1
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Liew JJM, Wicht DK, Gonzalez R, Dowling DP, Ellis HR. Current understanding of enzyme structure and function in bacterial two-component flavin-dependent desulfonases: Cleaving C-S bonds of organosulfur compounds. Arch Biochem Biophys 2024; 758:110048. [PMID: 38848996 DOI: 10.1016/j.abb.2024.110048] [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: 04/24/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
The inherent structural properties of enzymes are critical in defining catalytic function. Often, studies to evaluate the relationship between structure and function are limited to only one defined structural element. The two-component flavin-dependent desulfonase family of enzymes involved in bacterial sulfur acquisition utilize a comprehensive range of structural features to carry out the desulfonation of organosulfur compounds. These metabolically essential two-component FMN-dependent desulfonase systems have been proposed to utilize oligomeric changes, protein-protein interactions for flavin transfer, and common mechanistic steps for carbon-sulfur bond cleavage. This review is focused on our current functional and structural understanding of two-component FMN-dependent desulfonase systems from multiple bacterial sources. Mechanistic and structural comparisons from recent independent studies provide fresh insights into the overall functional properties of these systems and note areas in need of further investigation. The review acknowledges current studies focused on evaluating the structural properties of these enzymes in relationship to their distinct catalytic function. The role of these enzymes in maintaining adequate sulfur levels, coupled with the conserved nature of these enzymes in diverse bacteria, underscore the importance in understanding the functional and structural nuances of these systems.
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Affiliation(s)
- Jeremy J M Liew
- Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Denyce K Wicht
- Department of Biochemistry, Chemistry, Environment, and Physics, Suffolk University, Boston, MA, 02108, USA
| | - Reyaz Gonzalez
- Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Holly R Ellis
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC, 27834, USA.
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2
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Desai A, Mahajan V, Ramabhadran RO, Mukherjee R. Binding order of substrate and cofactor in sulfonamide monooxygenase during sulfa drug degradation: in silico studies. J Biomol Struct Dyn 2024:1-15. [PMID: 38263732 DOI: 10.1080/07391102.2024.2306495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
For decades, sulfonamide antibiotics have been used across industries such as agriculture and animal husbandry. However, the use and inadvertent misuse of these antibiotics have resulted in the advent of sulfonamide-drug-resistant strains due to antibiotic pollution. Enzymatic bioremediation of antibiotics remains a potential emerging solution to combat antibiotic pollution. Here, we propose an enzymatic model for the degradation of sulfonamides by Microbacterium sp. We have employed a multi-pronged computational strategy involving - protein structure modelling, ligand docking and molecular dynamics simulations to decipher a plausible binding order for the enzymatic degradation of sulfonamides by the bacterial sulfonamide monooxygenase, SulX. Our results enable us to predict that this degradation is achieved through the sequential binding of the antibiotic sulfonamide followed by the reduced flavin cofactor FMNH2, thereby laying the computational foundation for further advancements in enzyme-mediated degradation of the antibiotic. We also provide a list of experiments which may be performed to verify and follow-up on our in-silico studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amogh Desai
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Ved Mahajan
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Raju Mukherjee
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
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3
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Mangkalee M, Oonanant W, Aonbangkhen C, Pimviriyakul P, Tinikul R, Chaiyen P, Insin N, Sucharitakul J. Reaction mechanism and kinetics of the two-component flavoprotein dimethyl sulfone monooxygenase system: Using hydrogen peroxide for monooxygenation and substrate cleavage. FEBS J 2023; 290:5171-5195. [PMID: 37522421 DOI: 10.1111/febs.16916] [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: 05/30/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/01/2023]
Abstract
The dimethyl sulfone monooxygenase system is a two-component flavoprotein, catalyzing the monooxygenation of dimethyl sulfone (DMSO2 ) by oxidative cleavage producing methanesulfinate and formaldehyde. The reductase component (DMSR) is a flavoprotein with FMN as a cofactor, catalyzing flavin reduction using NADH. The monooxygenase (DMSMO) uses reduced flavin from the reductase and oxygen for substrate monooxygenation. DMSMO can bind to FMN and FMNH- with a Kd of 17.4 ± 0.9 μm and 4.08 ± 0.8 μm, respectively. The binding of FMN to DMSMO is required prior to binding DMSO2 . This also applies to the fast binding of reduced FMN to DMSMO followed by DMSO2 . Substituting reduced DMSR with FMNH- demonstrated the same oxidation kinetics, indicating that FMNH- from DMSR was transferred to DMSMO. The oxidation of FMNH- :DMSMO, with and without DMSO2 did not generate any flavin adducts for monooxygenation. Therefore, H2 O2 is likely to be the reactive agent to attack the substrate. The H2 O2 assay results demonstrated production of H2 O2 from the oxidation of FMNH- :DMSMO, whereas H2 O2 was not detected in the presence of DMSO2 , confirming H2 O2 utilization. The rate constant for methanesulfinate formation determined from rapid quenched flow and the rate constant for flavin oxidation were similar, indicating that H2 O2 rapidly reacts with DMSO2 , with flavin oxidation as the rate-limiting step. This is the first report of the kinetic mechanisms of both components using rapid kinetics and of a method for methanesulfinate detection using LC-MS.
