1
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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2
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Zhou TP, Deng WH, Wu Y, Liao RZ. QM/MM Calculations Suggested Concerted O‒O Bond Cleavage and Substrate Oxidation by Nonheme Diiron Toluene/o‐xylene Monooxygenase. Chem Asian J 2022; 17:e202200490. [DOI: 10.1002/asia.202200490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/01/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tai-Ping Zhou
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Wen-Hao Deng
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Yuzhou Wu
- Huazhong University of Science and Technology School of chemistry and chemical engineering CHINA
| | - Rong-Zhen Liao
- Huazhong University of Science and technology College of Chemistry and Chemical Engeneering Luoyulu 1037 430074 Wuhan CHINA
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3
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Zhang S, Li X, Wang Y, Yan L, Wei J, Liu Y. Computational Study of the C5-Hydroxylation Mechanism Catalyzed by the Diiron Monooxygenase PtmU3 as Part of the Platensimycin Biosynthesis. Inorg Chem 2021; 60:17783-17796. [PMID: 34762413 DOI: 10.1021/acs.inorgchem.1c02407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PtmU3 is a newly identified nonheme diiron monooxygenase, which installs a C-5 β-hydroxyl group into the C-19 CoA-ester intermediate involved in the biosynthesis of unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 possesses a noncanonical diiron active site architecture of a saturated six-coordinate iron center and lacks the μ-oxo bridge. Although the hydroxylation process is a simple reaction for nonheme mononuclear iron-dependent enzymes, how PtmU3 employs the diiron center to catalyze the H-abstraction and OH-rebound is still unknown. In particular, the electronic characteristic of diiron is also unclear. To understand the catalytic mechanism of PtmU3, we constructed two reactant models in which both the Fe1II-Fe2III-superoxo and Fe1II-Fe2IV═O are considered to trigger the H-abstraction and performed a series of quantum mechanics/molecular mechanics calculations. Our calculation results reveal that PtmU3 is a special monooxygenase, that is, both atoms of the dioxygen molecule can be incorporated into two molecules of the substrate by the successive reactions. In the first-round reaction, PtmU3 uses the Fe1II-Fe2III-superoxo to install a hydroxyl group into the substrate, generating the high-reactive Fe1II-Fe2IV═O complex. In the second-round reaction, the Fe1II-Fe2IV═O species is responsible for the hydroxylation of another molecule of the substrate. In the diiron center, Fe2 adopts the high spin state (S = 5/2) during the catalysis, whereas for Fe1, in addition to its structural role, it may also play an assistant role for Fe1 catalysis. In the two successive OH-installing steps, the H-abstraction is always the rate-liming step. E241 and D308 not only act as bridging ligands to connect two Fe ions but also take part in the electron reorganization. Owing to the high reactivity of Fe1II-Fe2IV═O compared to Fe1II-Fe2III-superoxo, besides the C5-hydroxylation, the C3- or C18-hydroxylation was also calculated to be feasible.
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Affiliation(s)
- Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
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4
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Abstract
Aerobic life is possible because the molecular structure of oxygen (O2) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperature. Nature has been able to tap this sequestered reservoir of energy with great spatial and temporal selectivity at ambient temperatures through the evolution of oxidase and oxygenase enzymes. One mechanism used by these enzymes for O2 activation has been studied in detail for the soluble form of the enzyme methane monooxygenase. These studies have revealed the step-by-step process of O2 activation and insertion into the ultimately stable C-H bond of methane. Additionally, an elegant regulatory mechanism has been defined that enlists size selection and quantum tunneling to allow methane oxidation to occur specifically in the presence of more easily oxidized substrates.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - Jason C Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
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5
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Jasniewski AJ, Que L. Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes. Chem Rev 2018; 118:2554-2592. [PMID: 29400961 PMCID: PMC5920527 DOI: 10.1021/acs.chemrev.7b00457] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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6
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Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A. A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
- IBB-National Research Council; Via Mezzocannone 16 80134 Napoli Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
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7
