1
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Buzsaki SR, Mason SM, Kattamuri PV, Serviano JMI, Rodriguez DN, Wilson CV, Hood DM, Ellefsen JD, Lu YC, Kan J, West JG, Miller SJ, Holland PL. Fe/Thiol Cooperative Hydrogen Atom Transfer Olefin Hydrogenation: Mechanistic Insights That Inform Enantioselective Catalysis. J Am Chem Soc 2024; 146:17296-17310. [PMID: 38875703 PMCID: PMC11209773 DOI: 10.1021/jacs.4c04047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Asymmetric hydrogenation of activated olefins using transition metal catalysis is a powerful tool for the synthesis of complex molecules, but traditional metal catalysts have difficulty with enantioselective reduction of electron-neutral, electron-rich, and minimally functionalized olefins. Hydrogenation based on radical, metal-catalyzed hydrogen atom transfer (mHAT) mechanisms offers an outstanding opportunity to overcome these difficulties, enabling the mild reduction of these challenging olefins with selectivity that is complementary to traditional hydrogenations with H2. Further, mHAT presents an opportunity for asymmetric induction through cooperative hydrogen atom transfer (cHAT) using chiral thiols. Here, we report insights from a mechanistic study of an iron-catalyzed achiral cHAT reaction and leverage these insights to deliver stereocontrol from chiral thiols. Kinetic analysis and variation of silane structure point to the transfer of hydride from silane to iron as the likely rate-limiting step. The data indicate that the selectivity-determining step is quenching of the alkyl radical by thiol, which becomes a more potent H atom donor when coordinated to iron(II). The resulting iron(III)-thiolate complex is in equilibrium with other iron species, including FeII(acac)2, which is shown to be the predominant off-cycle species. The enantiodetermining nature of the thiol trapping step enables enantioselective net hydrogenation of olefins through cHAT using a commercially available glucose-derived thiol catalyst with up to 80:20 enantiomeric ratio. To the best of our knowledge, this is the first demonstration of asymmetric hydrogenation via iron-catalyzed mHAT. These findings advance our understanding of cooperative radical catalysis and act as a proof of principle for the development of enantioselective iron-catalyzed mHAT reactions.
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Affiliation(s)
- Sarah R. Buzsaki
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
| | - Savannah M. Mason
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | | | - Juan M. I. Serviano
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Dinora N. Rodriguez
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
| | - Conner V. Wilson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Drew M. Hood
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
| | - Jonathan D. Ellefsen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Yen-Chu Lu
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
| | - Jolie Kan
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
| | - Julian G. West
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Patrick L. Holland
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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2
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Badgandi HB, Weichsel A, Montfort WR. Nitric oxide delivery and heme-assisted S-nitrosation by the bedbug nitrophorin. J Inorg Biochem 2023; 246:112263. [PMID: 37290359 PMCID: PMC10332259 DOI: 10.1016/j.jinorgbio.2023.112263] [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: 04/05/2023] [Revised: 05/10/2023] [Accepted: 05/20/2023] [Indexed: 06/10/2023]
Abstract
Nitrophorins are heme proteins used by blood feeding insects to deliver nitric oxide (NO) to a victim, leading to vasodilation and antiplatelet activity. Cimex lectularius (bedbug) nitrophorin (cNP) accomplishes this with a cysteine ligated ferric (Fe(III)) heme. In the acidic environment of the insect's salivary glands, NO binds tightly to cNP. During a blood meal, cNP-NO is delivered to the feeding site where dilution and increased pH lead to NO release. In a previous study, cNP was shown to not only bind heme, but to also nitrosate the proximal cysteine, leading to Cys-NO (SNO) formation. SNO formation requires oxidation of the proximal cysteine, which was proposed to be metal-assisted through accompanying reduction of ferric heme and formation of Fe(II)-NO. Here, we report the 1.6 Å crystal structure of cNP first chemically reduced and then exposed to NO, and show that Fe(II)-NO is formed but SNO is not, supporting a metal-assisted SNO formation mechanism. Crystallographic and spectroscopic studies of mutated cNP show that steric crowding of the proximal site inhibits SNO formation while a sterically relaxed proximal site enhances SNO formation, providing insight into specificity for this poorly understood modification. Experiments examining the pH dependence for NO implicate direct protonation of the proximal cysteine as the underlying mechanism. At lower pH, thiol heme ligation predominates, leading to a smaller trans effect and 60-fold enhanced NO affinity (Kd = 70 nM). Unexpectedly, we find that thiol formation interferes with SNO formation, suggesting cNP-SNO is unlikely to form in the insect salivary glands.
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Affiliation(s)
- Hemant B Badgandi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, United States of America
| | - Andrzej Weichsel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, United States of America
| | - William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, United States of America.
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3
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Fu J, Nisbett LM, Guo Y, Boon EM. NosP Detection of Heme Modulates Burkholderia thailandensis Biofilm Formation. Biochemistry 2023; 62:2426-2441. [PMID: 37498555 PMCID: PMC10478957 DOI: 10.1021/acs.biochem.3c00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Aggregated bacteria embedded within self-secreted extracellular polymeric substances, or biofilms, are resistant to antibiotics and cause chronic infections. As such, they are a significant public health threat. Heme is an abundant iron source for pathogenic bacteria during infection; many bacteria have systems to detect heme assimilated from host cells, which is correlated with the transition between acute and chronic infection states. Here, we investigate the heme-sensing function of a newly discovered multifactorial sensory hemoprotein called NosP and its role in biofilm regulation in the soil-dwelling bacterium Burkholderia thailandensis, the close surrogate of Bio-Safety-Level-3 pathogen Burkholderia pseudomallei. The NosP family protein has previously been shown to exhibit both nitric oxide (NO)- and heme-sensing functions and to regulate biofilms through NosP-associated histidine kinases and two-component systems. Our in vitro studies suggest that BtNosP exhibits heme-binding kinetics and thermodynamics consistent with a labile heme-responsive protein and that the holo-form of BtNosP acts as an inhibitor of its associated histidine kinase BtNahK. Furthermore, our in vivo studies suggest that increasing the concentration of extracellular heme decreases B. thailandensis biofilm formation, and deletion of nosP and nahK abolishes this phenotype, consistent with a model that BtNosP detects heme and exerts an inhibitory effect on BtNahK to decrease the biofilm.
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Affiliation(s)
- Jiayuan Fu
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Lisa-Marie Nisbett
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Yulong Guo
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Elizabeth M Boon
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
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4
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Mohamed H, Ghith A, Bell SG. The binding of nitrogen-donor ligands to the ferric and ferrous forms of cytochrome P450 enzymes. J Inorg Biochem 2023; 242:112168. [PMID: 36870164 DOI: 10.1016/j.jinorgbio.2023.112168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/24/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
The cytochrome P450 superfamily of heme-thiolate monooxygenase enzymes can catalyse various oxidation reactions. The addition of a substrate or an inhibitor ligand induces changes in the absorption spectrum of these enzymes and UV-visible (UV-vis) absorbance spectroscopy is the most common and readily available technique used to interrogate their heme and active site environment. Nitrogen-containing ligands can inhibit the catalytic cycle of heme enzymes by interacting with the heme. Here we evaluate the binding of imidazole and pyridine-based ligands to the ferric and ferrous forms of a selection of bacterial cytochrome P450 enzymes using UV-visible absorbance spectroscopy. The majority of these ligands interact with the heme as one would expect for type II nitrogen directly coordinated to a ferric heme-thiolate species. However, the spectroscopic changes observed in the ligand-bound ferrous forms indicated differences in the heme environment across these P450 enzyme/ligand combinations. Multiple species were observed in the UV-vis spectra of the ferrous ligand-bound P450s. None of the enzymes gave rise to the isolation of a single species with a Soret band at ∼442-447 nm, indicative of a 6-coordinate ferrous thiolate species with a nitrogen-donor ligand. A ferrous species with Soret band at ∼427 nm coupled with an α-band of increased intensity was observed with the imidazole ligands. With some enzyme-ligand combinations reduction resulted in breaking of the iron‑nitrogen bond yielding a 5-coordinate high-spin ferrous species. In other instances, the ferrous form was readily oxidised back to the ferric form on addition of the ligand.
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Affiliation(s)
- Hebatalla Mohamed
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | - Amna Ghith
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia.
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5
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Jenner LP, Crack JC, Kurth JM, Soldánová Z, Brandt L, Sokol KP, Reisner E, Bradley JM, Dahl C, Cheesman MR, Butt JN. Reaction of Thiosulfate Dehydrogenase with a Substrate Mimic Induces Dissociation of the Cysteine Heme Ligand Giving Insights into the Mechanism of Oxidative Catalysis. J Am Chem Soc 2022; 144:18296-18304. [PMID: 36173876 PMCID: PMC9562282 DOI: 10.1021/jacs.2c06062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Thiosulfate dehydrogenases are bacterial cytochromes
that contribute
to the oxidation of inorganic sulfur. The active sites of these enzymes
contain low-spin c-type heme with Cys–/His axial ligation. However, the reduction potentials of these hemes
are several hundred mV more negative than that of the thiosulfate/tetrathionate
couple (Em, +198 mV), making it difficult
to rationalize the thiosulfate oxidizing capability. Here, we describe
the reaction of Campylobacter jejuni thiosulfate dehydrogenase (TsdA) with sulfite, an analogue of thiosulfate.