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Affiliation(s)
- Montisa Mangkalee
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Research Unit in Integrative Immuno-Microbial Biochemistry and Bioresponsive Nanomaterials, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Worrapoj Oonanant
- Department of Basic Medical Science, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Chanat Aonbangkhen
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Numpon Insin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Research Unit in Integrative Immuno-Microbial Biochemistry and Bioresponsive Nanomaterials, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Skeletal Disorders Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
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4
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Aloh CH, Zeczycki TN, Ellis HR. Oligomeric Changes Regulate Flavin Transfer in Two-Component FMN Reductases Involved in Sulfur Metabolism. Biochemistry 2023; 62:2751-2762. [PMID: 37651343 DOI: 10.1021/acs.biochem.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The FMN reductases (SsuE and MsuE of the alkanesulfonate monooxygenase systems) supply reduced flavin to their partner monooxygenases for the desulfonation of alkanesulfonates. Flavin reductases that comprise two-component systems must be able to regulate both flavin reduction and transfer. One mechanism to control these distinct processes is through changes in the oligomeric state of the enzymes. Despite their similar overall structures, SsuE and MsuE showed clear differences in their oligomeric states in the presence of substrates. The oligomeric state of SsuE was converted from a tetramer to a dimer/tetramer equilibrium in the presence of FMN or NADPH in analytical ultracentrifugation studies. Conversely, MsuE shifted from a dimer to a single tetrameric state with FMN, and the NADPH substrate did not induce a similar oligomeric shift. There was a fast tetramer to dimer equilibrium shift occurring at the dimer/dimer interface in H/D-X investigations with apo SsuE. Formation of the SsuE/FMN complex slowed the tetramer/dimer conversion, leading to a slower exchange along the dimer/dimer interface. The oligomeric shift of the MsuE/FMN complex from a dimer to a distinct tetramer showed a decrease in H/D-X in the region around the π-helices at the dimer/dimer interface. Both SsuE and MsuE showed a comparable and significant increase in the melting temperature with the addition of FMN, indicating the conformers formed by each FMN-bound enzyme had increased stability. A mechanism that supports the different structural shifts is rationalized by the different roles these enzymes play in providing reduced flavin to single or multiple monooxygenase enzymes.
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Affiliation(s)
- Chioma H Aloh
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina 27834, United States
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina 27834, United States
| | - Holly R Ellis
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina 27834, United States
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5
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Somai S, Yue K, Acevedo O, Ellis HR. Shorter Alkanesulfonate Carbon Chains Destabilize the Active Site Architecture of SsuD for Desulfonation. Biochemistry 2023; 62:85-94. [PMID: 36534405 DOI: 10.1021/acs.biochem.2c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacteria have evolved to utilize alternative organosulfur sources when sulfur is limiting. The SsuE/SsuD and MsuE/MsuD enzymes expressed when sulfur sources are restricted, are responsible for providing specific bacteria with sulfur in the form of alkanesulfonates. In this study, we evaluated why two structurally and functionally similar FMNH2-dependent monooxygenase enzymes (MsuD and SsuD) are needed for the acquisition of alkanesulfonates in some bacteria. In desulfonation assays, MsuD was able to utilize the entire range of alkanesulfonates (C1-C10). However, SsuD was not able to utilize smaller alkanesulfonate substrates. Interestingly, SsuD had a similar binding affinity for methanesulfonate (MES) (15 ± 1 μM) as MsuD (12 ± 1 μM) even though SsuD was not able to catalyze the desulfonation of the MES substrate. SsuD and MsuD showed decreased proteolytic susceptibility in the presence of FMNH2 with MES and octanesulfonate (OCS). Tighter loop closure was observed for the MsuD/FMNH2 complex with MES and OCS compared to SsuD under comparable conditions. Analysis of the SsuD/FMNH2/MES structure using accelerated molecular dynamics simulations found three different conformations for MES, demonstrating the instability of the bound structure. Even when MES was bound in a similar fashion to OCS within the active site, the smaller alkane chain resulted in a shift of FMNH2 so that it was no longer in a position to catalyze the desulfonation of MES. The active site of SsuD requires a longer alkane chain to maintain the appropriate architecture for desulfonation.
