx–P450cam couple. Biochim Biophys Acta Gen Subj 2007; 1770:420-31. [PMID: 17014964 DOI: 10.1016/j.bbagen.2006.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Revised: 08/27/2006] [Accepted: 08/29/2006] [Indexed: 11/26/2022]
Abstract
Recently we have developed a new approach to study protein-protein interactions using Fourier transform infrared spectroscopy in combination with titration experiments and principal component analysis (FTIR-TPCA). In the present paper we review the FTIR-TPCA results obtained for the interaction between cytochrome P450 and the redox partner protein in two P450 systems, the Pseudomonas putida P450cam (CYP101) with putidaredoxin (P450cam-Pdx), and the Bacillus megaterium P450BM-3 (CYP102) heme domain with the FMN domain (P450BMP-FMND). Both P450 systems reveal similarities in the structural changes that occur upon redox partner complex formation. These involve an increase in beta-sheets and alpha-helix content, a decrease in the population of random coil/3(10)-helix structure, a redistribution of turn structures within the interacting proteins and changes in the protonation states or hydrogen-bonding of amino acid carboxylic side chains. We discuss in detail the P450cam-Pdx interaction in comparison with literature data and conclusions drawn from experiments obtained by other spectroscopic techniques. The results are also interpreted in the context of a 3D structural model of the Pdx-P450cam complex.
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Affiliation(s)
- Andrey Karyakin
- Max-Delbrück-Center for Molecular Medicine, Protein Dynamics Laboratory, Robert-Rössle Strasse 10, 13125 Berlin, Germany
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35
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OuYang B, Pochapsky SS, Pagani GM, Pochapsky TC. Specific effects of potassium ion binding on wild-type and L358P cytochrome P450cam. Biochemistry 2007; 45:14379-88. [PMID: 17128977 PMCID: PMC1764623 DOI: 10.1021/bi0617355] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The camphor monoxygenase cytochrome P450cam (CYP101) requires potassium ion (K+) to drive formation of the characteristic high-spin state of the heme Fe+3 upon substrate binding. Amide 1H, 15N correlations in perdeuterated [U-15N] CYP101 were monitored as a function of K+ concentration by 2D-TROSY-HSQC in both camphor-bound oxidized (CYP-S) and camphor- and CO-bound reduced CYP101 (CYP-S-CO). In both forms, K+-induced spectral perturbations are detected in the vicinity of the K+ binding site proposed from crystallographic structures, but are larger and more widespread structurally in CYP-S than in CYP-S-CO. In CYP-S-CO, K+-induced perturbations occur primarily near the proposed K+ binding site in the B-B' loop and B' helix, which are also perturbed by binding of effector, putidaredoxin (Pdx). The spectral effects of K+ binding in CYP-S-CO oppose those observed upon Pdxr titration. However, Pdxr titration of CYP-S-CO in the absence of K+ results in multiple conformations. The spin-state equilibrium in the L358P mutant of CYP101 is more sensitive to K+ concentration than WT CYP101, consistent with a hypothesis that L358P preferentially populates conformations enforced by Pdx binding in WT CYP101. Thallium(I), a K+ mimic, minimizes the effects of Pdx titration on the NMR spectrum of CYP-S-CO, but is competent to replace K+ in driving the formation of high-spin CYP-S. These observations suggest that the role of K+ is to stabilize conformers of CYP-S that drive the spin-state change prior to the first electron transfer, and that K+ stabilizes the CYP-S-CO conformer that interacts with Pdx. However, upon binding of Pdx, further conformational changes occur that disfavor K+ binding.