The reaction leads to stoichiometric conversion of the active site
Cys to cysteinyl sulfonate (Cα-CH2-S-SO3–) such that the protein exists in a form
closely resembling a proposed intermediate in the pathway for thiosulfate
oxidation that carries a cysteinyl thiosulfate (Cα-CH2-S-SSO3–). The active
site heme in the stable sulfonated protein displays an Em approximately 200 mV more positive than the Cys–/His-ligated state. This can explain the thiosulfate
oxidizing activity of the enzyme and allows us to propose a catalytic
mechanism for thiosulfate oxidation. Substrate-driven release of the
Cys heme ligand allows that side chain to provide the site of substrate
binding and redox transformation; the neighboring heme then simply
provides a site for electron relay to an appropriate partner. This
chemistry is distinct from that displayed by the Cys-ligated hemes
found in gas-sensing hemoproteins and in enzymes such as the cytochromes
P450. Thus, a further class of thiolate-ligated hemes is proposed,
as exemplified by the TsdA centers that have evolved to catalyze the
controlled redox transformations of inorganic oxo anions of sulfur.
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Affiliation(s)
- Leon P Jenner
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, United Kingdom
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, United Kingdom
| | - Julia M Kurth
- Institut für Mikrobiologie & Biotechnologie, Friedrich Wilhelms Universität Bonn, D-53115Bonn, Germany
| | - Zuzana Soldánová
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, United Kingdom
| | - Linda Brandt
- Institut für Mikrobiologie & Biotechnologie, Friedrich Wilhelms Universität Bonn, D-53115Bonn, Germany
| | - Katarzyna P Sokol
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Erwin Reisner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, United Kingdom
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Friedrich Wilhelms Universität Bonn, D-53115Bonn, Germany
| | - Myles R Cheesman
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, United Kingdom
| | - Julea N Butt
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, United Kingdom
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6
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Nienhaus K, Sharma V, Nienhaus GU, Podust LM. Homodimerization Counteracts the Detrimental Effect of Nitrogenous Heme Ligands on the Enzymatic Activity of Acanthamoeba castellanii CYP51. Biochemistry 2022; 61:1363-1377. [PMID: 35730528 DOI: 10.1021/acs.biochem.2c00198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acanthamoeba castellanii is a free-living amoeba that can cause severe eye and brain infections in humans. At present, there is no uniformly effective treatment for any of these infections. However, sterol 14α-demethylases (CYP51s), heme-containing cytochrome P450 enzymes, are known to be validated drug targets in pathogenic fungi and protozoa. The catalytically active P450 form of CYP51 from A. castellanii (AcCYP51) is stabilized against conversion to the inactive P420 form by dimerization. In contrast, Naegleria fowleri CYP51 (NfCYP51) is monomeric in its active P450 and inactive P420 forms. For these two CYP51 enzymes, we have investigated the interplay between the enzyme activity and oligomerization state using steady-state and time-resolved UV-visible absorption spectroscopy. In both enzymes, the P450 → P420 transition is favored under reducing conditions. The transition is accelerated at higher pH, which excludes a protonated thiol as the proximal ligand in P420. Displacement of the proximal thiolate ligand is also promoted by adding exogenous nitrogenous ligands (N-ligands) such as imidazole, isavuconazole, and clotrimazole that bind at the opposite, distal heme side. In AcCYP51, the P450 → P420 transition is faster in the monomer than in the dimer, indicating that the dimeric assembly is critical for stabilizing thiolate coordination to the heme and thus for sustaining AcCYP51 activity. The spectroscopic experiments were complemented with size-exclusion chromatography and X-ray crystallography studies. Collectively, our results indicate that effective inactivation of the AcCYP51 function by azole drugs is due to synergistic interference with AcCYP51 dimerization and promoting irreversible displacement of the proximal heme-thiolate ligand.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), D-76049 Karlsruhe, Germany
| | - Vandna Sharma
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), D-76049 Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany.,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
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7
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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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8
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Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp-Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH-Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α-Helical Metalloprotein. Angew Chem Int Ed Engl 2020; 60:3974-3978. [PMID: 33215801 DOI: 10.1002/anie.202012673] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/19/2020] [Indexed: 11/09/2022]
Abstract
De Novo metalloprotein design assesses the relationship between metal active site architecture and catalytic reactivity. Herein, we use an α-helical scaffold to control the iron coordination geometry when a heme cofactor is allowed to bind to either histidine or cysteine ligands, within a single artificial protein. Consequently, we uncovered a reversible pH-induced switch of the heme axial ligation within this simplified scaffold. Characterization of the specific heme coordination modes was done by using UV/Vis and Electron Paramagnetic Resonance spectroscopies. The penta- or hexa-coordinate thiolate heme (9≤pH≤11) and the penta-coordinate imidazole heme (6≤pH≤8.5) reproduces well the heme ligation in chloroperoxidases or cyt P450 monooxygenases and peroxidases, respectively. The stability of heme coordination upon ferric/ferrous redox cycling is a crucial property of the construct. At basic pHs, the thiolate mini-heme protein can catalyze O2 reduction when adsorbed onto a pyrolytic graphite electrode.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2), Centrale Marseille, Aix-Marseille Univ., CNRS, Marseille, France
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
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9
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Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp‐Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH‐Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α‐Helical Metalloprotein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Borries Demeler
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge AB T1K 3M4 Canada
| | - Barbara Schoepp‐Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2) Centrale Marseille Aix-Marseille Univ. CNRS Marseille France
| | | | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
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10
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Sharma V, Shing B, Hernandez-Alvarez L, Debnath A, Podust LM. Domain-Swap Dimerization of Acanthamoeba castellanii CYP51 and a Unique Mechanism of Inactivation by Isavuconazole. Mol Pharmacol 2020; 98:770-780. [PMID: 33008918 DOI: 10.1124/molpharm.120.000092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/17/2020] [Indexed: 01/14/2023] Open
Abstract
Cytochromes P450 (P450, CYP) metabolize a wide variety of endogenous and exogenous lipophilic molecules, including most drugs. Sterol 14α-demethylase (CYP51) is a target for antifungal drugs known as conazoles. Using X-ray crystallography, we have discovered a domain-swap homodimerization mode in CYP51 from a human pathogen, Acanthamoeba castellanii CYP51 (AcCYP51). Recombinant AcCYP51 with a truncated transmembrane helix was purified as a heterogeneous mixture corresponding to the dimer and monomer units. Spectral analyses of these two populations have shown that the CO-bound ferrous form of the dimeric protein absorbed at 448 nm (catalytically competent form), whereas the monomeric form absorbed at 420 nm (catalytically incompetent form). AcCYP51 dimerized head-to-head via N-termini swapping, resulting in formation of a nonplanar protein-protein interface exceeding 2000 Å2 with a total solvation energy gain of -35.4 kcal/mol. In the dimer, the protomers faced each other through the F and G α-helices, thus blocking the substrate access channel. In the presence of the drugs clotrimazole and isavuconazole, the AcCYP51 drug complexes crystallized as monomers. Although clotrimazole-bound AcCYP51 adopted a typical CYP monomer structure, isavuconazole-bound AcCYP51 failed to refold 74 N-terminal residues. The failure of AcCYP51 to fully refold upon inhibitor binding in vivo would cause an irreversible loss of a structurally aberrant enzyme through proteolytic degradation. This assumption explains the superior potency of isavuconazole against A. castellanii The dimerization mode observed in this work is compatible with membrane association and may be relevant to other members of the CYP family of biologic, medical, and pharmacological importance. SIGNIFICANCE STATEMENT: We investigated the mechanism of action of antifungal drugs in the human pathogen Acanthamoeba castellanii. We discovered that the enzyme target [Acanthamoeba castellanii sterol 14α-demethylase (AcCYP51)] formed a dimer via an N-termini swap, whereas drug-bound AcCYP51 was monomeric. In the AcCYP51-isavuconazole complex, the protein target failed to refold 74 N-terminal residues, suggesting a fundamentally different mechanism of AcCYP51 inactivation than only blocking the active site. Proteolytic degradation of a structurally aberrant enzyme would explain the superior potency of isavuconazole against A. castellanii.
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Affiliation(s)
- Vandna Sharma
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California (V.S., B.S., L.H.-A., A.D., L.M.P.) and Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil (L.H.-A.)
| | - Brian Shing
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California (V.S., B.S., L.H.-A., A.D., L.M.P.) and Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil (L.H.-A.)
| | - Lilian Hernandez-Alvarez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California (V.S., B.S., L.H.-A., A.D., L.M.P.) and Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil (L.H.-A.)
| | - Anjan Debnath
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California (V.S., B.S., L.H.-A., A.D., L.M.P.) and Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil (L.H.-A.)
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California (V.S., B.S., L.H.-A., A.D., L.M.P.) and Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil (L.H.-A.)