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Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A. A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation. Angew Chem Int Ed Engl 2017; 56:15580-15583. [DOI: 10.1002/anie.201707637] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
- IBB-National Research Council; Via Mezzocannone 16 80134 Napoli Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
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8
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Solomon EI, Park K. Structure/function correlations over binuclear non-heme iron active sites. J Biol Inorg Chem 2016; 21:575-88. [PMID: 27369780 PMCID: PMC5010389 DOI: 10.1007/s00775-016-1372-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Abstract
Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea
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9
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Sazinsky MH, Lippard SJ. Methane Monooxygenase: Functionalizing Methane at Iron and Copper. Met Ions Life Sci 2015; 15:205-56. [DOI: 10.1007/978-3-319-12415-5_6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Liang A, Lippard SJ. Component interactions and electron transfer in toluene/o-xylene monooxygenase. Biochemistry 2014; 53:7368-75. [PMID: 25402597 PMCID: PMC4255640 DOI: 10.1021/bi500892n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 10/28/2014] [Indexed: 01/19/2023]
Abstract
The multicomponent protein toluene/o-xylene monooxygenase (ToMO) activates molecular oxygen to oxidize aromatic hydrocarbons. Prior to dioxygen activation, two electrons are injected into each of two diiron(III) units of the hydroxylase, a process that involves three redox active proteins: the ToMO hydroxylase (ToMOH), Rieske protein (ToMOC), and an NADH oxidoreductase (ToMOF). In addition to these three proteins, a small regulatory protein is essential for catalysis (ToMOD). Through steady state and pre-steady state kinetics studies, we show that ToMOD attenuates electron transfer from ToMOC to ToMOH in a concentration-dependent manner. At substoichiometric concentrations, ToMOD increases the rate of turnover, which we interpret to be a consequence of opening a pathway for oxygen transport to the catalytic diiron center in ToMOH. Excess ToMOD inhibits steady state catalysis in a manner that depends on ToMOC concentration. Through rapid kinetic assays, we demonstrate that ToMOD attenuates formation of the ToMOC-ToMOH complex. These data, coupled with protein docking studies, support a competitive model in which ToMOD and ToMOC compete for the same binding site on the hydroxylase. These results are discussed in the context of other studies of additional proteins in the superfamily of bacterial multicomponent monooxygenases.
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Affiliation(s)
- Alexandria
Deliz Liang
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Acheson JF, Bailey LJ, Elsen NL, Fox BG. Structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system. Nat Commun 2014; 5:5009. [PMID: 25248368 PMCID: PMC4200526 DOI: 10.1038/ncomms6009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/18/2014] [Indexed: 12/23/2022] Open
Abstract
Productive biomolecular recognition requires exquisite control of affinity and specificity. Accordingly, nature has devised many strategies to achieve proper binding interactions. Bacterial multicomponent monooxygenases provide a fascinating example, where a diiron hydroxylase must reversibly interact with both ferredoxin and catalytic effector in order to achieve electron transfer and O2 activation during catalysis. Because these two accessory proteins have distinct structures, and because the hydroxylase-effector complex covers the entire surface closest to the hydroxylase diiron centre, how ferredoxin binds to the hydroxylase has been unclear. Here we present high-resolution structures of toluene 4-monooxygenase hydroxylase complexed with its electron transfer ferredoxin and compare them with the hydroxylase-effector structure. These structures reveal that ferredoxin or effector protein binding produce different arrangements of conserved residues and customized interfaces on the hydroxylase in order to achieve different aspects of catalysis.
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Affiliation(s)
- Justin F Acheson
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Lucas J Bailey
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Nathaniel L Elsen
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin, Biochemistry Addition, 433 Babcock Drive, Madison, Wisconsin 53706, USA
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12
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Liang AD, Wrobel AT, Lippard SJ. A flexible glutamine regulates the catalytic activity of toluene o-xylene monooxygenase. Biochemistry 2014; 53:3585-92. [PMID: 24873259 PMCID: PMC4059525 DOI: 10.1021/bi500387y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Toluene/o-xylene
monooxygenase (ToMO) is a bacterial
multicomponent monooxygenase capable of oxidizing aromatic substrates.