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Affiliation(s)
- Shruti Somai
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina27834, United States
| | - Kun Yue
- Department of Chemistry, University of Miami, Coral Gables, Florida33146, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida33146, United States
| | - Holly R Ellis
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina27834, United States
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6
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Perera M, Wijesundera S, Wijayarathna CD, Seneviratne G, Jayasena S. Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis. Front Microbiol 2022; 13:898456. [PMID: 36110294 PMCID: PMC9468676 DOI: 10.3389/fmicb.2022.898456] [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] [Received: 03/17/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyzed using a computational approach. By analyzing publicly available protein databases, we identified six uncharacterized proteins in A. flavus NRRL 3357, of which five were identified as class LadAα and one as class LadAβ, which are eukaryotic homologs of bacterial long-chain alkane monooxygenase (LadA). Computational models of A. flavus LadAα homologs (Af1-Af5) showed overall structural similarity to the bacterial LadA and the unique sequence and structural elements that bind the cofactor Flavin mononucleotide (FMN). A receptor-cofactor-substrate docking protocol was established and validated to demonstrate the substrate binding in the A. flavus LadAα homologs. The modeled Af1, Af3, Af4, and Af5 captured long-chain n-alkanes inside the active pocket, above the bound FMN. Isoalloxazine ring of reduced FMN formed a π–alkyl interaction with the terminal carbon atom of captured alkanes, C16–C30, in Af3–Af5 and C16–C24 in Af1. Our results confirmed the ability of identified A. flavus LadAα monooxygenases to bind long-chain alkanes inside the active pocket. Hence A. flavus LadAα monooxygenases potentially initiate the degradation of long-chain alkanes by oxidizing bound long-chain alkanes into their corresponding alcohol.
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Affiliation(s)
- Madushika Perera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Sulochana Wijesundera
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | | | | | - Sharmila Jayasena
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- *Correspondence: Sharmila Jayasena,
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7
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Matthews A, Schönfelder J, Lagies S, Schleicher E, Kammerer B, Ellis HR, Stull F, Teufel R. Bacterial flavoprotein monooxygenase YxeK salvages toxic S-(2-succino)-adducts via oxygenolytic C-S bond cleavage. FEBS J 2021; 289:787-807. [PMID: 34510734 DOI: 10.1111/febs.16193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 01/23/2023]
Abstract
Thiol-containing nucleophiles such as cysteine react spontaneously with the citric acid cycle intermediate fumarate to form S-(2-succino)-adducts. In Bacillus subtilis, a salvaging pathway encoded by the yxe operon has recently been identified for the detoxification and exploitation of these compounds as sulfur sources. This route involves acetylation of S-(2-succino)cysteine to N-acetyl-2-succinocysteine, which is presumably converted to oxaloacetate and N-acetylcysteine, before a final deacetylation step affords cysteine. The critical oxidative cleavage of the C-S bond of N-acetyl-S-(2-succino)cysteine was proposed to depend on the predicted flavoprotein monooxygenase YxeK. Here, we characterize YxeK and verify its role in S-(2-succino)-adduct detoxification and sulfur metabolism. Detailed biochemical and mechanistic investigation of YxeK including 18 O-isotope-labeling experiments, homology modeling, substrate specificity tests, site-directed mutagenesis, and (pre-)steady-state kinetics provides insight into the enzyme's mechanism of action, which may involve a noncanonical flavin-N5-peroxide species for C-S bond oxygenolysis.
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Affiliation(s)
| | | | - Simon Lagies
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Erik Schleicher
- Institute of Physical Chemistry, University of Freiburg, Germany
| | - Bernd Kammerer
- Institute of Organic Chemistry, University of Freiburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
| | - Holly R Ellis
- Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Germany
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8
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Phintha A, Prakinee K, Jaruwat A, Lawan N, Visitsatthawong S, Kantiwiriyawanitch C, Songsungthong W, Trisrivirat D, Chenprakhon P, Mulholland A, van Pée KH, Chitnumsub P, Chaiyen P. Dissecting the low catalytic capability of flavin-dependent halogenases. J Biol Chem 2021; 296:100068. [PMID: 33465708 PMCID: PMC7948982 DOI: 10.1074/jbc.ra120.016004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022] Open
Abstract
Although flavin-dependent halogenases (FDHs) are attractive biocatalysts, their practical applications are limited because of their low catalytic efficiency. Here, we investigated the reaction mechanisms and structures of tryptophan 6-halogenase (Thal) from Streptomyces albogriseolus using stopped-flow, rapid-quench flow, quantum/mechanics molecular mechanics calculations, crystallography, and detection of intermediate (hypohalous acid [HOX]) liberation. We found that the key flavin intermediate, C4a-hydroperoxyflavin (C4aOOH-FAD), formed by Thal and other FDHs (tryptophan 7-halogenase [PrnA] and tryptophan 5-halogenase [PyrH]), can react with I-, Br-, and Cl- but not F- to form C4a-hydroxyflavin and HOX. Our experiments revealed that I- reacts with C4aOOH-FAD the fastest with the lowest energy barrier and have shown for the first time that a significant amount of the HOX formed leaks out as free HOX. This leakage is probably a major cause of low product coupling ratios in all FDHs. Site-saturation mutagenesis of Lys79 showed that changing Lys79 to any other amino acid resulted in an inactive enzyme. However, the levels of liberated HOX of these variants are all similar, implying that Lys79 probably does not form a chloramine or bromamine intermediate as previously proposed. Computational calculations revealed that Lys79 has an abnormally lower pKa compared with other Lys residues, implying that the catalytic Lys may act as a proton donor in catalysis. Analysis of new X-ray structures of Thal also explains why premixing of FDHs with reduced flavin adenine dinucleotide generally results in abolishment of C4aOOH-FAD formation. These findings reveal the hidden factors restricting FDHs capability which should be useful for future development of FDHs applications.