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11
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Steck V, Kolev JN, Ren X, Fasan R. Mechanism-Guided Design and Discovery of Efficient Cytochrome P450-Derived C-H Amination Biocatalysts. J Am Chem Soc 2020; 142:10343-10357. [PMID: 32407077 DOI: 10.1021/jacs.9b12859] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochromes P450 have been recently identified as a promising class of biocatalysts for mediating C-H aminations via nitrene transfer, a valuable transformation for forging new C-N bonds. The catalytic efficiency of P450s in these non-native transformations is however significantly inferior to that exhibited by these enzymes in their native monooxygenase function. Using a mechanism-guided strategy, we report here the rational design of a series of P450BM3-based variants with dramatically enhanced C-H amination activity acquired through disruption of the native proton relay network and other highly conserved structural elements within this class of enzymes. This approach further guided the identification of XplA and BezE, two "atypical" natural P450s implicated in the degradation of a man-made explosive and in benzastatins biosynthesis, respectively, as very efficient C-H aminases. Both XplA and BezE could be engineered to further improve their C-H amination reactivity, which demonstrates their evolvability for abiological reactions. These engineered and natural P450 catalysts can promote the intramolecular C-H amination of arylsulfonyl azides with over 10 000-14 000 catalytic turnovers, ranking among the most efficient nitrene transfer biocatalysts reported to date. Mechanistic and structure-reactivity studies provide insights into the origin of the C-H amination reactivity enhancement and highlight the divergent structural requirements inherent to supporting C-H amination versus C-H monooxygenation reactivity within this class of enzymes. Overall, this work provides new promising scaffolds for the development of nitrene transferases and demonstrates the value of mechanism-driven rational design as a strategy for improving the catalytic efficiency of metalloenzymes in the context of abiological transformations.
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Affiliation(s)
- Viktoria Steck
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Joshua N Kolev
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Xinkun Ren
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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12
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A comparison of steroid and lipid binding cytochrome P450s from Mycobacterium marinum and Mycobacterium tuberculosis. J Inorg Biochem 2020; 209:111116. [PMID: 32473484 DOI: 10.1016/j.jinorgbio.2020.111116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 11/22/2022]
Abstract
The steroid lipid binding cytochrome P450 (CYP) enzymes of Mycobacterium tuberculosis are essential for organism survival through metabolism of cholesterol and its derivatives. The counterparts to these enzymes from Mycobacterium marinum were studied to determine the degree of functional conservation between them. Spectroscopic analyses of substrate and inhibitor binding for the four M. marinum enzymes CYP125A6, CYP125A7, CYP142A3 and CYP124A1 were performed and compared to the equivalent enzymes of M. tuberculosis. The sequence of CYP125A7 from M. marinum was more similar to CYP125A1 from M. tuberculosis than CYP125A6 but both showed differences in the resting heme spin state and in the binding modes and affinities of certain azole inhibitors. CYP125A7 did not show a significant Type II inhibitor-like shift with any of the azoles tested. CYP142A3 bound a similar range of steroids and inhibitors to CYP142A1. However, there were some differences in the extent of the Type I shifts to the high-spin form with steroids and a higher affinity for the azole inhibitors compared to CYP142A1. The two CYP124 enzymes had similar substrate binding properties. M. marinum CYP124 was characterised by X-ray crystallography and displayed strong conservation of active site residues, except near the region where the carboxylate terminus of the phytanic acid substrate would be bound. As these enzymes in M. tuberculosis have been identified as candidates for inhibition the data here demonstrates that alternative strategies for inhibitor design may be required to target CYP family members from distinct pathogenic Mycobacterium species or other bacteria.
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13
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Zuccarello L, Berthomieu C, Boussac A, Brubach JB, Díaz-Moreno I, Díaz Quintana AJ, Hienerwadel R. Protonation of the Cysteine Axial Ligand Investigated in His/Cys c-Type Cytochrome by UV-Vis and Mid- and Far-IR Spectroscopy. J Phys Chem Lett 2020; 11:4198-4205. [PMID: 32364390 DOI: 10.1021/acs.jpclett.0c01016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
His/Cys coordination was recently found in several c-type cytochromes, which could act as sensors, in electron transport or in regulation. Toward a better understanding of Cys function and reactivity in these cytochromes, we compare cytochrome c6 (c6wt) from the cyanobacterium Nostoc PCC 7120 with its Met58Cys mutant. We probe the axial ligands and heme properties by combining visible and mid- to far-FTIR difference spectroscopies. Cys58 determines the strong negative redox potential and pH dependence of M58C (EmM58C = -375 mV, versus Emc6wt = +339 mV). Mid-IR (notably Cys ν(SH), His ν(C5N1), heme δ(CmH)) and far-IR (ν(Fe(II)-His), ν(His-Fe(III)-Cys)) markers of the heme and ligands show that Cys58 remains a strong thiolate ligand of reduced Met58Cys at alkaline pH, while it is protonated at pH 7.5, is stabilized by a strong hydrogen bonding interaction, and weakly interacts with Fe(II). These data provide a benchmark for further analysis of c-type cytochromes with natural His/Cys coordination.
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Affiliation(s)
- Lidia Zuccarello
- CEA, CNRS, Aix Marseille Univ., BIAM, Interactions Protéine Métal UMR 7265, 13108 Saint Paul-Lez-Durance, France
- Aix Marseille Univ., CEA, CNRS, BIAM, Luminy Genetics and Biophysic of Plants, UMR 7265, 13288 Marseille Cedex, France
| | - Catherine Berthomieu
- CEA, CNRS, Aix Marseille Univ., BIAM, Interactions Protéine Métal UMR 7265, 13108 Saint Paul-Lez-Durance, France
| | - Alain Boussac
- I2BC, UMR CNRS 9198, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Jean-Blaise Brubach
- Synchrotron SOLEIL, AILES Beamline, L'Orme des Merisier, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex, France
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Antonio J Díaz Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, Sevilla 41092, Spain
| | - Rainer Hienerwadel
- Aix Marseille Univ., CEA, CNRS, BIAM, Luminy Genetics and Biophysic of Plants, UMR 7265, 13288 Marseille Cedex, France
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14
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Akram M, Reimann J, Dietl A, Menzel A, Versantvoort W, Kartal B, Jetten MSM, Barends TRM. A nitric oxide-binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase. J Biol Chem 2019; 294:16712-16728. [PMID: 31548310 DOI: 10.1074/jbc.ra119.008788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/17/2019] [Indexed: 01/17/2023] Open
Abstract
Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.
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Affiliation(s)
- Mohd Akram
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen 6525AJ, The Netherlands
| | - Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Andreas Menzel
- Coherent X-ray Scattering Group, Paul Scherrer Institute, WLGA/223, Villigen 5232, Switzerland
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen 6525AJ, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen 6525AJ, The Netherlands
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
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15
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Lau ICK, Feyereisen R, Nelson DR, Bell SG. Analysis and preliminary characterisation of the cytochrome P450 monooxygenases from Frankia sp. EuI1c (Frankia inefficax sp.). Arch Biochem Biophys 2019; 669:11-21. [PMID: 31082352 DOI: 10.1016/j.abb.2019.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Frankia bacteria are nitrogen fixing species from the Actinobacterium phylum which live on the root nodules of plants. They have been hypothesised to have significant potential for natural product biosynthesis. The cytochrome P450 monooxygenase complement of Frankia sp. EuI1c (Frankia inefficax sp.), which comprises 68 members, was analysed. Several members belonged to previously uncharacterised bacterial P450 families. There was an unusually high number of CYP189 family members (21) suggesting that this family has undergone gene duplication events which are classified as "blooms". The likely electron transfer partners for the P450 enzymes were also identified and analysed. These consisted of predominantly [3Fe-4S] cluster containing ferredoxins (eight), a single [2Fe-2S] ferredoxin and a couple of ferredoxin reductases. Three of these CYP family members were produced and purified, using Escherichia coli as a host, and their substrate range was characterised. CYP1027H1 and CYP150A20 bound a broad range of norisoprenoids and terpenoids. CYP1074A2 was highly specific for certain steroids including testosterone, progesterone, stanolone and 4-androstene-3,17-dione. It is likely that steroids are the physiological substrates of CYP1074A2. These results also give an indication that terpenoids are the likely substrates of CYP1027H1 and CYP150A2. The large number of P450s belonging to distinct families as well as the associated electron transfer partners found in different Frankia strains highlights the importance of this family of enzymes has in the secondary metabolism of these bacteria.
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Affiliation(s)
- Ian C K Lau
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - René Feyereisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David R Nelson
- University of Tennessee Health Science Center, Dept. of Microbiology, Immunology and Biochemistry, 858 Madison Ave. Suite G01, Memphis, TN, 38163, USA
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia.
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16
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Picciano AL, Crane BR. A nitric oxide synthase-like protein from Synechococcus produces NO/NO 3- from l-arginine and NADPH in a tetrahydrobiopterin- and Ca 2+-dependent manner. J Biol Chem 2019; 294:10708-10719. [PMID: 31113865 PMCID: PMC6615690 DOI: 10.1074/jbc.ra119.008399] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/17/2019] [Indexed: 01/01/2023] Open
Abstract
Nitric oxide synthases (NOSs) are heme-based monooxygenases that convert l-Arg to l-citrulline and nitric oxide (NO), a key signaling molecule and cytotoxic agent in mammals. Bacteria also contain NOS proteins, but the role of NO production within these organisms, where understood, differs considerably from that of mammals. For example, a NOS protein in the marine cyanobacterium Synechococcus sp. PCC 7335 (syNOS) has recently been proposed to function in nitrogen assimilation from l-Arg. syNOS retains the oxygenase (NOSox) and reductase (NOSred) domains present in mammalian NOS enzymes (mNOSs), but also contains an N-terminal globin domain (NOSg) homologous to bacterial flavohemoglobin proteins. Herein, we show that syNOS functions as a dimer and produces NO from l-Arg and NADPH in a tetrahydrobiopterin (H4B)-dependent manner at levels similar to those produced by other NOSs but does not require Ca2+-calmodulin, which regulates NOSred-mediated NOSox reduction in mNOSs. Unlike other bacterial NOSs, syNOS cannot function with tetrahydrofolate and requires high Ca2+ levels (>200 μm) for its activation. NOSg converts NO to NO3- in the presence of O2 and NADPH; however, NOSg did not protect Escherichia coli strains against nitrosative stress, even in a mutant devoid of NO-protective flavohemoglobin. We also found that syNOS does not have NOS activity in E. coli (which lacks H4B) and that the recombinant protein does not confer growth advantages on l-Arg as a nitrogen source. Our findings indicate that syNOS has both NOS and NO oxygenase activities, requires H4B, and may play a role in Ca2+-mediated signaling.