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Affiliation(s)
| | | | | | - Thomas C. Pochapsky
- Departments of Chemistry
- Biochemistry, and the
- Rosensteil Basic Medical Science Research Institute Brandeis University, 415 South St., MS 015 Waltham, MA 02454-9110
- *to whom correspondence should be addressed. ., Website: http://www.chem.brandeis.edu/pochapsky. Phone: 781-736-2559. Fax: 781-736-2516
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36
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Kuznetsov VY, Poulos TL, Sevrioukova IF. Putidaredoxin-to-cytochrome P450cam electron transfer: differences between the two reductive steps required for catalysis. Biochemistry 2006; 45:11934-44. [PMID: 17002293 PMCID: PMC2533851 DOI: 10.1021/bi0611154] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450cam (P450cam) is the terminal monooxygenase in a three-component camphor-hydroxylating system from Pseudomonas putida. The reaction cycle requires two distinct electron transfer (ET) processes from the [2Fe-2S] containing putidaredoxin (Pdx) to P450cam. Even though the mechanism of interaction and ET between the two proteins has been under investigation for over 30 years, the second reductive step and the effector role of Pdx are not fully understood. We utilized mutagenesis, kinetic, and computer modeling approaches to better understand differences between the two Pdx-to-P450cam ET events. Our results indicate that interacting residues and the ET pathways in the complexes formed between reduced Pdx (Pdx(r)) and the ferric and ferrous dioxygen-bound forms of P450cam (oxy-P450cam) are different. Pdx Asp38 and Trp106 were found to be key players in both reductive steps. Compared to the wild-type Pdx, the D38A, W106A, and delta106 mutants exhibited considerably higher Kd values for ferric P450cam and retained ca. 20% of the first electron transferring ability. In contrast, the binding affinity of the mutants for oxy-P450cam was not substantially altered while the second ET rates were <1%. On the basis of the kinetic and modeling data we conclude that (i) P450cam-Pdx interaction is highly specific in part because it is guided/controlled by the redox state of both partners; (ii) there are alternative ET routes from Pdx(r) to ferric P450cam and a unique pathway to oxy-P450cam involving Asp38; (iii) Pdx Trp106 is a key structural element that couples the second ET event to product formation possibly via its "push" effect on the heme-binding loop.
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Affiliation(s)
- Vadim Yu. Kuznetsov
- Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
- Departments of Physiology and Biophysics, University of California, Irvine, California 92697-3900
- Departments of Chemistry, University of California, Irvine, California 92697-3900
- Center in Chemical and Structural Biology, University of California, Irvine, California 92697-3900
| | - Irina F. Sevrioukova
- Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
- To whom correspondence should be addressed: Tel: 949-824-1953, Fax: 949-824-3280, E-mail:
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37
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Rui L, Pochapsky SS, Pochapsky TC. Comparison of the complexes formed by cytochrome P450cam with cytochrome b5 and putidaredoxin, two effectors of camphor hydroxylase activity. Biochemistry 2006; 45:3887-97. [PMID: 16548516 PMCID: PMC2265421 DOI: 10.1021/bi052318f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural perturbations in cytochrome P450cam (CYP101) induced by the soluble fragment of cytochrome b5, a nonphysiological effector of CYP101, were investigated by NMR spectroscopy and compared with the perturbations induced by the physiological reductant and effector putidaredoxin (Pdx). Chemical shifts of perdeuterated [U-15N]CYP101 backbone amide (NH) resonances were monitored as a function of cytochrome b5 concentration by 1H-15N TROSY-HSQC experiments. The association of cytochrome b5 with the reduced CYP101-camphor-carbon monoxide complex (CYP-S-CO) perturbs many of the same resonances that Pdx does, including regions of the CYP101 molecule implicated in substrate access and orientation. The perturbations are smaller in magnitude than those observed with Pdx(r) due to a lower binding affinity (a Kd of 13 +/- 3 mM, for the reduced cytochrome b5-CYP-S-CO complex compared to a Kd of 26 +/- 12 microM for the Pdx-CYP-S-CO complex). The results are in accord with our previous suggestion that the observed perturbations are related to effector activity and support the proposal that the primary role of the effector is to populate the active conformation of CYP101 to prevent uncoupling [Pochapsky, S. S., et al. (2003) Biochemistry 42, 5649-5656]. A titratable perturbation is observed at the 1H resonance of the 8-CH3 group of CYP101-bound camphor upon addition of cytochrome b5, a phenomenon also associated with the formation of the CYP101 x Pdx complex, albeit with larger perturbations [Wei, J. Y., et al. (2005) J. Am. Chem. Soc. 127, 6974-6976]. The effector activity of the particular rat cytochrome b5 construct used for NMR studies was confirmed by monitoring the enzymatic turnover that yielded 5-exo-hydroxycamphor using gas chromatography and mass spectrometry. Finally, the common features of the perturbations observed in the NMR spectra of the two complexes are discussed, and their relevance to effector activity is considered.