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Affiliation(s)
- Aisaraphon Phintha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Aritsara Jaruwat
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Surawit Visitsatthawong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chadaporn Kantiwiriyawanitch
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Warangkhana Songsungthong
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, Thailand
| | - Adrian Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Karl-Heinz van Pée
- General Biochemistry, Faculty of Chemistry and Food Chemistry, Technical University of Dresden, Dresden, Germany
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand.
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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9
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Bottos EM, Al-Shabib EY, Shaw DMJ, McAmmond BM, Sharma A, Suchan DM, Cameron ADS, Van Hamme JD. Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6:2 fluorotelomer sulfonamidoalkyl betaine or 6:2 fluorotelomer sulfonate as sole sulfur source. Biodegradation 2020; 31:407-422. [PMID: 33150552 PMCID: PMC7661421 DOI: 10.1007/s10532-020-09917-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Abstract Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are environmental contaminants of concern. We previously described biodegradation of two PFAS that represent components and transformation products of aqueous film-forming foams (AFFF), 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) and 6:2 fluorotelomer sulfonate (6:2 FTSA), by Gordonia sp. strain NB4-1Y. To identify genes involved in the breakdown of these compounds, the transcriptomic response of NB4-1Y was examined when grown on 6:2 FTAB, 6:2 FTSA, a non-fluorinated analog of 6:2 FTSA (1-octanesulfonate), or MgSO4, as sole sulfur source. Differentially expressed genes were identified as those with ± 1.5 log2-fold-differences (± 1.5 log2FD) in transcript abundances in pairwise comparisons. Transcriptomes of cells grown on 6:2 FTAB and 6:2 FTSA were most similar (7.9% of genes expressed ± 1.5 log2FD); however, several genes that were expressed in greater abundance in 6:2 FTAB treated cells compared to 6:2 FTSA treated cells were noted for their potential role in carbon–nitrogen bond cleavage in 6:2 FTAB. Responses to sulfur limitation were observed in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments, as 20 genes relating to global sulfate stress response were more highly expressed under these conditions compared to the MgSO4 treatment. More highly expressed oxygenase genes in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments were found to code for proteins with lower percent sulfur-containing amino acids compared to both the total proteome and to oxygenases showing decreased expression. This work identifies genetic targets for further characterization and will inform studies aimed at evaluating the biodegradation potential of environmental samples through applied genomics. Graphic Abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s10532-020-09917-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Ebtihal Y Al-Shabib
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Dayton M J Shaw
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Breanne M McAmmond
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Aditi Sharma
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Danae M Suchan
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada.