The carboxylate-rich diiron active site is located in the hydroxylase
component of ToMO (ToMOH), buried 12 Å from the surface of the
protein. A small, hydrophilic pore is the shortest pathway between
the diiron active site and the protein exterior. In this study of
ToMOH from Pseudomonas sp. OX1, the
functions of two residues lining this pore, N202 and Q228, were investigated
using site-directed mutagenesis. Steady-state characterization of
WT and the three mutant enzymes demonstrates that residues N202 and
Q228 are critical for turnover. Kinetic isotope effects and pH profiles
reveal that these residues govern the kinetics of water egress and
prevent quenching of activated oxygen intermediates formed at the
diiron active site. We propose that this activity arises from movement
of these residues, opening and closing the pore during catalysis,
as seen in previous X-ray crystallographic studies. In addition, N202
and Q228 are important for the interactions of the reductase and regulatory
components to ToMOH, suggesting that they bind competitively to the
hydroxylase. The role of the pore in the hydroxylase components of
other bacterial multicomponent monooxygenases within the superfamily
is discussed in light of these conclusions.
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Affiliation(s)
- Alexandria Deliz Liang
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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13
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Hosseini A, Brouk M, Lucas MF, Glaser F, Fishman A, Guallar V. Atomic picture of ligand migration in toluene 4-monooxygenase. J Phys Chem B 2014; 119:671-8. [PMID: 24798294 DOI: 10.1021/jp502509a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational modeling combined with mutational and activity assays was used to underline the substrate migration pathways in toluene 4-monooxygenase, a member of the important family of bacterial multicomponent monooxygenases (BMMs). In all structurally defined BMM hydroxylases, several hydrophobic cavities in the α-subunit map a preserved path from the protein surface to the diiron active site. Our results confirm the presence of two pathways by which different aromatic molecules can enter/escape the active site. While the substrate is observed to enter from both channels, the more hydrophilic product is withdrawn mainly from the shorter channel ending at residues D285 and E214. The long channel ends in the vicinity of S395, whose variants have been seen to affect activity and specificity. These mutational effects are clearly reproduced and rationalized by the in silico studies. Furthermore, the combined computational and experimental results highlight the importance of residue F269, which is located at the intersection of the two channels.
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Affiliation(s)
- Ali Hosseini
- Department of Life Sciences, Barcelona Supercomputing Center , Nexus II Building, 08034 Barcelona, Spain
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14
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Politis A, Stengel F, Hall Z, Hernández H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R. A mass spectrometry-based hybrid method for structural modeling of protein complexes. Nat Methods 2014; 11:403-406. [PMID: 24509631 PMCID: PMC3972104 DOI: 10.1038/nmeth.2841] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/12/2013] [Indexed: 01/22/2023]
Abstract
We describe a method that integrates data derived from different mass spectrometry (MS)-based techniques with a modeling strategy for structural characterization of protein assemblies. We encoded structural data derived from native MS, bottom-up proteomics, ion mobility-MS and chemical cross-linking MS into modeling restraints to compute the most likely structure of a protein assembly. We used the method to generate near-native models for three known structures and characterized an assembly intermediate of the proteasomal base.
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Affiliation(s)
- Argyris Politis
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Zoe Hall
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Helena Hernández
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Thomas Walzthoeni
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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15
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Affiliation(s)
- Artur Gora
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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16
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Sanchez-Ballester NM, Shrestha LK, Elsegood MRJ, Schmitt W, Ariga K, Anson CE, Hill JP, Powell AK. Ligand displacement for fixing manganese: relevance to cellular metal ion transport and synthesis of polymeric coordination complexes. Dalton Trans 2013; 42:2779-85. [DOI: 10.1039/c2dt32547k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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17
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Sousounis K, Haney CE, Cao J, Sunchu B, Tsonis PA. Conservation of the three-dimensional structure in non-homologous or unrelated proteins. Hum Genomics 2012; 6:10. [PMID: 23244440 PMCID: PMC3500211 DOI: 10.1186/1479-7364-6-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 12/12/2022] Open
Abstract
In this review, we examine examples of conservation of protein structural motifs in unrelated or non-homologous proteins. For this, we have selected three DNA-binding motifs: the histone fold, the helix-turn-helix motif, and the zinc finger, as well as the globin-like fold. We show that indeed similar structures exist in unrelated proteins, strengthening the concept that three-dimensional conservation might be more important than the primary amino acid sequence.