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Affiliation(s)
- Lingyun Rui
- Departments of Chemistry, Brandeis University, 415 South St., MS 015 Waltham, MA 02454-9110
| | - Susan S. Pochapsky
- Departments of Chemistry, Brandeis University, 415 South St., MS 015 Waltham, MA 02454-9110
| | - Thomas C. Pochapsky
- Departments of Chemistry, Brandeis University, 415 South St., MS 015 Waltham, MA 02454-9110
- Departments of Biochemistry, Brandeis University, 415 South St., MS 015 Waltham, MA 02454-9110
- *to whom correspondence should be addressed. . Website: http://www.chem.brandeis.edu/pochapsky. Phone: 781-736-2559. Fax: 781-736-2516
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38
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Poulos TL. Structural biology of heme monooxygenases. Biochem Biophys Res Commun 2005; 338:337-45. [PMID: 16185651 DOI: 10.1016/j.bbrc.2005.07.204] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 07/20/2005] [Indexed: 10/25/2022]
Abstract
Over the past few years the number of crystal structures available for heme monooxygenases has substantially increased. Those most closely related to one another are cytochrome P450, nitric oxide synthase, and heme oxygenase. The present mini-review provides a summary of some recently published work on how crystallography and solution studies have provided new insights on function and especially the oxygen activation process. It now appears that in all three monooxygenases highly ordered solvent in the active site serves as direct proton donors to the iron-linked dioxygen; a requirement for splitting the O-O bond. This is in sharp contrast to the related peroxidase family of enzymes where strategically positioned amino acid side chains serve the function of shuttling protons. The P450cam-oxy-complex as well as various mutants in a complex with either oxygen or carbon monoxide have enabled a fairly detailed picture to be developed on the role of specific amino acids and conformational changes in both electron transfer and oxygen activation.
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Affiliation(s)
- Thomas L Poulos
- Department of Molecular Biology, The Center in Chemical and Structural Biology, University of California, Irvine, Irvine, CA 92697-3900, USA.
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39
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Strushkevich NV, Azeva TN, Lepesheva GI, Usanov SA. Role of positively charged residues lys267, lys270, and arg411 of cytochrome p450scc (CYP11A1) in interaction with adrenodoxin. BIOCHEMISTRY (MOSCOW) 2005; 70:664-71. [PMID: 16038609 DOI: 10.1007/s10541-005-0167-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cytochrome P450scc and adrenodoxin are redox proteins of the electron transfer chain of the inner mitochondrial membrane steroid hydroxylases. In the present work site-directed mutagenesis of the charged residues of cytochrome P450scc and adrenodoxin, which might be involved in interaction, was used to study the nature of electrostatic contacts between the hemeprotein and the ferredoxin. The target residues for mutagenesis were selected based on the theoretical model of cytochrome P450scc-adrenodoxin complex and previously reported chemical modification studies of cytochrome P450scc. In the present work, to clarify the molecular mechanism of hemeprotein interaction with ferredoxin, we constructed cytochrome P450scc Lys267, Lys270, and Arg411 mutants and Glu47 mutant of adrenodoxin and analyzed their possible role in electrostatic interaction and the role of these residues in the functional activity of the proteins. Charge neutralization at positions Lys267 or Lys270 of cytochrome P450scc causes no significant effect on the physicochemical and functional properties of cytochrome P450scc. However, cytochrome P450scc mutant Arg411Gln was found to exhibit decreased binding affinity to adrenodoxin and lower activity in the cholesterol side chain cleavage reaction. Studies of the functional properties of Glu47Gln and Glu47Arg adrenodoxin mutants indicate that a negatively charged residue in the loop covering the Fe2S2 cluster, being important for maintenance of the correct architecture of these structural elements of ferredoxin, is not directly involved in electrostatic interaction with cytochrome P450scc. Moreover, our results indicate the presence of at least two different binding (contact) sites on the proximal surface of cytochrome P450scc with different electrostatic input to interaction with adrenodoxin. In the binary complex, the positively charged sites of the proximal surface of cytochrome P450scc well correspond to the two negatively charged sites of adrenodoxin: the "interaction" domain site and the "core" domain site.