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Affiliation(s)
- Angela L Picciano
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Brian R Crane
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
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17
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Horn M, Nienhaus K, Nienhaus GU. Kinetic Study of Ligand Binding and Conformational Changes in Inducible Nitric Oxide Synthase. J Phys Chem B 2018; 122:11048-11057. [PMID: 29965771 DOI: 10.1021/acs.jpcb.8b05137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nitric oxide synthases (NOSs) are heme enzymes that generate highly reactive nitric oxide from l-arginine (l-Arg) in a complex mechanism that is still only partially understood. We have studied carbon monoxide (CO) binding to the oxygenase domain of murine inducible NOS (iNOS) by using flash photolysis. The P420 and P450 forms of the enzyme, assigned to a protonated and unprotonated proximal cysteine, through which the heme is anchored to the protein, show markedly different CO rebinding properties. The data suggest that P420 has a widely open distal pocket that admits water. CO rebinding to the P450 form strongly depends on the presence of the substrate l-Arg, the intermediate Nω-hydroxy-l-arginine, and the cofactor tetrahydrobiopterin. After adding these small molecules to the enzyme solution, the CO kinetics change slowly over the hours. This process can be described as a relaxation from a fast rebinding, metastable species to a slowly rebinding, thermodynamically stable species, which we associate with the enzymatically active form. Our results allow us to determine kinetic parameters of l-Arg binding to the ferrous deoxy iNOS protein for the first time and also provide clues regarding the nature of structural differences between the two interconverting species.
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Affiliation(s)
- Michael Horn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
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18
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Yadav R, Scott EE. Endogenous insertion of non-native metalloporphyrins into human membrane cytochrome P450 enzymes. J Biol Chem 2018; 293:16623-16634. [PMID: 30217815 DOI: 10.1074/jbc.ra118.005417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/13/2018] [Indexed: 11/06/2022] Open
Abstract
Human cytochrome P450 enzymes are membrane-bound heme-containing monooxygenases. As is the case for many heme-containing enzymes, substitution of the metal in the center of the heme can be useful for mechanistic and structural studies of P450 enzymes. For many heme proteins, the iron protoporphyrin prosthetic group can be extracted and replaced with protoporphyrin containing another metal, but human membrane P450 enzymes are not stable enough for this approach. The method reported herein was developed to endogenously produce human membrane P450 proteins with a nonnative metal in the heme. This approach involved coexpression of the P450 of interest, a heme uptake system, and a chaperone in Escherichia coli growing in iron-depleted minimal medium supplemented with the desired trans-metallated protoporphyrin. Using the steroidogenic P450 enzymes CYP17A1 and CYP21A2 and the drug-metabolizing CYP3A4, we demonstrate that this approach can be used with several human P450 enzymes and several different metals, resulting in fully folded proteins appropriate for mechanistic, functional, and structural studies including solution NMR.
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Affiliation(s)
- Rahul Yadav
- From the Departments of Medicinal Chemistry and
| | - Emily E Scott
- From the Departments of Medicinal Chemistry and .,Pharmacology, University of Michigan, Ann Arbor, Michigan 48109
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19
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Spectroscopic evidence supporting neutral thiol ligation to ferrous heme iron. J Biol Inorg Chem 2018; 23:1085-1092. [DOI: 10.1007/s00775-018-1611-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
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20
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Kinetic mechanism of time-dependent inhibition of CYP2D6 by 3,4-methylenedioxymethamphetamine (MDMA): Functional heterogeneity of the enzyme and the reversibility of its inactivation. Biochem Pharmacol 2018; 156:86-98. [PMID: 30114388 DOI: 10.1016/j.bcp.2018.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/08/2018] [Indexed: 12/16/2022]
Abstract
We investigate the mechanism of time-dependent inhibition (TDI) of human cytochrome P450 2D6 (CYP2D6) by 3,4-methylenedioxymethamphetamine (MDMA, ecstasy), one of the most widespread recreational drugs of abuse. In an effort to unravel the kinetic mechanism of the formation of metabolic inhibitory complex (MIC) of CYP2D6 with MDMA-derived carbene we carried out a series of spectrophotometric studies paralleled with registration of the kinetics of time-dependent inhibition (TDI) in CYP2D6-incorporated proteoliposomes. The high amplitude of spectral signal in this system allowed us to characterize the spectral properties of the formed MIC in details and obtain an accurate spectral signature of MIC formation. This information was then used in the studies with CYP2D6-containing microsomes of insect cells (CYP2D6 Supersomes™). Our results demonstrate that in both systems the formation of the ferrous carbene-derived MIC is relatively slow, reversible and is not associated with the accumulation of the ferric carbene intermediate, as takes place in the case of CYP3A4 and podophylotoxin. Furthermore, the limited amplitude of MIC formation suggests that only a fraction (∼50%) of spectrally detectable CYP2D6 in both proteoliposomes and Supersomes participates in the formation of MIC and is therefore involved in the MDMA metabolism. This observation reveals yet another example of a cytochrome P450 that exhibits persistent functional heterogeneity of its population in microsomal membranes. Our study provides a solid methodological background for further mechanistic studies of MIC formation in human liver microsomes and demonstrates that the potency and physiological relevance of MDMA-dependent TDI of CYP2D6 may be overestimated.
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21
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Structure and function of the cytochrome P450 peroxygenase enzymes. Biochem Soc Trans 2018; 46:183-196. [PMID: 29432141 PMCID: PMC5818669 DOI: 10.1042/bst20170218] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/12/2017] [Accepted: 12/18/2017] [Indexed: 11/17/2022]
Abstract
The cytochromes P450 (P450s or CYPs) constitute a large heme enzyme superfamily, members of which catalyze the oxidative transformation of a wide range of organic substrates, and whose functions are crucial to xenobiotic metabolism and steroid transformation in humans and other organisms. The P450 peroxygenases are a subgroup of the P450s that have evolved in microbes to catalyze the oxidative metabolism of fatty acids, using hydrogen peroxide as an oxidant rather than NAD(P)H-driven redox partner systems typical of the vast majority of other characterized P450 enzymes. Early members of the peroxygenase (CYP152) family were shown to catalyze hydroxylation at the α and β carbons of medium-to-long-chain fatty acids. However, more recent studies on other CYP152 family P450s revealed the ability to oxidatively decarboxylate fatty acids, generating terminal alkenes with potential applications as drop-in biofuels. Other research has revealed their capacity to decarboxylate and to desaturate hydroxylated fatty acids to form novel products. Structural data have revealed a common active site motif for the binding of the substrate carboxylate group in the peroxygenases, and mechanistic and transient kinetic analyses have demonstrated the formation of reactive iron-oxo species (compounds I and II) that are ultimately responsible for hydroxylation and decarboxylation of fatty acids, respectively. This short review will focus on the biochemical properties of the P450 peroxygenases and on their biotechnological applications with respect to production of volatile alkenes as biofuels, as well as other fine chemicals.
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22
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Yan JA, Chen YS, Chang YH, Tsai CY, Lyu CL, Luo CG, Lee GH, Hsu HF. Redox Interconversion of Non-Oxido Vanadium Complexes Accompanied by Acid–Base Chemistry of Thiol and Thiolate. Inorg Chem 2017; 56:9055-9063. [DOI: 10.1021/acs.inorgchem.7b01040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jyun-An Yan
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Yu-Sen Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Ya-Ho Chang
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng-Yun Tsai
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Chiao-Ling Lyu
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Gang Luo
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Gene-Hsiang Lee
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hua-Fen Hsu
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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23
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Matthews S, Belcher JD, Tee KL, Girvan HM, McLean KJ, Rigby SEJ, Levy CW, Leys D, Parker DA, Blankley RT, Munro AW. Catalytic Determinants of Alkene Production by the Cytochrome P450 Peroxygenase OleT JE. J Biol Chem 2017; 292:5128-5143. [PMID: 28053093 PMCID: PMC5377825 DOI: 10.1074/jbc.m116.762336] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/03/2017] [Indexed: 12/22/2022] Open
Abstract
The Jeotgalicoccus sp. peroxygenase cytochrome P450 OleTJE (CYP152L1) is a hydrogen peroxide-driven oxidase that catalyzes oxidative decarboxylation of fatty acids, producing terminal alkenes with applications as fine chemicals and biofuels. Understanding mechanisms that favor decarboxylation over fatty acid hydroxylation in OleTJE could enable protein engineering to improve catalysis or to introduce decarboxylation activity into P450s with different substrate preferences. In this manuscript, we have focused on OleTJE active site residues Phe79, His85, and Arg245 to interrogate their roles in substrate binding and catalytic activity. His85 is a potential proton donor to reactive iron-oxo species during substrate decarboxylation. The H85Q mutant substitutes a glutamine found in several peroxygenases that favor fatty acid hydroxylation. H85Q OleTJE still favors alkene production, suggesting alternative protonation mechanisms. However, the mutant undergoes only minor substrate binding-induced heme iron spin state shift toward high spin by comparison with WT OleTJE, indicating the key role of His85 in this process. Phe79 interacts with His85, and Phe79 mutants showed diminished affinity for shorter chain (C10–C16) fatty acids and weak substrate-induced high spin conversion. F79A OleTJE is least affected in substrate oxidation, whereas the F79W/Y mutants exhibit lower stability and cysteine thiolate protonation on reduction. Finally, Arg245 is crucial for binding the substrate carboxylate, and R245E/L mutations severely compromise activity and heme content, although alkene products are formed from some substrates, including stearic acid (C18:0). The results identify crucial roles for the active site amino acid trio in determining OleTJE catalytic efficiency in alkene production and in regulating protein stability, heme iron coordination, and spin state.