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18
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McCormick MS, Lippard SJ. Analysis of substrate access to active sites in bacterial multicomponent monooxygenase hydroxylases: X-ray crystal structure of xenon-pressurized phenol hydroxylase from Pseudomonas sp. OX1. Biochemistry 2011; 50:11058-69. [PMID: 22136180 PMCID: PMC3243792 DOI: 10.1021/bi201248b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In all structurally characterized bacterial multicomponent monooxygenase (BMM) hydroxylase proteins, a series of hydrophobic cavities in the α-subunit trace a conserved path from the protein exterior to the carboxylate-bridged diiron active site. This study examines these cavities as a potential route for transport of dioxygen to the active site by crystallographic characterization of a xenon-pressurized sample of the hydroxylase component of phenol hydroxylase from Pseudomonas sp. OX1. Computational analyses of the hydrophobic cavities in the hydroxylase α-subunits of phenol hydroxylase (PHH), soluble methane monooxygenase (MMOH), and toluene/o-xylene monooxygenase (ToMOH) are also presented. The results, together with previous findings from crystallographic studies of xenon-pressurized sMMO hydroxylase, clearly identify the propensity for these cavities to bind hydrophobic gas molecules in the protein interior. This proposed functional role is supported by recent stopped flow kinetic studies of ToMOH variants [Song, W. J., et al. (2011) Proc. Natl. Acad. Sci. U.S.A.108, 14795-14800]. In addition to information about the Xe sites, the structure determination revealed significantly weakened binding of regulatory protein to the hydroxylase in comparison to that in the previously reported structure of PHH, as well as the presence of a newly identified metal-binding site in the α-subunit that adopts a linear coordination environment consistent with Cu(I), and a glycerol molecule bound to Fe1 in a fashion that is unique among hydrocarbon-diiron site adducts reported to date in BMM hydroxylase structures. Finally, a comparative analysis of the α-subunit structures of PHH, MMOH, and ToMOH details proposed routes for the other three BMM substrates, the hydrocarbon, electrons, and protons, comprising cavities, channels, hydrogen-bonding networks, and pores in the structures of their α-subunits.
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Affiliation(s)
- Michael S. McCormick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA 02139
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19
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Song WJ, Gucinski G, Sazinsky MH, Lippard SJ. Tracking a defined route for O₂ migration in a dioxygen-activating diiron enzyme. Proc Natl Acad Sci U S A 2011; 108:14795-800. [PMID: 21859951 PMCID: PMC3169157 DOI: 10.1073/pnas.1106514108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/o-xylene monooxygenase hydroxylase is a dioxygen-activating enzyme. Structural analysis suggests two possible pathways for dioxygen access through the α-subunit to the diiron center: a channel or a series of hydrophobic cavities. To distinguish which is utilized as the O(2) migration pathway, the dimensions of the cavities and the channel were independently varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate constants for dioxygen access to the diiron center were derived from the formation rates of a peroxodiiron(III) intermediate, generated upon treatment of the diiron(II) enzyme with O(2). This reaction depends on the concentration of dioxygen to the first order. Altering the dimensions of the cavities, but not the channel, changed the rate of dioxygen reactivity with the enzyme. These results strongly suggest that voids comprising the cavities in toluene/o-xylene monooxygenase hydroxylase are not artifacts of protein packing/folding, but rather programmed routes for dioxygen migration through the protein matrix. Because the cavities are not fully connected into the diiron active center in the enzyme resting state, conformational changes will be required to facilitate dioxygen access to the diiron center. We propose that such temporary opening and closing of the cavities may occur in all bacterial multicomponent monooxygenases to control O(2) consumption for efficient catalysis. Our findings suggest that other gas-utilizing enzymes may employ similar structural features to effect substrate passage through a protein matrix.