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10
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Thakur A, Somai S, Yue K, Ippolito N, Pagan D, Xiong J, Ellis HR, Acevedo O. Substrate-Dependent Mobile Loop Conformational Changes in Alkanesulfonate Monooxygenase from Accelerated Molecular Dynamics. Biochemistry 2020; 59:3582-3593. [PMID: 32881481 DOI: 10.1021/acs.biochem.0c00633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Abhishek Thakur
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Shruti Somai
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Kun Yue
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Nicole Ippolito
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Dianne Pagan
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Jingyuan Xiong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Holly R. Ellis
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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11
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Protective Role of Bacterial Alkanesulfonate Monooxygenase under Oxidative Stress. Appl Environ Microbiol 2020; 86:AEM.00692-20. [PMID: 32503904 DOI: 10.1128/aem.00692-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Bacterial alkane metabolism is associated with a number of cellular stresses, including membrane stress and oxidative stress, and the limited uptake of charged ions such as sulfate. In the present study, the genes ssuD and tauD in Acinetobacter oleivorans DR1 cells, which encode an alkanesulfonate monooxygenase and a taurine dioxygenase, respectively, were found to be responsible for hexadecanesulfonate (C16SO3H) and taurine metabolism, and Cbl was experimentally identified as a potential regulator of ssuD and tauD expression. The expression of ssuD and tauD occurred under sulfate-limited conditions generated during n-hexadecane degradation. Interestingly, expression analysis and knockout experiments suggested that both genes are required to protect cells against oxidative stress, including that generated by n-hexadecane degradation and H2O2 exposure. Measurable levels of intracellular hexadecanesulfonate were also produced during n-hexadecane degradation. Phylogenetic analysis suggested that ssuD and tauD are mainly present in soil-dwelling aerobes within the Betaproteobacteria and Gammaproteobacteria classes, which suggests that they function as controllers of the sulfur cycle and play a protective role against oxidative stress in sulfur-limited conditions.IMPORTANCE ssuD and tauD, which play a role in the degradation of organosulfonate, were expressed during n-hexadecane metabolism and oxidative stress conditions in A. oleivorans DR1. Our study confirmed that hexadecanesulfonate was accidentally generated during bacterial n-hexadecane degradation in sulfate-limited conditions. Removal of this by-product by SsuD and TauD must be necessary for bacterial survival under oxidative stress generated during n-hexadecane degradation.
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12
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Hao DAC, Song SM, Cheng Y, Qin ZQ, Ge GB, An BL, Xiao PG. Functional and Transcriptomic Characterization of a Dye-decolorizing Fungus from Taxus Rhizosphere. Pol J Microbiol 2019; 67:417-430. [PMID: 30550228 PMCID: PMC7256826 DOI: 10.21307/pjm-2018-050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 01/18/2023] Open
Abstract
We isolated three laccase-producing fungus strains from Taxus rhizosphere. Myrotheium verrucaria strain DJTU-sh7 had the highest laccase activity of 216.2 U/ml, which was increased to above 300 U/ml after optimization. DJTU-sh7 had the best decolorizing effect for three classes of reactive dyes. The DJTU-sh7-containing fungal consortium displayed the robust decolorizing ability. Both color removal efficiency and chemical oxygen demand were increased in the consortium mediated biotransformation. Transcriptome changes of M. verrucaria elicited by azo dye and phenolic were quantified by the high throughput transcriptome sequencing, and the activities of the selected oxidases and reductases were determined. The possible involvement of oxidases and reductases, especially laccase, aryl alcohol oxidase, and ferric reductase in the biotransformation of dye and phenolic compounds was revealed at both transcriptomic and phenotypic levels. Revealing the transcriptomic mechanisms of fungi in dealing with organic pollutants facilitates the fine-tuned manipulation of strains in developing novel bioremediation and biodegradation strategies. We isolated three laccase-producing fungus strains from Taxus rhizosphere. Myrotheium verrucaria strain DJTU-sh7 had the highest laccase activity of 216.2 U/ml, which was increased to above 300 U/ml after optimization. DJTU-sh7 had the best decolorizing effect for three classes of reactive dyes. The DJTU-sh7-containing fungal consortium displayed the robust decolorizing ability. Both color removal efficiency and chemical oxygen demand were increased in the consortium mediated biotransformation. Transcriptome changes of M. verrucaria elicited by azo dye and phenolic were quantified by the high throughput transcriptome sequencing, and the activities of the selected oxidases and reductases were determined. The possible involvement of oxidases and reductases, especially laccase, aryl alcohol oxidase, and ferric reductase in the biotransformation of dye and phenolic compounds was revealed at both transcriptomic and phenotypic levels. Revealing the transcriptomic mechanisms of fungi in dealing with organic pollutants facilitates the fine-tuned manipulation of strains in developing novel bioremediation and biodegradation strategies.