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Affiliation(s)
- Sarah Matthews
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - James D Belcher
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Kang Lan Tee
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Hazel M Girvan
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Kirsty J McLean
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Stephen E J Rigby
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Colin W Levy
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David A Parker
- the Westhollow Technology Center, Houston, Texas 77028-3101, and
| | | | - Andrew W Munro
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom,
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24
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Xu H, Ning L, Yang W, Fang B, Wang C, Wang Y, Xu J, Collin S, Laeuffer F, Fourage L, Li S. In vitro oxidative decarboxylation of free fatty acids to terminal alkenes by two new P450 peroxygenases. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:208. [PMID: 28912830 PMCID: PMC5588734 DOI: 10.1186/s13068-017-0894-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/28/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND P450 fatty acid decarboxylases represented by the unusual CYP152 peroxygenase family member OleTJE have been receiving great attention recently since these P450 enzymes are able to catalyze the simple and direct production of 1-alkenes for potential applications in biofuels and biomaterials. To gain more mechanistic insights, broader substrate spectra, and improved decarboxylative activities, it is demanded to discover and investigate more P450 fatty acid decarboxylases. RESULTS Here, we describe for the first time the expression, purification, and in vitro biochemical characterization of two new CYP152 peroxygenases, CYP-Aa162 and CYP-Sm46Δ29, that are capable of decarboxylating straight-chain saturated fatty acids. Both enzymes were found to catalyze the decarboxylation and hydroxylation of a broad range of free fatty acids (C10-C20) with overlapping substrate specificity, yet distinct chemoselectivity. CYP-Sm46Δ29 works primarily as a fatty (lauric) acid decarboxylase (66.1 ± 3.9% 1-undecene production) while CYP-Aa162 more as a fatty (lauric) acid hydroxylase (72.2 ± 0.9% hydroxy lauric acid production). Notably, the optical spectroscopic analysis of functional CYP-Sm46Δ29 revealed no characteristic P450 band, suggesting a unique heme coordination environment. Active-site mutagenesis analysis showed that substitution with the proposed key decarboxylation-modulating residues, His85 and Ile170, enhanced the decarboxylation activity of CYP-Aa162 and P450BSβ, emphasizing the importance of these residues in directing the decarboxylation pathway. Furthermore, the steady-state kinetic analysis of CYP-Aa162 and CYP-Sm46Δ29 revealed both cooperative and substrate inhibition behaviors which are substrate carbon chain length dependent. CONCLUSIONS Our data identify CYP-Sm46Δ29 as an efficient OleTJE-like fatty acid decarboxylase. Oxidative decarboxylation chemoselectivity of the CYP152 decarboxylases is largely dependent upon the carbon chain length of fatty acid substrates and their precise positioning in the enzyme active site. Finally, the kinetic mode analysis of the enzymes could provide important guidance for future process design.
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Affiliation(s)
- Huifang Xu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Linlin Ning
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenxia Yang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Bo Fang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Cong Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Yun Wang
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Jian Xu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
| | - Severine Collin
- Total Refinery and Chemistry, SDR/Biofuels, Tour Coupole, 2, PI. Jean Millier, 92400 Courbevoie, France
| | - Frederic Laeuffer
- Total Refinery and Chemistry, SDR/Biofuels, Tour Coupole, 2, PI. Jean Millier, 92400 Courbevoie, France
| | - Laurent Fourage
- Total Refinery and Chemistry, SDR/Biofuels, Tour Coupole, 2, PI. Jean Millier, 92400 Courbevoie, France
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 Shandong China
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25
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Ye H, Yang Z, Li H, Gao Z. NPY binds with heme to form a NPY–heme complex: enhancing peroxidase activity in free heme and promoting NPY nitration and inactivation. Dalton Trans 2017; 46:10315-10323. [DOI: 10.1039/c7dt01822c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NPY binding with heme enhances the peroxidase activity of free heme, resulting in the important tyrosine nitration, which will attenuate its bioactivity.
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Affiliation(s)
- Huixian Ye
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
- People's Republic of China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
| | - Zhen Yang
- Department of Chemical and Biomolecular Engineering
- University of Houston
- Houston
- USA
| | - Hailing Li
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
- People's Republic of China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
| | - Zhonghong Gao
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
- People's Republic of China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
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26
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Lee C, Lee SY. Hemin-bound cysteinyl bolaamphiphile self-assembly as a horseradish peroxidase-mimetic catalyst. RSC Adv 2017. [DOI: 10.1039/c7ra06547g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
A horseradish peroxidase (HRP) mimetic catalyst was constructed by tethering hemin to the cysteinyl bolaamphiphile assembly through thiol–Fe bond. The prepared catalyst showed high catalytic activity comparable to HRP even at the high temperature.
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Affiliation(s)
- Chaemyeong Lee
- Department of Chemical and Biomolecular Engineering
- Yonsei University
- Seoul
- South Korea
| | - Sang-Yup Lee
- Department of Chemical and Biomolecular Engineering
- Yonsei University
- Seoul
- South Korea
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27
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Rodriguez KJ, Hanlon AM, Lyon CK, Cole JP, Tuten BT, Tooley CA, Berda EB, Pazicni S. Porphyrin-Cored Polymer Nanoparticles: Macromolecular Models for Heme Iron Coordination. Inorg Chem 2016; 55:9493-9496. [DOI: 10.1021/acs.inorgchem.6b01113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Kyle J. Rodriguez
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Ashley M. Hanlon
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Christopher K. Lyon
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Justin P. Cole
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Bryan T. Tuten
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Christian A. Tooley
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Erik B. Berda
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Samuel Pazicni
- Department of Chemistry and ‡Materials Science
Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
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28
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Girvan HM, Bradley JM, Cheesman MR, Kincaid JR, Liu Y, Czarnecki K, Fisher K, Leys D, Rigby SEJ, Munro AW. Analysis of Heme Iron Coordination in DGCR8: The Heme-Binding Component of the Microprocessor Complex. Biochemistry 2016; 55:5073-83. [DOI: 10.1021/acs.biochem.6b00204] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hazel M. Girvan
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Justin M. Bradley
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Myles R. Cheesman
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - James R. Kincaid
- Department
of Chemistry, Marquette University, 535 North 14th Street, Milwaukee, Wisconsin 53233, United States
| | - Yilin Liu
- Department
of Chemistry, Marquette University, 535 North 14th Street, Milwaukee, Wisconsin 53233, United States
| | - Kazimierz Czarnecki
- Department
of Chemistry, Marquette University, 535 North 14th Street, Milwaukee, Wisconsin 53233, United States
| | - Karl Fisher
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - David Leys
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Stephen E. J. Rigby
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Andrew W. Munro
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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29
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Morozov AN, Pardillo AD, Chatfield DC. Chloroperoxidase-Catalyzed Epoxidation of Cis-β-Methylstyrene: NH-S Hydrogen Bonds and Proximal Helix Dipole Change the Catalytic Mechanism and Significantly Lower the Reaction Barrier. J Phys Chem B 2015; 119:14350-63. [PMID: 26452587 DOI: 10.1021/acs.jpcb.5b06731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH-S) is a conserved feature of heme-thiolate enzymes such as chloroperoxidase (CPO) and cytochrome P450 (P450). In CPO, the effect of NH-S bonds is amplified by the dipole moment of the proximal helix. Our gas-phase DFT studies show that the proximal pocket effect significantly enhances CPO's reactivity toward the epoxidation of olefinic substrates. Comparison of models with and without proximal pocket residues shows that with them, the barrier for Cβ-O bond formation is lowered by about ∼4.6 kcal/mol, while Cα-O-Cβ ring closure becomes barrierless. The dipole moment of the proximal helix was estimated to contribute 1/3 of the decrease, while the rest is attributed to the effect of NH-S bonds. The decrease of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket. The effect is most pronounced on the doublet spin surface and involves a change in the electron-transfer mechanism. A full enzyme QMMM study on the doublet spin surface gives about the same barrier as the gas-phase DFT study. The free-energy barrier was estimated to be in agreement with the experimental results for the CPO-catalyzed epoxidation of styrene.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - Armando D Pardillo
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
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30
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Smith AT, Pazicni S, Marvin KA, Stevens DJ, Paulsen KM, Burstyn JN. Functional divergence of heme-thiolate proteins: a classification based on spectroscopic attributes. Chem Rev 2015; 115:2532-58. [PMID: 25763468 DOI: 10.1021/cr500056m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron T Smith
- †Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208, United States
| | - Samuel Pazicni
- ‡Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Katherine A Marvin
- §Department of Chemistry, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032, United States
| | - Daniel J Stevens
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Katherine M Paulsen
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Judith N Burstyn
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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31
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Khatri Y, Hannemann F, Girhard M, Kappl R, Hutter M, Urlacher VB, Bernhardt R. A natural heme-signature variant of CYP267A1 fromSorangium cellulosumSo ce56 executes diverse ω-hydroxylation. FEBS J 2014; 282:74-88. [DOI: 10.1111/febs.13104] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/30/2014] [Accepted: 10/06/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Yogan Khatri
- Department of Biochemistry; Saarland University; Saarbrücken Germany
| | - Frank Hannemann
- Department of Biochemistry; Saarland University; Saarbrücken Germany
| | - Marco Girhard
- Institute of Biochemistry; Heinrich-Heine-Universität Düsseldorf; Germany
| | - Reinhard Kappl
- Department of Biophysics; Saarland University; Homburg Germany
| | - Michael Hutter
- Center for Bioinformatics; Saarland University; Saarbrücken Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry; Heinrich-Heine-Universität Düsseldorf; Germany
| | - Rita Bernhardt
- Department of Biochemistry; Saarland University; Saarbrücken Germany
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32
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Berryman VEJ, Baker MG, Boyd RJ. Effect of Amino Acid Ligands on the Structure of Iron Porphyrins and Their Ability to Bind Oxygen. J Phys Chem A 2014; 118:4565-74. [DOI: 10.1021/jp502541y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Matthew G. Baker
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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33
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Human P450-like oxidation of diverse proton pump inhibitor drugs by ‘gatekeeper’ mutants of flavocytochrome P450 BM3. Biochem J 2014; 460:247-59. [DOI: 10.1042/bj20140030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structurally destabilizing and conformation altering ‘gatekeeper’ mutants of the biotechnologically important flavocytochrome P450 BM3 mono-oxygenase were shown to catalyse oxidation of several proton pump inhibitor drugs, and to generate products identical to those formed by major human drug metabolizing P450s.