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Affiliation(s)
- N V Strushkevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, ul. Kuprevicha5, 220141 Minsk, Belarus
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40
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Wade RC, Motiejunas D, Schleinkofer K, Winn PJ, Banerjee A, Kariakin A, Jung C. Multiple molecular recognition mechanisms. Cytochrome P450--a case study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1754:239-44. [PMID: 16226496 DOI: 10.1016/j.bbapap.2005.07.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 07/18/2005] [Accepted: 07/19/2005] [Indexed: 11/30/2022]
Abstract
Biomolecular recognition is complex. The balance between the different molecular properties that contribute to molecular recognition, such as shape, electrostatics, dynamics and entropy, varies from case to case. This, along with the extent of experimental characterization, influences the choice of appropriate computational approaches to study biomolecular interactions. Here, we present computational studies of cytochrome P450 enzymes and their interactions with small molecules and with other proteins. These interactions exemplify some of the diversity of molecular determinants of binding affinity and specificity observed for proteins and we discuss some of the challenges that they pose for molecular modelling and simulation.
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Affiliation(s)
- Rebecca C Wade
- Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.
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41
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Prasad S, Murugan R, Mitra S. An artificial electron donor supported catalytic cycle of Pseudomonas putida cytochrome P450cam. Biochem Biophys Res Commun 2005; 335:590-5. [PMID: 16084834 DOI: 10.1016/j.bbrc.2005.07.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 07/19/2005] [Indexed: 11/22/2022]
Abstract
Putidaredoxin (PdX), the physiological effector of cytochrome P450cam (P450cam), serves to gate electron transfer into oxy-P450cam during the catalytic cycle of the enzyme. Redox-linked structural changes in PdX are necessary for the effective P450cam turnover reaction. PdX is believed to be difficult to be replaced by an artificial electron donor in the reaction pathway of P450cam. We demonstrate that the catalytic cycle of wild-type P450cam can be supported in the presence of an artificial reductant, potassium ferrocyanide. Upon rapid mixing of ferrocyanide ion with P450cam, we observed an intermediate with spectral features characteristic of compound I. The rate constant for the formation of compound I in the presence of ferrocyanide supported reaction cycle was found to be comparable to the ones observed for H2O2 supported compound I formation in wild-type P450cam, but was much lower than those observed for classical peroxidases. The results presented in this paper form the first kinetic analysis of this intermediate for an artificial electron-driven P450cam catalytic pathway in solution.
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Affiliation(s)
- Swati Prasad
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
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42
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Poulos TL. Intermediates in P450 catalysis. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:793-806; discussion 1035-40. [PMID: 15901536 DOI: 10.1098/rsta.2004.1537] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cytochromes P450 catalyse the insertion of one O2-derived oxygen atom in unactivated C-H bonds, and as such, are potent oxidants. A significant amount is known about the P450 catalytic cycle owing partly to the single heme group at the active site that provides spectroscopic handles in tracking various intermediates. A sophisticated array of electron paramagnetic, electron double nuclear resonance, and more traditional absorption spectroscopies have been able to identify key intermediates, while crystallography has defined the structure of the substrate-free, -bound, and oxy-complexes. What has remained elusive is the Fe(IV)=O intermediate, thought to be the active hydroxylating agent. Here, theory and especially density functional calculations have provided valuable insights.
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Affiliation(s)
- Thomas L Poulos
- Department of Molecular Biology and Biochemistry and the Program in Chemical and Structural Biology, University of California, Irvine, CA 92697-3900, USA.