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Affiliation(s)
- DA Cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University , Dalian , China
| | - Si Meng Song
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University , Dalian , China
| | - Yan Cheng
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University , Dalian , China
| | - Zhi Qiang Qin
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University , Dalian , China
| | - Guang Bo Ge
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , China.,Shanghai University of Traditional Chinese Medicine , Shanghai , China
| | - Bai Lin An
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University , Dalian , China
| | - Pei Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences , Beijing , China
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13
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Sedláček V, Kučera I. Functional and mechanistic characterization of an atypical flavin reductase encoded by the pden_5119 gene in Paracoccus denitrificans. Mol Microbiol 2019; 112:166-183. [PMID: 30977245 DOI: 10.1111/mmi.14260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2019] [Indexed: 01/25/2023]
Abstract
Pden_5119, annotated as an NADPH-dependent FMN reductase, shows homology to proteins assisting in utilization of alkanesulfonates in other bacteria. Here, we report that inactivation of the pden_5119 gene increased susceptibility to oxidative stress, decreased growth rate and increased growth yield; growth on lower alkanesulfonates as sulfur sources was not specifically influenced. Pden_5119 transcript rose in response to oxidative stressors, respiratory chain inhibitors and terminal oxidase downregulation. Kinetic analysis of a fusion protein suggested a sequential mechanism in which FMN binds first, followed by NADH. The affinity of flavin toward the protein decreased only slightly upon reduction. The observed strong viscosity dependence of kcat demonstrated that reduced FMN formed tends to remain bound to the enzyme where it can be re-oxidized by oxygen or, less efficiently, by various artificial electron acceptors. Stopped flow data were consistent with the enzyme-FMN complex being a functional oxidase that conducts the reduction of oxygen by NADH. Hydrogen peroxide was identified as the main product. As shown by isotope effects, hydride transfer occurs from the pro-S C4 position of the nicotinamide ring and partially limits the overall turnover rate. Collectively, our results point to a role for the Pden_5119 protein in maintaining the cellular redox state.
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Affiliation(s)
- Vojtěch Sedláček
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Igor Kučera
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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14
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Robbins JM, Ellis HR. Investigations of two-component flavin-dependent monooxygenase systems. Methods Enzymol 2019; 620:399-422. [DOI: 10.1016/bs.mie.2019.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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McFarlane JS, Hagen RA, Chilton AS, Forbes DL, Lamb AL, Ellis HR. Not as easy as π: An insertional residue does not explain the π-helix gain-of-function in two-component FMN reductases. Protein Sci 2018; 28:123-134. [PMID: 30171650 DOI: 10.1002/pro.3504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/25/2018] [Accepted: 08/27/2018] [Indexed: 11/08/2022]
Abstract
The π-helix located at the tetramer interface of two-component FMN-dependent reductases contributes to the structural divergence from canonical FMN-bound reductases within the NADPH:FMN reductase family. The π-helix in the SsuE FMN-dependent reductase of the alkanesulfonate monooxygenase system has been proposed to be generated by the insertion of a Tyr residue in the conserved α4-helix. Variants of Tyr118 were generated, and their X-ray crystal structures determined, to evaluate how these alterations affect the structural integrity of the π-helix. The structure of the Y118A SsuE π-helix was converted to an α-helix, similar to the FMN-bound members of the NADPH:FMN reductase family. Although the π-helix was altered, the FMN binding region remained unchanged. Conversely, deletion of Tyr118 disrupted the secondary structural properties of the π-helix, generating a random coil region in the middle of helix 4. Both the Y118A and Δ118 SsuE SsuE variants crystallize as a dimer. The MsuE FMN reductase involved in the desulfonation of methanesulfonates is structurally similar to SsuE, but the π-helix contains a His insertional residue. Exchanging the π-helix insertional residue of each enzyme did not result in equivalent kinetic properties. Structure-based sequence analysis further demonstrated the presence of a similar Tyr residue in an FMN-bound reductase in the NADPH:FMN reductase family that is not sufficient to generate a π-helix. Results from the structural and functional studies of the FMN-dependent reductases suggest that the insertional residue alone is not solely responsible for generating the π-helix, and additional structural adaptions occur to provide the altered gain of function.
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Affiliation(s)
- Jeffrey S McFarlane
- The Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Richard A Hagen
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, 36849
| | - Annemarie S Chilton
- The Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Dianna L Forbes
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, 36849
| | - Audrey L Lamb
- The Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Holly R Ellis
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, 36849
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16
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Musila JM, L Forbes D, Ellis HR. Functional Evaluation of the π-Helix in the NAD(P)H:FMN Reductase of the Alkanesulfonate Monooxygenase System. Biochemistry 2018; 57:4469-4477. [PMID: 29979040 DOI: 10.1021/acs.biochem.8b00544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A subgroup of enzymes in the NAD(P)H:FMN reductase family is comprised of flavin reductases from two-component monooxygenase systems. The diverging structural feature in these FMN reductases is a π-helix centrally located at the tetramer interface that is generated by the insertion of an amino acid in a conserved α4 helix. The Tyr insertional residue of SsuE makes specific contacts across the dimer interface that may assist in the altered mechanistic properties of this enzyme. The Y118F SsuE variant maintained the π-π stacking interactions at the tetramer interface and had kinetic parameters similar to those of wild-type SsuE. Substitution of the π-helical residue (Tyr118) to Ala or Ser transformed the enzymes into flavin-bound SsuE variants that could no longer support flavin reductase and desulfonation activities. These variants existed as dimers and could form protein-protein interactions with SsuD even though flavin transfer was not sustained. The ΔY118 SsuE variant was flavin-free as purified and did not undergo the tetramer to dimer oligomeric shift with the addition of flavin. The absence of desulfonation activity can be attributed to the inability of ΔY118 SsuE to promote flavin transfer and undergo the requisite oligomeric changes to support desulfonation. Results from these studies provide insights into the role of the SsuE π-helix in promoting flavin transfer and oligomeric changes that support protein-protein interactions with SsuD.