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Affiliation(s)
- Woon Ju Song
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Grant Gucinski
- Department of Chemistry, Pomona College, Claremont, CA 91711
| | | | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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20
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Bochevarov AD, Li J, Song WJ, Friesner RA, Lippard SJ. Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. J Am Chem Soc 2011; 133:7384-97. [PMID: 21517016 PMCID: PMC3092846 DOI: 10.1021/ja110287y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The methane and toluene monooxygenase hydroxylases (MMOH and TMOH, respectively) have almost identical active sites, yet the physical and chemical properties of their oxygenated intermediates, designated P*, H(peroxo), Q, and Q* in MMOH and ToMOH(peroxo) in a subclass of TMOH, ToMOH, are substantially different. We review and compare the structural differences in the vicinity of the active sites of these enzymes and discuss which changes could give rise to the different behavior of H(peroxo) and Q. In particular, analysis of multiple crystal structures reveals that T213 in MMOH and the analogous T201 in TMOH, located in the immediate vicinity of the active site, have different rotatory configurations. We study the rotational energy profiles of these threonine residues with the use of molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) computational methods and put forward a hypothesis according to which T213 and T201 play an important role in the formation of different types of peroxodiiron(III) species in MMOH and ToMOH. The hypothesis is indirectly supported by the QM/MM calculations of the peroxodiiron(III) models of ToMOH and the theoretically computed Mössbauer spectra. It also helps explain the formation of two distinct peroxodiiron(III) species in the T201S mutant of ToMOH. Additionally, a role for the ToMOD regulatory protein, which is essential for intermediate formation and protein functioning in the ToMO system, is advanced. We find that the low quadrupole splitting parameter in the Mössbauer spectrum observed for a ToMOH(peroxo) intermediate can be explained by protonation of the peroxo moiety, possibly stabilized by the T201 residue. Finally, similarities between the oxygen activation mechanisms of the monooxygenases and cytochrome P450 are discussed.
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21
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Lasker K, Sali A, Wolfson HJ. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins 2011; 78:3205-11. [PMID: 20827723 DOI: 10.1002/prot.22845] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structural models of macromolecular assemblies are instrumental for gaining a mechanistic understanding of cellular processes. Determining these structures is a major challenge for experimental techniques, such as X-ray crystallography, NMR spectroscopy and electron microscopy (EM). Thus, computational modeling techniques, including molecular docking, are required. The development of most molecular docking methods has so far been focused on modeling of binary complexes. We have recently introduced the MultiFit method for modeling the structure of a multisubunit complex by simultaneously optimizing the fit of the model into an EM density map of the entire complex and the shape complementarity between interacting subunits. Here, we report algorithmic advances of the MultiFit method that result in an efficient and accurate assembly of the input subunits into their density map. The successful predictions and the increasing number of complexes being characterized by EM suggests that the CAPRI challenge could be extended to include docking-based modeling of macromolecular assemblies guided by EM.
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Affiliation(s)
- Keren Lasker
- Raymond and Beverly Sackler Faculty of Exact Sciences, Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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22
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Grishin AM, Ajamian E, Zhang L, Cygler M. Crystallization and preliminary X-ray analysis of PaaAC, the main component of the hydroxylase of the Escherichia coli phenylacetyl-coenzyme A oxygenase complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1045-9. [PMID: 20823522 DOI: 10.1107/s174430911002748x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 07/11/2010] [Indexed: 11/10/2022]
Abstract
The Escherichia coli paa operon encodes enzymes of the phenylacetic acid-utilization pathway that metabolizes phenylacetate in the form of a coenzyme A (CoA) derivative. The phenylacetyl-coenzyme A oxygenase complex, which has been postulated to contain five components designated PaaABCDE, catalyzes ring hydroxylation of phenylacetyl-CoA. The PaaAC subcomplex shows low sequence similarity to other bacterial multicomponent monooxygenases (BMMs) and forms a separate branch on the phylogenetic tree. PaaAC, which catalyzes the hydroxylation reaction, was purified and crystallized in the absence of a bound ligand as well as in complexes with CoA, 3-hydroxybutyryl-CoA, benzoyl-CoA and the true substrate phenylacetyl-CoA. Crystals of the ligand-free enzyme belonged to space group P2(1)2(1)2(1) and diffracted to 2.65 A resolution, whereas complexes with CoA and its derivatives crystallized in space group P4(1)2(1)2 and diffracted to approximately 2.0 A resolution. PaaAC represents the first crystallized BMM hydroxylase that utilizes a CoA-linked substrate.