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34
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Carter EL, Ragsdale SW. Modulation of nuclear receptor function by cellular redox poise. J Inorg Biochem 2014; 133:92-103. [PMID: 24495544 DOI: 10.1016/j.jinorgbio.2014.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/28/2013] [Accepted: 01/09/2014] [Indexed: 02/09/2023]
Abstract
Nuclear receptors (NRs) are ligand-responsive transcription factors involved in diverse cellular processes ranging from metabolism to circadian rhythms. This review focuses on NRs that contain redox-active thiol groups, a common feature within the superfamily. We will begin by describing NRs, how they regulate various cellular processes and how binding ligands, corepressors and/or coactivators modulate their activity. We will then describe the general area of redox regulation, especially as it pertains to thiol-disulfide interconversion and the cellular systems that respond to and govern this redox equilibrium. Lastly, we will discuss specific examples of NRs whose activities are regulated by redox-active thiols. Glucocorticoid, estrogen, and the heme-responsive receptor, Rev-erb, will be described in the most detail as they exhibit archetypal redox regulatory mechanisms.
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Affiliation(s)
- Eric L Carter
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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35
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Redox-dependent stability, protonation, and reactivity of cysteine-bound heme proteins. Proc Natl Acad Sci U S A 2014; 111:E306-15. [PMID: 24398520 DOI: 10.1073/pnas.1317173111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cysteine-bound hemes are key components of many enzymes and biological sensors. Protonation (deprotonation) of the Cys ligand often accompanies redox transformations of these centers. To characterize these phenomena, we have engineered a series of Thr78Cys/Lys79Gly/Met80X mutants of yeast cytochrome c (cyt c) in which Cys78 becomes one of the axial ligands to the heme. At neutral pH, the protonation state of the coordinated Cys differs for the ferric and ferrous heme species, with Cys binding as a thiolate and a thiol, respectively. Analysis of redox-dependent stability and alkaline transitions of these model proteins, as well as comparisons to Cys binding studies with the minimalist heme peptide microperoxidase-8, demonstrate that the protein scaffold and solvent interactions play important roles in stabilizing a particular Cys-heme coordination. The increased stability of ferric thiolate compared with ferrous thiol arises mainly from entropic factors. This robust cyt c model system provides access to all four forms of Cys-bound heme, including the ferric thiol. Protein motions control the rates of heme redox reactions, and these effects are amplified at low pH, where the proteins are less stable. Thermodynamic signatures and redox reactivity of the model Cys-bound hemes highlight the critical role of the protein scaffold and its dynamics in modulating redox-linked transitions between thiols and thiolates.
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36
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Sun Y, Zeng W, Benabbas A, Ye X, Denisov I, Sligar SG, Du J, Dawson JH, Champion PM. Investigations of heme ligation and ligand switching in cytochromes p450 and p420. Biochemistry 2013; 52:5941-51. [PMID: 23905516 DOI: 10.1021/bi400541v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
It is generally accepted that the inactive P420 form of cytochrome P450 (CYP) involves the protonation of the native cysteine thiolate to form a neutral thiol heme ligand. On the other hand, it has also been suggested that recruitment of a histidine to replace the native cysteine thiolate ligand might underlie the P450 → P420 transition. Here, we discuss resonance Raman investigations of the H93G myoglobin (Mb) mutant in the presence of tetrahydrothiophene (THT) or cyclopentathiol (CPSH), and on pressure-induced cytochrome P420cam (CYP101), that show a histidine becomes the heme ligand upon CO binding. The Raman mode near 220 cm⁻¹, normally associated with the Fe-histidine vibration in heme proteins, is not observed in either reduced P420cam or the reduced H93G Mb samples, indicating that histidine is not the ligand in the reduced state. The absence of a mode near 220 cm⁻¹ is also inconsistent with a generalization of the suggestion that the 221 cm⁻¹ Raman mode, observed in the P420-CO photoproduct of inducible nitric oxide synthase (iNOS), arises from a thiol-bound ferrous heme. This leads us to assign the 218 cm⁻¹ mode observed in the 10 ns P420cam-CO photoproduct Raman spectrum to a Fe-histidine vibration, in analogy to many other histidine-bound heme systems. Additionally, the inverse correlation plots of the νFe-His and νCO frequencies for the CO adducts of P420cam and the H93G analogs provide supporting evidence that histidine is the heme ligand in the P420-CO-bound state. We conclude that, when CO binds to the ferrous P420 state, a histidine ligand is recruited as the heme ligand. The common existence of an HXC-Fe motif in many CYP systems allows the C → H ligand switch to occur with only minor conformational changes. One suggested conformation of P420-CO involves the addition of another turn in the proximal L helix so that, when the protonated Cys ligand is dissociated from the heme, it can become part of the helix, and the heme is ligated by the His residue from the adjoining loop region. In other systems, such as iNOS and CYP3A4 (where the HXC-Fe motif is not found), a somewhat larger conformational change would be necessary to recuit a nearby histidine.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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37
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Butler CF, Peet C, Mason AE, Voice MW, Leys D, Munro AW. Key mutations alter the cytochrome P450 BM3 conformational landscape and remove inherent substrate bias. J Biol Chem 2013; 288:25387-25399. [PMID: 23828198 DOI: 10.1074/jbc.m113.479717] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s) have enormous potential in the production of oxychemicals, due to their unparalleled regio- and stereoselectivity. The Bacillus megaterium P450 BM3 enzyme is a key model system, with several mutants (many distant from the active site) reported to alter substrate selectivity. It has the highest reported monooxygenase activity of the P450 enzymes, and this catalytic efficiency has inspired protein engineering to enable its exploitation for biotechnologically relevant oxidations with structurally diverse substrates. However, a structural rationale is lacking to explain how these mutations have such effects in the absence of direct change to the active site architecture. Here, we provide the first crystal structures of BM3 mutants in complex with a human drug substrate, the proton pump inhibitor omeprazole. Supported by solution data, these structures reveal how mutation alters the conformational landscape and decreases the free energy barrier for transition to the substrate-bound state. Our data point to the importance of such "gatekeeper" mutations in enabling major changes in substrate recognition. We further demonstrate that these mutants catalyze the same 5-hydroxylation reaction as performed by human CYP2C19, the major human omeprazole-metabolizing P450 enzyme.
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Affiliation(s)
- Christopher F Butler
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Caroline Peet
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - Amy E Mason
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and
| | - Andrew W Munro
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom and.
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Leal MC, Magnani N, Villordo S, Buslje CM, Evelson P, Castaño EM, Morelli L. Transcriptional regulation of insulin-degrading enzyme modulates mitochondrial amyloid β (Aβ) peptide catabolism and functionality. J Biol Chem 2013; 288:12920-31. [PMID: 23525105 DOI: 10.1074/jbc.m112.424820] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Studies of post-mortem brains from Alzheimer disease patients suggest that oxidative damage induced by mitochondrial amyloid β (mitAβ) accumulation is associated with mitochondrial dysfunction. However, the regulation of mitAβ metabolism is unknown. One of the proteases involved in mitAβ catabolism is the long insulin-degrading enzyme (IDE) isoform (IDE-Met(1)). However, the mechanisms of its expression are unknown, and its presence in brain is uncertain. We detected IDE-Met(1) in brain and showed that its expression is regulated by the mitochondrial biogenesis pathway (PGC-1α/NRF-1). A strong positive correlation between PGC-1α or NRF-1 and long IDE isoform transcripts was found in non-demented brains. This correlation was weaker in Alzheimer disease. In vitro inhibition of IDE increased mitAβ and impaired mitochondrial respiration. These changes were restored by inhibition of γ-secretase or promotion of mitochondrial biogenesis. Our results suggest that IDE-Met(1) links the mitochondrial biogenesis pathway with mitAβ levels and organelle functionality.