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43
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Sevrioukova IF. Redox-dependent Structural Reorganization in Putidaredoxin, a Vertebrate-type [2Fe-2S] Ferredoxin from Pseudomonas putida. J Mol Biol 2005; 347:607-21. [PMID: 15755454 DOI: 10.1016/j.jmb.2005.01.047] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Revised: 01/19/2005] [Accepted: 01/21/2005] [Indexed: 11/24/2022]
Abstract
Putidaredoxin (Pdx), a vertebrate-type [2Fe-2S] ferredoxin from Pseudomonas putida, transfers electrons from NADH-putidaredoxin reductase to cytochrome P450cam. Pdx exhibits redox-dependent binding affinities for P450cam and is thought to play an effector role in the monooxygenase reaction catalyzed by this hemoprotein. To understand how the reduced form of Pdx is stabilized and how reduction of the [2Fe-2S] cluster affects molecular properties of the iron-sulfur protein, crystal structures of reduced C73S and C73S/C85S Pdx were solved to 1.45 angstroms and 1.84 angstroms resolution, respectively, and compared to the corresponding 2.0 angstroms and 2.03 angstroms X-ray models of the oxidized mutants. To prevent photoreduction, the latter models were determined using in-house radiation source and the X-ray dose received by Pdx crystals was significantly decreased. Structural analysis showed that in reduced Pdx the Cys45-Ala46 peptide bond flip initiates readjustment of hydrogen bonding interactions between the [2Fe-2S] cluster, the Sgamma atoms of the cysteinyl ligands, and the backbone amide nitrogen atoms that results in tightening of the Cys39-Cys48 metal cluster binding loop around the prosthetic group and shifting of the metal center toward the Cys45-Thr47 peptide. From the metal center binding loop, the redox changes are transmitted to the linked Ile32-Asp38 peptide triggering structural rearrangement between the Tyr33-Asp34, Ser7-Asp9 and Pro102-Asp103 fragments of Pdx. The newly established hydrogen bonding interactions between Ser7, Asp9, Tyr33, Asp34, and Pro102, in turn, not only stabilize the tightened conformation of the [2Fe-2S] cluster binding loop but also assist in formation of a specific structural patch on the surface of Pdx that can be recognized by P450cam. This redox-linked change in surface properties is likely to be responsible for different binding affinity of oxidized and reduced Pdx to the hemoprotein.
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Affiliation(s)
- Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92612-3900, USA.
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44
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Kuznetsov VY, Blair E, Farmer PJ, Poulos TL, Pifferitti A, Sevrioukova IF. The putidaredoxin reductase-putidaredoxin electron transfer complex: theoretical and experimental studies. J Biol Chem 2005; 280:16135-42. [PMID: 15716266 DOI: 10.1074/jbc.m500771200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interaction and electron transfer between putidaredoxin reductase (Pdr) and putidaredoxin (Pdx) from Pseudomonas putida was studied by molecular modeling, mutagenesis, and stopped flow techniques. Based on the crystal structures of Pdr and Pdx, a complex between the proteins was generated using computer graphics methods. In the model, Pdx is docked above the isoalloxazine ring of FAD of Pdr with the distance between the flavin and [2Fe-2S] of 14.6 A. This mode of interaction allows Pdx to easily adjust and optimize orientation of its cofactor relative to Pdr. The key residues of Pdx located at the center, Asp(38) and Trp(106), and at the edge of the protein-protein interface, Tyr(33) and Arg(66), were mutated to test the Pdr-Pdx computer model. The Y33F, Y33A, D38N, D38A, R66A, R66E, W106F, W106A, and Delta106 mutations did not affect assembly of the [2Fe-2S] cluster and resulted in a marginal change in the redox potential of Pdx. The electron-accepting ability of Delta106 Pdx was similar to that of the wild-type protein, whereas electron transfer rates from Pdr to other mutants were diminished to various degrees with the smallest and largest effects on the kinetic parameters of the Pdr-to-Pdx electron transfer reaction caused by the Trp(106) and Tyr(33)/Arg(66) substitutions, respectively. Compared with wild-type Pdx, the binding affinity of all studied mutants to Pdr was significantly higher. Experimental results were in agreement with theoretical predictions and suggest that: (i) Pdr-Pdx complex formation is mainly driven by steric complementarity, (ii) bulky side chains of Tyr(33), Arg(66), and Trp(106) prevent tight binding of oxidized Pdx and facilitate dissociation of the reduced iron-sulfur protein from Pdr, and (iii) transfer of an electron from FAD to [2Fe-2S] can occur with various orientations between the cofactors through multiple electron transfer pathways that do not involve Trp(106) but are likely to include Asp(38) and Cys(39).
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Affiliation(s)
- Vadim Yu Kuznetsov
- Department of Molecular Biology, University of California, Irvine, California 92612-3900, USA
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45
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Pylypenko O, Schlichting I. Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s. Annu Rev Biochem 2004; 73:991-1018. [PMID: 15189165 DOI: 10.1146/annurev.biochem.73.011303.073711] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytochrome P450 enzymes are heme-containing monooxygenases that are named after an absorption band at 450 nm when complexed with carbon monoxide. They catalyze a wide variety of reactions and are unique in their ability to hydroxylate nonactivated hydrocarbons. P450 enzymes are involved in numerous biological processes, which include the biosynthesis of lipids, steroids, antibiotics, and the degradation of xenobiotics. In line with the variety of reactions catalyzed, the size of their substrates varies significantly. Some P450s have open active sites (e.g., BM3), and some have shielded active sites that open only transiently (e.g., P450cam), whereas others bind the substrate only when attached to carrier proteins (e.g., Oxy proteins). Structural aspects of both organic and gaseous ligand binding and electron transfer are described.