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Affiliation(s)
- Andrey M Grishin
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
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23
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Friedle S, Lippard SJ. Synthesis, Characterization, and Oxygenation Studies of Carboxylate-Bridged Diiron(II) Complexes with Aromatic Substrates Tethered to Pyridine Ligands and the Formation of a Unique Trinuclear Complex. Eur J Inorg Chem 2009; 2009:5506-5515. [PMID: 20376288 DOI: 10.1002/ejic.200900821] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this study, diiron(II) complexes were synthesized as small molecule mimics of the reduced active sites in the hydroxylase components of bacterial multicomponent monooxygenases (BMMs). Tethered aromatic substrates were introduced in the form of 2-phenoxypyridines, incorporating hydroxy and methoxy functionalities into windmill-type diiron(II) compounds [Fe(2)(μ-O(2)CAr(R))(2)-(O(2)CAr(R))(2)(L)(2)] (1-4), where (-)O(2)CAr(R) is a sterically encumbering carboxylate, 2,6-di(4-fluorophenyl)- or 2,6-di(p-tolyl)benzoate (R = 4-FPh or Tol, respectively). The inability of 1-4 to hydroxylate the aromatic substrates was ascertained. Upon reaction with dioxygen, compounds 2 and 3 (L = 2-(m-MeOPhO)Py, 2-(p-MeOPhO)Py, respectively) decompose by a known bimolecular pathway to form mixed-valent diiron(II,III) species at low temperature. Use of 2-(pyridin-2-yloxy)phenol as the ligand L resulted in a doubly-bridged diiron complex (4) and an unprecedented phenoxide-bridged triiron(II) complex (5) under slightly modified reaction conditions.
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Affiliation(s)
- Simone Friedle
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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24
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Bailey LJ, Fox BG. Crystallographic and Catalytic Studies of the Peroxide-Shunt Reaction in a Diiron Hydroxylase. Biochemistry 2009; 48:8932-9. [DOI: 10.1021/bi901150a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucas J. Bailey
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706-1544
| | - Brian G. Fox
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706-1544
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25
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26
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Nie FM, Leibeling G, Demeshko S, Dechert S, Meyer F. Magnetostructural correlations in μ-pyrazolato-μ-acetato dinickel(II) complexes: Subtle effects of acetate tilting. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.03.101] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Bailey LJ, McCoy JG, Phillips GN, Fox BG. Structural consequences of effector protein complex formation in a diiron hydroxylase. Proc Natl Acad Sci U S A 2008; 105:19194-8. [PMID: 19033467 PMCID: PMC2614738 DOI: 10.1073/pnas.0807948105] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Indexed: 11/18/2022] Open
Abstract
Carboxylate-bridged diiron hydroxylases are multicomponent enzyme complexes responsible for the catabolism of a wide range of hydrocarbons and as such have drawn attention for their mechanism of action and potential uses in bioremediation and enzymatic synthesis. These enzyme complexes use a small molecular weight effector protein to modulate the function of the hydroxylase. However, the origin of these functional changes is poorly understood. Here, we report the structures of the biologically relevant effector protein-hydroxylase complex of toluene 4-monooxygenase in 2 redox states. The structures reveal a number of coordinated changes that occur up to 25 A from the active site and poise the diiron center for catalysis. The results provide a structural basis for the changes observed in a number of the measurable properties associated with effector protein binding. This description provides insight into the functional role of effector protein binding in all carboxylate-bridged diiron hydroxylases.
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Affiliation(s)
- Lucas J. Bailey
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
| | - Jason G. McCoy
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
| | - Brian G. Fox
- Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706-1544
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28
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Feingersch R, Shainsky J, Wood TK, Fishman A. Protein engineering of toluene monooxygenases for synthesis of chiral sulfoxides. Appl Environ Microbiol 2008; 74:1555-66. [PMID: 18192418 PMCID: PMC2258606 DOI: 10.1128/aem.01849-07] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 12/27/2007] [Indexed: 11/20/2022] Open
Abstract
Enantiopure sulfoxides are valuable asymmetric starting materials and are important chiral auxiliaries in organic synthesis. Toluene monooxygenases (TMOs) have been shown previously to catalyze regioselective hydroxylation of substituted benzenes and phenols. Here we show that TMOs are also capable of performing enantioselective oxidation reactions of aromatic sulfides. Mutagenesis of position V106 in the alpha-hydroxylase subunit of toluene ortho-monooxygenase (TOM) of Burkholderia cepacia G4 and the analogous position I100 in toluene 4-monooxygenase (T4MO) of Pseudomonas mendocina KR1 improved both rate and enantioselectivity. Variant TomA3 V106M of TOM oxidized methyl phenyl sulfide to the corresponding sulfoxide at a rate of 3.0 nmol/min/mg protein compared with 1.6 for the wild-type enzyme, and the enantiomeric excess (pro-S) increased from 51% for the wild type to 88% for this mutant. Similarly, T4MO variant TmoA I100G increased the wild-type oxidation rate by 1.7-fold, and the enantiomeric excess rose from 86% to 98% (pro-S). Both wild-type enzymes showed lower activity with methyl para-tolyl sulfide as a substrate, but the improvement in the activity and enantioselectivity of the mutants was more dramatic. For example, T4MO variant TmoA I100G oxidized methyl para-tolyl sulfide 11 times faster than the wild type did and changed the selectivity from 41% pro-R to 77% pro-S. A correlation between regioselectivity and enantioselectivity was shown for TMOs studied in this work. Using in silico homology modeling, it is shown that residue I100 in T4MO aids in steering the substrate into the active site at the end of the long entrance channel. It is further hypothesized that the main function of V106 in TOM is the proper positioning or docking of the substrate with respect to the diiron atoms. The results from this work suggest that when the substrate is not aligned correctly in the active site, the oxidation rate is decreased and enantioselectivity is impaired, resulting in products with both chiral configurations.