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Affiliation(s)
- María C Leal
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)), Avenida Patricias Argentinas 435, Ciudad Autónoma de Buenos Aires C1405BWE, Argentina
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Mono- and bis-phosphine-ligated H93G myoglobin: spectral models for ferrous-phosphine and ferrous-CO cytochrome P450. J Inorg Biochem 2013; 127:238-45. [PMID: 23639797 DOI: 10.1016/j.jinorgbio.2013.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/13/2013] [Accepted: 03/13/2013] [Indexed: 11/21/2022]
Abstract
To further investigate the properties of phosphines as structural and functional probes of heme proteins, mono- and bis-phosphine [tris(hydroxymethyl)phosphine, THMP] adducts of H93G myoglobin (Mb) have been prepared by stepwise THMP titrations of exogenous ligand-free ferric and ferrous H93G Mb, respectively. Bubbling with CO or stepwise titration with imidazole (Im) of the bis-THMP-ligated ferrous protein generated a mixed ligand (THMP/CO or THMP/Im, respectively) ferrous complexes. Stable oxyferrous H93G(THMP) Mb was formed at -40°C by bubbling the mono-THMP-Fe(II) protein with O2. A THMP-ligated ferryl H93G Mb moiety has been partially formed upon addition of H2O2 to the ferric mono-THMP adduct. All the species prepared above have been characterized with UV-visible (UV-vis) absorption and magnetic circular dichroism (MCD) spectroscopy in this study. The six-coordinate ferrous bis-phosphine and mono-phosphine/CO complexes of H93G Mb exhibit characteristic spectral features (red-shifted Soret/unique-shaped MCD visible bands and hyperporphyrin spectra, respectively) that only have been seen for the analogous phosphine or CO-complexes of thiolate-ligated heme proteins such as cytochrome P450 (P450) and Caldariomyces fumago chloroperoxidase (CPO). However, such resemblance is not seen in phosphine-ligated ferric H93G Mb even though phosphine-bound ferric P450 and CPO display hyperporphyrin spectra. In fact, bis-THMP-bound ferric H93G Mb exhibits MCD and UV-vis absorption spectra that are similar to those of bis-amine- and bis-thioether-ligated H93G Mb complexes. This study also further demonstrates the utility of the H93G cavity mutant for preparing novel heme iron coordination structures.
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40
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Munro AW, Girvan HM, Mason AE, Dunford AJ, McLean KJ. What makes a P450 tick? Trends Biochem Sci 2013; 38:140-50. [DOI: 10.1016/j.tibs.2012.11.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/15/2012] [Accepted: 11/21/2012] [Indexed: 12/31/2022]
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Weak coordination of neutral S- and O-donor proximal ligands to a ferrous porphyrin nitrosyl. Characterization of 6-coordinate complexes at low T. J Inorg Biochem 2013; 121:129-33. [PMID: 23376554 DOI: 10.1016/j.jinorgbio.2012.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/27/2012] [Accepted: 12/28/2012] [Indexed: 11/23/2022]
Abstract
The interaction of the S- and O-donor ligands tetrahydrothiophen (THT) and tetrahydrofuran (THF) with the ferrous nitrosyl complex Fe(TTP)(NO) (TTP(2-) is meso-tetra-p-tolyl-porphyrinatodianion) was studied at various temperatures both in solid state and solution using electronic and infrared absorption spectroscopy. Upon addition of these ligands to a cryostat containing sublimed layers of Fe(TTP)(NO), no complex formation was detected at room temperature. However, upon lowering the temperature, spectral changes were observed that are consistent with ligand binding in axial position trans to the NO (the proximal site) and formation of the six-coordinate adducts. Analogous behavior was observed in solution. In both media, the six-coordinate adducts are stable only at low temperature and dissociate to the 5-coordinate nitrosyl complexes upon warming. The NO stretching frequencies of the six-coordinate thioether and ether complexes were recorded and binding constants for the weak bonding of proximal THF and THT ligands were determined from the spectral changes. These parameters are compared with those obtained for the N-donor ligand pyrrolidine.
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42
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Schneider E, Clark DS. Cytochrome P450 (CYP) enzymes and the development of CYP biosensors. Biosens Bioelectron 2013; 39:1-13. [DOI: 10.1016/j.bios.2012.05.043] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/29/2012] [Accepted: 05/30/2012] [Indexed: 11/29/2022]
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Gao JL, Lu Y, Browne G, Yap BCM, Trewhella J, Hunter N, Nguyen KA. The role of heme binding by DNA-protective protein from starved cells (Dps) in the Tolerance of Porphyromonas gingivalis to heme toxicity. J Biol Chem 2012; 287:42243-58. [PMID: 23086936 DOI: 10.1074/jbc.m112.392787] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The widely expressed DNA-protective protein from starved-cells (Dps) family proteins are considered major contributors to prokaryotic resistance to stress. We show here that Porphyromonas gingivalis Dps (PgDps), previously described as an iron-storage and DNA-binding protein, also mediates heme sequestration. We determined that heme binds strongly to PgDps with an apparent K(d) of 3.7 × 10(-8) m and is coordinated by a single surface-located cysteine at the fifth axial ligand position. Heme and iron sequestered in separate sites by PgDps provide protection of DNA from H(2)O(2)-mediated free radical damage and were found to be important for growth of P. gingivalis under excess heme as the only iron source. Conservation of the heme-coordinating cysteine among Dps isoforms from the Bacteroidales order suggests that this function may be a common feature within these anaerobic bacteria.
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Affiliation(s)
- Jin-Long Gao
- University of Sydney, New South Wales 2006, Australia
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Hannibal L, Collins D, Brassard J, Chakravarti R, Vempati R, Dorlet P, Santolini J, Dawson JH, Stuehr DJ. Heme binding properties of glyceraldehyde-3-phosphate dehydrogenase. Biochemistry 2012; 51:8514-29. [PMID: 22957700 DOI: 10.1021/bi300863a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that also functions in transcriptional regulation, oxidative stress, vesicular trafficking, and apoptosis. Because GAPDH is required for the insertion of cellular heme into inducible nitric oxide synthase [Chakravarti, R., et al. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 18004-18009], we extensively characterized the heme binding properties of GAPDH. Substoichiometric amounts of ferric heme bound to GAPDH (one heme per GAPDH tetramer) to form a low-spin complex with UV-visible maxima at 362, 418, and 537 nm and when reduced to ferrous gave maxima at 424, 527, and 559 nm. Ferric heme association and dissociation rate constants at 10 °C were as follows: k(on) = 17800 M(-1) s(-1), k(off1) = 7.0 × 10(-3) s(-1), and k(off2) = 3.3 × 10(-4) s(-1) (giving approximate affinities of 19-390 nM). Ferrous heme bound more poorly to GAPDH and dissociated with a k(off) of 4.2 × 10(-3) s(-1). Magnetic circular dichroism, resonance Raman, and electron paramagnetic resonance spectroscopic data on the ferric, ferrous, and ferrous-CO complexes of GAPDH showed that the heme is bis-ligated with His as the proximal ligand. The distal ligand in the ferric complex was not displaced by CN(-) or N(3)(-) but in the ferrous complex could be displaced by CO at a rate of 1.75 s(-1) (for >0.2 mM CO). Studies with heme analogues revealed selectivity toward the coordinating metal and porphyrin ring structure. The GAPDH-heme complex was isolated from bacteria induced to express rabbit GAPDH in the presence of δ-aminolevulinic acid. Our finding of heme binding to GAPDH expands the protein's potential roles. The strength, selectivity, reversibility, and redox sensitivity of heme binding to GAPDH are consistent with it performing heme sensing or heme chaperone-like functions in cells.