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Affiliation(s)
- Jonathan M Musila
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Dianna L Forbes
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Holly R Ellis
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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17
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Hazra AB, Ballou DP, Taga ME. Unique Biochemical and Sequence Features Enable BluB To Destroy Flavin and Distinguish BluB from the Flavin Monooxygenase Superfamily. Biochemistry 2018; 57:1748-1757. [PMID: 29457884 DOI: 10.1021/acs.biochem.7b01193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Vitamin B12 (cobalamin) is an essential micronutrient for humans that is synthesized by only a subset of bacteria and archaea. The aerobic biosynthesis of 5,6-dimethylbenzimidazole, the lower axial ligand of cobalamin, is catalyzed by the "flavin destructase" enzyme BluB, which fragments reduced flavin mononucleotide following its reaction with oxygen to yield this ligand. BluB is similar in sequence and structure to members of the flavin oxidoreductase superfamily, yet the flavin destruction process has remained elusive. Using stopped-flow spectrophotometry, we find that the flavin destructase reaction of BluB from Sinorhizobium meliloti is initiated with canonical flavin-O2 chemistry. A C4a-peroxyflavin intermediate is rapidly formed in BluB upon reaction with O2, and has properties similar to those of flavin-dependent hydroxylases. Analysis of reaction mixtures containing flavin analogues indicates that both formation of the C4a-peroxyflavin and the subsequent destruction of the flavin to form 5,6-dimethylbenzimidazole are influenced by the electronic properties of the flavin isoalloxazine ring. The flavin destruction phase of the reaction, which results from the decay of the C4a-peroxyflavin intermediate, occurs more efficiently at pH >7.5. Furthermore, the BluB mutants D32N and S167G are specifically impaired in the flavin destruction phase of the reaction; nevertheless, both form the C4a-peroxyflavin nearly quantitatively. Coupled with a phylogenetic analysis of BluB and related flavin-dependent enzymes, these results demonstrate that the BluB flavin destructase family can be identified by the presence of active site residues D32 and S167.
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Affiliation(s)
- Amrita B Hazra
- Department of Plant & Microbial Biology , University of California, Berkeley , Berkeley , California 94720 , United States.,Department of Chemistry , Indian Institute of Science Education and Research Pune , Pune - 411008 , India
| | - David P Ballou
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology , University of California, Berkeley , Berkeley , California 94720 , United States
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18
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Pimviriyakul P, Thotsaporn K, Sucharitakul J, Chaiyen P. Kinetic Mechanism of the Dechlorinating Flavin-dependent Monooxygenase HadA. J Biol Chem 2017; 292:4818-4832. [PMID: 28159841 DOI: 10.1074/jbc.m116.774448] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/30/2017] [Indexed: 01/26/2023] Open
Abstract
The accumulation of chlorophenols (CPs) in the environment, due to their wide use as agrochemicals, has become a serious environmental problem. These organic halides can be degraded by aerobic microorganisms, where the initial steps of various biodegradation pathways include an oxidative dechlorinating process in which chloride is replaced by a hydroxyl substituent. Harnessing these dechlorinating processes could provide an opportunity for environmental remediation, but detailed catalytic mechanisms for these enzymes are not yet known. To close this gap, we now report transient kinetics and product analysis of the dechlorinating flavin-dependent monooxygenase, HadA, from the aerobic organism Ralstonia pickettii DTP0602, identifying several mechanistic properties that differ from other enzymes in the same class. We first overexpressed and purified HadA to homogeneity. Analyses of the products from single and multiple turnover reactions demonstrated that HadA prefers 4-CP and 2-CP over CPs with multiple substituents. Stopped-flow and rapid-quench flow experiments of HadA with 4-CP show the involvement of specific intermediates (C4a-hydroperoxy-FAD and C4a-hydroxy-FAD) in the reaction, define rate constants and the order of substrate binding, and demonstrate that the hydroxylation step occurs prior to chloride elimination. The data also identify the non-productive and productive paths of the HadA reactions and demonstrate that product formation is the rate-limiting step. This is the first elucidation of the kinetic mechanism of a two-component flavin-dependent monooxygenase that can catalyze oxidative dechlorination of various CPs, and as such it will serve as the basis for future investigation of enzyme variants that will be useful for applications in detoxifying chemicals hazardous to human health.