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Affiliation(s)
- Roi Feingersch
- Department of Biotechnology and Food Engineering and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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29
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Murray LJ, García-Serres R, McCormick MS, Davydov R, Naik S, Kim SH, Hoffman BM, Huynh BH, Lippard SJ. Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase. Biochemistry 2007; 46:14795-809. [PMID: 18044971 PMCID: PMC2494530 DOI: 10.1021/bi7017128] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At its carboxylate-bridged diiron active site, the hydroxylase component of toluene/o-xylene monooxygenase activates dioxygen for subsequent arene hydroxylation. In an I100W variant of this enzyme, we characterized the formation and decay of two species formed by addition of dioxygen to the reduced, diiron(II) state by rapid-freeze quench (RFQ) EPR, Mössbauer, and ENDOR spectroscopy. The dependence of the formation and decay rates of this mixed-valent transient on pH and the presence of phenol, propylene, or acetylene was investigated by double-mixing stopped-flow optical spectroscopy. Modification of the alpha-subunit of the hydroxylase after reaction of the reduced protein with dioxygen-saturated buffer was investigated by tryptic digestion coupled mass spectrometry. From these investigations, we conclude that (i) a diiron(III,IV)-W* transient, kinetically linked to a preceding diiron(III) intermediate, arises from the one-electron oxidation of W100, (ii) the tryptophan radical is deprotonated, (iii) rapid exchange of either a terminal water or hydroxide ion with water occurs at the ferric ion in the diiron(III,IV) cluster, and (iv) the diiron(III,IV) core and W* decay to the diiron(III) product by a common mechanism. No transient radical was observed by stopped-flow optical spectroscopy for reactions of the reduced hydroxylase variants I100Y, L208F, and F205W with dioxygen. The absence of such species, and the deprotonated state of the tryptophanyl radical in the diiron(III,IV)-W* transient, allow for a conservative estimate of the reduction potential of the diiron(III) intermediate as lying between 1.1 and 1.3 V. We also describe the X-ray crystal structure of the I100W variant of ToMOH.
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Affiliation(s)
- Leslie J. Murray
- Department of Chemistry, Massachusetts Institute of Technology Cambridge, MA 02139
| | | | - Michael S. McCormick
- Department of Chemistry, Massachusetts Institute of Technology Cambridge, MA 02139
| | - Roman Davydov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Sunil Naik
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Sun-Hee Kim
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Boi Hanh Huynh
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology Cambridge, MA 02139
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30
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Murray LJ, Naik SG, Ortillo DO, García-Serres R, Lee JK, Huynh BH, Lippard SJ. Characterization of the arene-oxidizing intermediate in ToMOH as a diiron(III) species. J Am Chem Soc 2007; 129:14500-10. [PMID: 17967027 PMCID: PMC2494525 DOI: 10.1021/ja076121h] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the generation and characterization of a diiron(III) intermediate formed during reaction with dioxygen of the reduced hydroxylase component of toluene/o-xylene monooxygenase from Pseudomonas sp. OX1. The decay rate of this species is accelerated upon mixing with phenol, a substrate for this system. Under steady-state conditions, hydrogen peroxide was generated in the absence of substrate. The oxidized hydroxylase also decomposed hydrogen peroxide to liberate dioxygen in the absence of reducing equivalents. This activity suggests that dioxygen activation may be reversible. The linear free energy relationship determined from hydroxylation of para-substituted phenols under steady-state turnover has a negative slope. A value of rho < 0 is consistent with electrophilic attack by the oxidizing intermediate on the aromatic substrates. The results from these steady and pre-steady-state experiments provide compelling evidence that the diiron(III) intermediate is the active oxidant in the toluene/o-xylene monooxygenase system and is a peroxodiiron(III) transient, despite differences between its optical and Mössbauer spectroscopic parameters and those of other peroxodiiron(III) centers.