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Affiliation(s)
- Luciana Hannibal
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Bradley JM, Marritt SJ, Kihlken MA, Haynes K, Hemmings AM, Berks BC, Cheesman MR, Butt JN. Redox and chemical activities of the hemes in the sulfur oxidation pathway enzyme SoxAX. J Biol Chem 2012; 287:40350-9. [PMID: 23060437 DOI: 10.1074/jbc.m112.396192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND SoxAX enzymes initiate microbial oxidation of reduced inorganic sulfur compounds. Their catalytic mechanism is unknown. RESULTS Cyanide displaces the CysS(-) ligand to the active site heme following reduction by S(2)O(4)(2-) but not Eu(II). CONCLUSION An active site heme ligand becomes labile on exposure to substrate analogs. SIGNIFICANCE Elucidation of SoxAX mechanism is necessary to understand a widespread pathway for sulfur compound oxidation. SoxAX enzymes couple disulfide bond formation to the reduction of cytochrome c in the first step of the phylogenetically widespread Sox microbial sulfur oxidation pathway. Rhodovulum sulfidophilum SoxAX contains three hemes. An electrochemical cell compatible with magnetic circular dichroism at near infrared wavelengths has been developed to resolve redox and chemical properties of the SoxAX hemes. In combination with potentiometric titrations monitored by electronic absorbance and EPR, this method defines midpoint potentials (E(m)) at pH 7.0 of approximately +210, -340, and -400 mV for the His/Met, His/Cys(-), and active site His/CysS(-)-ligated heme, respectively. Exposing SoxAX to S(2)O(4)(2-), a substrate analog with E(m) ~-450 mV, but not Eu(II) complexed with diethylene triamine pentaacetic acid (E(m) ~-1140 mV), allows cyanide to displace the cysteine persulfide (CysS(-)) ligand to the active site heme. This provides the first evidence for the dissociation of CysS(-) that has been proposed as a key event in SoxAX catalysis.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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Du J, Sono M, Dawson JH. Ferric His93Gly myoglobin cavity mutant and its complexes with thioether and selenolate as heme protein models. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424610002872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The composition of ferric exogenous ligand-free His93Gly sperm whale myoglobin (H93G Mb) at neutral pH has been determined by examination of the spectral properties of the protein over the pH range from 3.0 to 10.5. An apparent pKa value of ~6.6 has been observed for the conversion of a postulated six-coordinate bis-water-bound coordination structure at pH 5.0 to a five-coordinate hydroxide-bound form at pH 10.5. Starting from the exogenous ligand-free ferric H93G protein, ferric mono- and bis-thioether (tetrahydrothiophene, THT)-ligated adducts have been prepared and characterized by UV-visible (UV-vis) absorption and magnetic circular dichroism (MCD) spectroscopy. The mon-THT ferric H93G Mb species has hydroxide as the sixth ligand. The bis-THT derivative is a model for the low-spin ferric heme binding site of native bis-Met-ligated bacterioferritin or streptococcal heme-associated protein (Shp). A novel THT-bound ferryl H93G Mb moiety has been partially formed. The high-spin five-coordinate ferric H93G(selenolate) Mb complex has been prepared using benzeneselenol and characterized by UV-vis and MCD spectroscopy as a model for Se-Cys-ligated ferric cytochrome P450. The results described herein further demonstrate the versatility of the H93G cavity mutant for modeling the coordination structures of novel heme iron protein active sites.
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Affiliation(s)
- Jing Du
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
| | - Masanori Sono
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
- School of Medicine, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
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Warman AJ, Robinson JW, Luciakova D, Lawrence AD, Marshall KR, Warren MJ, Cheesman MR, Rigby SEJ, Munro AW, McLean KJ. Characterization of Cupriavidus metallidurans CYP116B1--a thiocarbamate herbicide oxygenating P450-phthalate dioxygenase reductase fusion protein. FEBS J 2012; 279:1675-93. [PMID: 22356105 DOI: 10.1111/j.1742-4658.2012.08543.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The novel cytochrome P450/redox partner fusion enzyme CYP116B1 from Cupriavidus metallidurans was expressed in and purified from Escherichia coli. Isolated CYP116B1 exhibited a characteristic Fe(II)CO complex with Soret maximum at 449 nm. EPR and resonance Raman analyses indicated low-spin, cysteinate-coordinated ferric haem iron at both 10 K and ambient temperature, respectively, for oxidized CYP116B1. The EPR of reduced CYP116B1 demonstrated stoichiometric binding of a 2Fe-2S cluster in the reductase domain. FMN binding in the reductase domain was confirmed by flavin fluorescence studies. Steady-state reduction of cytochrome c and ferricyanide were supported by both NADPH/NADH, with NADPH used more efficiently (K(m[NADPH]) = 0.9 ± 0.5 μM and K(m[NADH]) = 399.1 ± 52.1 μM). Stopped-flow studies of NAD(P)H-dependent electron transfer to the reductase confirmed the preference for NADPH. The reduction potential of the P450 haem iron was -301 ± 7 mV, with retention of haem thiolate ligation in the ferrous enzyme. Redox potentials for the 2Fe-2S and FMN cofactors were more positive than that of the haem iron. Multi-angle laser light scattering demonstrated CYP116B1 to be monomeric. Type I (substrate-like) binding of selected unsaturated fatty acids (myristoleic, palmitoleic and arachidonic acids) was shown, but these substrates were not oxidized by CYP116B1. However, CYP116B1 catalysed hydroxylation (on propyl chains) of the herbicides S-ethyl dipropylthiocarbamate (EPTC) and S-propyl dipropylthiocarbamate (vernolate), and the subsequent N-dealkylation of vernolate. CYP116B1 thus has similar thiocarbamate-oxidizing catalytic properties to Rhodoccocus erythropolis CYP116A1, a P450 involved in the oxidative degradation of EPTC.
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Affiliation(s)
- Ashley J Warman
- Department of Biochemistry, University of Leicester, Leicester, UK
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Rebouças JS, Patrick BO, James BR. Thiol, disulfide, and trisulfide complexes of Ru porphyrins: potential models for iron-sulfur bonds in heme proteins. J Am Chem Soc 2012; 134:3555-70. [PMID: 22224472 DOI: 10.1021/ja211226e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Thirty-two Ru(porp)L(2) complexes have been synthesized, where porp = the dianion of meso-tetramesitylporphyrin (TMP) or meso-tetrakis(4-methylphenyl)porphyrin (H(2)T-pMe-PP), and L = a thiol, a sulfide, a disulfide, or a trisulfide. Species studied were with RSH [R = Me, Et, (n)Pr, (i)Pr, (t)Bu, Bn (benzyl), and Ph], RSR (R = Me, Bn), RSSR (R = Me, Et, (n)Pr, Bn) and MeSS(t)Bu, and RSSSR (R = Me, Bn). All the species except two, which were the isolated Ru(T-pMe-PP)((t)BuSH)(2) and Ru(TMP)(MeSSMe)(2), were characterized in situ. The disulfide complex was characterized by X-ray analysis. (1)H NMR data for the coordinated thiols are the first reported within metalloporphyrin systems, and are especially informative because of the upfield shifts of the axial sulfur-containing ligands due to the porphyrin π-ring current effect, which is also present in the di- and trisulfide species. The disulfide in the solid state structure of Ru(TMP)(MeSSMe)(2) is η(1)(end-on) coordinated, the first example of such bonding in a nontethered, acyclic dialkyl disulfide; (1)H-(1)H EXSY NMR data in solution show that the species undergoes 1,2-S-metallotropic shifts. Stepwise formation of the bis(disulfide) complex from Ru(TMP)(MeCN)(2) in solution occurs with a cooperativity effect, resembling behavior of Fe(II)-porphyrin systems where crystal field effects dominate, but ligand trans-effects are more likely in the Ru system. The η(1)(end-on) coordination mode is also favored for the trisulfide ligand. Discussed also are the remarkable linear correlations that exist between the ring-current shielding shifts for the axial ligand C(1) protons of Ru(porp)(RS(x)R)(2) and x (the number of S atoms). The Introduction briefly reviews literature on Ru- and Fe porphyrins (including heme proteins) with sulfur-containing ligands or substrates, and relationships between our findings and this literature are discussed throughout the paper.
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Affiliation(s)
- Júlio S Rebouças
- Departamento de Química, CCEN, Universidade Federal da Paraíba, João Pessoa, PB, 58.051-900, Brazil.
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Perera R, Dawson JH. Modeling heme protein active sites with the his93gly cavity mutant of sperm whale myoglobin: complexes with nitrogen-, oxygen- and sulfur-donor proximal ligands. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424604000234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent investigations of the His93Gly (H93G) "cavity" mutant of myoglobin as a versatile scaffold for modeling heme states are described. The difference in accessibility of the two sides of the heme in H93G myoglobin makes it possible to generate mixed ligand adducts in the ferric state that are difficult to prepare with heme models in organic solvents. In addition, the protection provided to the heme by the protein environment allows for the preparation of stable oxyferrous and oxo-iron(IV) complexes at near-ambient temperatures with variable ligands trans to the normally reactive dioxygen and oxo substituents. The extensive range of possible complexes that can be generated using the H93G system is illustrated with examples involving imidazole, phenolate, benzoate, thiolate and thiol ligands bound to the proximal side of the heme iron.
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Affiliation(s)
- Roshan Perera
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
- School of Medicine, University of South Carolina, Columbia, SC 29208, USA
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Ferric, not ferrous, heme activates RNA-binding protein DGCR8 for primary microRNA processing. Proc Natl Acad Sci U S A 2012; 109:1919-24. [PMID: 22308374 DOI: 10.1073/pnas.1114514109] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The RNA-binding protein DiGeorge Critical Region 8 (DGCR8) and its partner nuclease Drosha are essential for processing of microRNA (miRNA) primary transcripts (pri-miRNAs) in animals. Previous work showed that DGCR8 forms a highly stable and active complex with ferric [Fe(III)] heme using two endogenous cysteines as axial ligands. Here we report that reduction of the heme iron to the ferrous [Fe(II)] state in DGCR8 abolishes the pri-miRNA processing activity. The reduction causes a dramatic increase in the rate of heme dissociation from DGCR8, rendering the complex labile. Electronic absorption, magnetic circular dichroism, and resonance Raman spectroscopies indicate that reduction of the heme iron is accompanied by loss of the cysteines as axial ligands. ApoDGCR8 dimers, generated through reduction and removal of the heme, show low levels of activity in pri-miRNA processing in vitro. Importantly, ferric, but not ferrous, heme restores the activity of apoDGCR8 to the level of the native ferric complex. This study demonstrates binding specificity of DGCR8 for ferric heme, provides direct biochemical evidence for ferric heme serving as an activator for miRNA maturation, and suggests that an intracellular environment increasing the availability of ferric heme may enhance the efficiency of pri-miRNA processing.
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