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Affiliation(s)
- Olena Pylypenko
- Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany.
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46
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Prudêncio M, Ubbink M. Transient complexes of redox proteins: structural and dynamic details from NMR studies. J Mol Recognit 2004; 17:524-39. [PMID: 15386621 DOI: 10.1002/jmr.686] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Redox proteins participate in many metabolic routes, in particular those related to energy conversion. Protein-protein complexes of redox proteins are characterized by a weak affinity and a short lifetime. Two-dimensional NMR spectroscopy has been applied to many redox protein complexes, providing a wealth of information about the process of complex formation, the nature of the interface and the dynamic properties of the complex. These studies have shown that some complexes are non-specific and exist as a dynamic ensemble of orientations while in other complexes the proteins assume a single orientation. The binding interface in these complexes consists of a small hydrophobic patch for specificity, surrounded by polar, uncharged residues that may enhance dissociation, and, in most complexes, a ring or patch of charged residues that enhances the association by electrostatic interactions. The entry and exit port of the electrons is located within the hydrophobic interaction site, ensuring rapid electron transfer from one redox centre to the next.
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Affiliation(s)
- Miguel Prudêncio
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, PO Box 9502, 2300 RA Leiden, The Netherlands
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47
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Sevrioukova IF, Li H, Poulos TL. Crystal structure of putidaredoxin reductase from Pseudomonas putida, the final structural component of the cytochrome P450cam monooxygenase. J Mol Biol 2004; 336:889-902. [PMID: 15095867 DOI: 10.1016/j.jmb.2003.12.067] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Revised: 12/22/2003] [Accepted: 12/29/2003] [Indexed: 11/28/2022]
Abstract
The crystal structure of recombinant putidaredoxin reductase (Pdr), an FAD-containing NADH-dependent flavoprotein component of the cytochrome P450cam monooxygenase from Pseudomonas putida, has been determined to 1.90 A resolution. The protein has a fold similar to that of disulfide reductases and consists of the FAD-binding, NAD-binding, and C-terminal domains. Compared to homologous flavoenzymes, the reductase component of biphenyl dioxygenase (BphA4) and apoptosis-inducing factor, Pdr lacks one of the arginine residues that compensates partially for the negative charge on the pyrophosphate of FAD. This uncompensated negative charge is likely to decrease the electron-accepting ability of the flavin. The aromatic side-chain of the "gatekeeper" Tyr159 is in the "out" conformation and leaves the nicotinamide-binding site of Pdr completely open. The presence of electron density in the NAD-binding channel indicates that NAD originating from Escherichia coli is partially bound to Pdr. A structural comparison of Pdr with homologous flavoproteins indicates that an open and accessible nicotinamide-binding site, the presence of an acidic residue in the middle part of the NAD-binding channel that binds the nicotinamide ribose, and multiple positively charged arginine residues surrounding the entrance of the NAD-binding channel are the special structural elements that assist tighter and more specific binding of the oxidized pyridine nucleotide by the BphA4-like flavoproteins. The crystallographic model of Pdr explains differences in the electron transfer mechanism in the Pdr-putidaredoxin redox couple and their mammalian counterparts, adrenodoxin reductase and adrenodoxin.
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Affiliation(s)
- Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92612-3900, USA.
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48
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Schiffler B, Bernhardt R. Bacterial (CYP101) and mitochondrial P450 systems—how comparable are they? Biochem Biophys Res Commun 2003; 312:223-8. [PMID: 14630046 DOI: 10.1016/j.bbrc.2003.09.214] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The bacterial CYP101 system and mitochondrial P450 systems show high similarity. Both systems contain the same protein components, a FAD containing reductase, a ferredoxin of the [2Fe2S] type, and a cytochrome P450. At a first glance they seem to be comparable but there are considerable differences among both proteins. Thus, the ferredoxin components of the two systems display significant structural homology but cannot substitute for each other in functional assays. Going into more detail, pronounced differences between the two systems that affect their biological functions are found.