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Affiliation(s)
- Leslie J. Murray
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sunil G. Naik
- Department of Physics, Emory University, Atlanta, GA 30322
| | | | | | - Jessica K. Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Boi Hanh Huynh
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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31
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Gil MA, Maringgele W, Dechert S, Meyer F. Structural Flexibility of Carboxylate Bridging Exemplified by a Series of μ-Acetato Dizinc Complexes. Z Anorg Allg Chem 2007. [DOI: 10.1002/zaac.200700200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Murray LJ, Lippard SJ. Substrate trafficking and dioxygen activation in bacterial multicomponent monooxygenases. Acc Chem Res 2007; 40:466-74. [PMID: 17518435 DOI: 10.1021/ar600040e] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-heme carboxylate-bridged diiron centers in the hydroxylase components of the bacterial multicomponent monooxygenases process four substrates during catalysis: electrons, protons, dioxygen, and hydrocarbons. Understanding how protein-protein interactions mediate the transport of these substrates to the diiron center to achieve the selective oxidation of the hydrocarbon is a significant challenge. In this Account, we summarize our current knowledge of these processes with a focus on the methane monooxygenase system. We also describe recent results for the toluene/ o-xylene monooxygenase and phenol hydroxylase systems from Pseudomonas sporium OX1. The observation in these latter systems of a diiron(III) oxygenated intermediate having different Mössbauer parameters from analogous species in other carboxylate-bridged diiron proteins is discussed. The results indicate that the ability of the protein framework to tune the reactivity of the diiron center at structurally similar active sites is substantially more complex than previously recognized.
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Affiliation(s)
- Leslie J Murray
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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33
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Sazinsky MH, Dunten PW, McCormick MS, DiDonato A, Lippard SJ. X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase. Biochemistry 2006; 45:15392-404. [PMID: 17176061 PMCID: PMC1829208 DOI: 10.1021/bi0618969] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenol hydroxylase (PH) belongs to a family of bacterial multicomponent monooxygenases (BMMs) with carboxylate-bridged diiron active sites. Included are toluene/o-xylene (ToMO) and soluble methane (sMMO) monooxygenase. PH hydroxylates aromatic compounds, but unlike sMMO, it cannot oxidize alkanes despite having a similar dinuclear iron active site. Important for activity is formation of a complex between the hydroxylase and a regulatory protein component. To address how structural features of BMM hydroxylases and their component complexes may facilitate the catalytic mechanism and choice of substrate, we determined X-ray structures of native and SeMet forms of the PH hydroxylase (PHH) in complex with its regulatory protein (PHM) to 2.3 A resolution. PHM binds in a canyon on one side of the (alphabetagamma)2 PHH dimer, contacting alpha-subunit helices A, E, and F approximately 12 A above the diiron core. The structure of the dinuclear iron center in PHH resembles that of mixed-valent MMOH, suggesting an Fe(II)Fe(III) oxidation state. Helix E, which comprises part of the iron-coordinating four-helix bundle, has more pi-helical character than analogous E helices in MMOH and ToMOH lacking a bound regulatory protein. Consequently, conserved active site Thr and Asn residues translocate to the protein surface, and an approximately 6 A pore opens through the four-helix bundle. Of likely functional significance is a specific hydrogen bond formed between this Asn residue and a conserved Ser side chain on PHM. The PHM protein covers a putative docking site on PHH for the PH reductase, which transfers electrons to the PHH diiron center prior to O2 activation, suggesting that the regulatory component may function to block undesired reduction of oxygenated intermediates during the catalytic cycle. A series of hydrophobic cavities through the PHH alpha-subunit, analogous to those in MMOH, may facilitate movement of the substrate to and/or product from the active site pocket. Comparisons between the ToMOH and PHH structures provide insights into their substrate regiospecificities.
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Affiliation(s)
- Matthew H Sazinsky
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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