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Affiliation(s)
- Burkhard Schiffler
- Universität des Saarlandes, Gebäude 9.2, P.O. Box 151150, 66041 Saarbrücken, Germany
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49
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Tosha T, Yoshioka S, Takahashi S, Ishimori K, Shimada H, Morishima I. NMR study on the structural changes of cytochrome P450cam upon the complex formation with putidaredoxin. Functional significance of the putidaredoxin-induced structural changes. J Biol Chem 2003; 278:39809-21. [PMID: 12842870 DOI: 10.1074/jbc.m304265200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We investigated putidaredoxin-induced structural changes in carbonmonoxy P450cam by using NMR spectroscopy. The resonance from the beta-proton of the axial cysteine was upfield shifted by 0.12 ppm upon the putidaredoxin binding, indicating that the axial cysteine approaches to the heme-iron by about 0.1 A. The approach of the axial cysteine to the heme-iron would enhance the electronic donation from the axial thiolate to the heme-iron, resulting in the enhanced heterolysis of the dioxygen bond. In addition to the structural perturbation on the axial ligand, the structural changes in the substrate and ligand binding site were observed. The resonances from the 5-exo- and 9-methyl-protons of d-camphor, which were newly identified in this study, were upfield shifted by 1.28 and 0.20 ppm, respectively, implying that d-camphor moves to the heme-iron by 0.15-0.7 A. Based on the radical rebound mechanism, the approach of d-camphor to the heme-iron could promote the oxygen transfer reaction. On the other hand, the downfield shift of the resonance from the gamma-methyl group of Thr-252 reflects the movement of the side chain away from the heme-iron by approximately 0.25 A. Because Thr-252 regulates the heterolysis of the dioxygen bond, the positional rearrangement of Thr-252 might assist the scission of the dioxygen bond. We, therefore, conclude that putidaredoxin induces the specific heme environmental changes of P450cam, which would facilitate the oxygen activation and the oxygen transfer reaction.
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Affiliation(s)
- Takehiko Tosha
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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Sevrioukova IF, Garcia C, Li H, Bhaskar B, Poulos TL. Crystal Structure of Putidaredoxin, the [2Fe–2S] Component of the P450cam Monooxygenase System from Pseudomonas putida. J Mol Biol 2003; 333:377-92. [PMID: 14529624 DOI: 10.1016/j.jmb.2003.08.028] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stability of the [2Fe-2S]-containing putidaredoxin (Pdx), the electron donor to cytochrome P450cam in Pseudomonas putida, was improved by mutating non-ligating cysteine residues, Cys73 and Cys85, to serine singly and in combination. The increasing order of stability is Cys73Ser/Cys85Ser>Cys73Ser>Cys85Ser>WT Pdx. Crystal structures of Cys73Ser/Cys85Ser and Cys73Ser mutants of Pdx, solved by single-wavelength anomalous dispersion phasing using the [2Fe-2S] iron atoms to 1.47 A and 1.65 A resolution, respectively, are nearly identical and very similar to those of bovine adrenodoxin (Adx) and Escherichia coli ferredoxin. However, unlike the Adx structure, no motion between the core and interaction domains of Pdx is observed. This higher conformational stability of Pdx might be due to the presence of a more extensive hydrogen bonding network at the interface between the two structural domains around the conserved His49. In particular, formation of a hydrogen bond between the side-chain of Tyr51 and the carbonyl oxygen atom of Glu77 and the presence of two well-ordered water molecules linking the interaction domain and the C-terminal peptide to the core of the molecule are unique to Pdx. The folding topology of the NMR model is similar to that of the X-ray structure of Pdx. The overall rmsd of Calpha positions between the two models is 1.59 A. The largest positional differences are observed for residues 18-21 and 33-37 in the loop regions and the C terminus. The latter two peptides display conformational heterogeneity in the crystal structures. Owing to flexibility, the aromatic ring of the C-terminal Trp106 can closely approach the side-chains of Asp38 and Thr47 (3.2-3.9 A) or move away and leave the active site solvent-exposed. Therefore, Trp106, previously shown to be important in the Pdr-to-Pdx and Pdx-to-P450cam electron transfer reactions is in a position to regulate and/or mediate electron transfer to or from the [2Fe-2S] center of Pdx.
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Affiliation(s)
- Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92612-3900, USA.
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