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Affiliation(s)
- Panu Pimviriyakul
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400 and
| | - Kittisak Thotsaporn
- the Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok 10300, Thailand
| | - Jeerus Sucharitakul
- the Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok 10300, Thailand
| | - Pimchai Chaiyen
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400 and
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19
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Musila JM, Ellis HR. Transformation of a Flavin-Free FMN Reductase to a Canonical Flavoprotein through Modification of the π-Helix. Biochemistry 2016; 55:6389-6394. [DOI: 10.1021/acs.biochem.6b00452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan M. Musila
- Department
of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department
of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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20
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Dayal PV, Singh H, Busenlehner LS, Ellis HR. Exposing the Alkanesulfonate Monooxygenase Protein–Protein Interaction Sites. Biochemistry 2015; 54:7531-8. [DOI: 10.1021/acs.biochem.5b00935] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paritosh V. Dayal
- Department
of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Harsimran Singh
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Laura S. Busenlehner
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Holly R. Ellis
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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21
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Driggers CM, Dayal PV, Ellis HR, Karplus PA. Crystal Structure of Escherichia coli SsuE: Defining a General Catalytic Cycle for FMN Reductases of the Flavodoxin-like Superfamily. Biochemistry 2014; 53:3509-19. [DOI: 10.1021/bi500314f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Camden M. Driggers
- Department
of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural
and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - Paritosh V. Dayal
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural
and Life Sciences Building, Corvallis, Oregon 97331, United States
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22
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Armacost K, Musila J, Gathiaka S, Ellis HR, Acevedo O. Exploring the Catalytic Mechanism of Alkanesulfonate Monooxygenase Using Molecular Dynamics. Biochemistry 2014; 53:3308-17. [DOI: 10.1021/bi5002085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kira Armacost
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Jonathan Musila
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Symon Gathiaka
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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23
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Robbins JM, Ellis HR. Steady-state kinetic isotope effects support a complex role of Arg226 in the proposed desulfonation mechanism of alkanesulfonate monooxygenase. Biochemistry 2013; 53:161-8. [PMID: 24321058 DOI: 10.1021/bi401234e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alkanesulfonate monooxygenase system catalyzes the desulfonation of alkanesulfonates through proposed acid-base mechanistic steps that involves the abstraction of a proton from the alkane peroxyflavin intermediate and protonation of the FMN-O(-) intermediate. Both solvent and kinetic isotope studies were performed to define the proton transfer steps involved in the SsuD reaction. Substitution of the protium at the C1 position of octanesulfonate with deuterium resulted in an observed primary isotope effect of 3.0 ± 0.2 on the kcat parameter, supporting abstraction of the α-proton from the alkane peroxyflavin as the rate-limiting step in catalysis. Previous studies implicated Arg226 as the acid involved in the reprotonation of the hydroxyflavin intermediate. Solvent isotope kinetic studies gave an inverse isotope effect on (D2O)kcat of 0.75 ± 0.04 with no observable effect on (D2O)kcat/Km. This resulted in equivalent solvent isotope effects on (D2O)kcat and (D2O)(kcat)D, suggesting a solvent equilibrium isotope effect on a step occurring after the first irreversible step through product release. Data from proton inventory studies on kcat were best fit to a dome-shaped curve consistent with a conformational change to an open conformation during product release. The solvent isotope effect data coupled with the corresponding proton inventory results support and extend our previous observations that Arg226 donates a proton to the FMN-O(-) intermediate, triggering a conformational change that opens the enzyme to solvation and promotes product release.
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Affiliation(s)
- John M Robbins
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
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24
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Ferrario V, Braiuca P, Tessaro P, Knapic L, Gruber C, Pleiss J, Ebert C, Eichhorn E, Gardossi L. Elucidating the structural and conformational factors responsible for the activity and substrate specificity of alkanesulfonate monooxygenase. J Biomol Struct Dyn 2012; 30:74-88. [PMID: 22571434 DOI: 10.1080/07391102.2012.674268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The mechanism and substrate specificity of alkanesulfonate monooxygenase (SsuD) was investigated by combining molecular dynamics simulations, docking, and a comprehensive quantitative structure activity relationships (QSAR) analysis. The FMNH(2) dependent monooxygenase undergoes a dynamic conformational change of the active site, passing from a closed to an open state. As a consequence, substrates have access to the active site and the cofactor is then regenerated by the associated oxidoreductase FMN reductase SsuE.. Computational analysis of the interaction of SsuD with FMNH(2) based on molecular docking and multiple 20 ns molecular dynamics simulations pointed out that the conformational change is mainly driven by salt bridge formation between Arg297 and Glu20 or Asp111. A set of substrates accepted by SsuD were described by means of ALMOND chemical descriptors and a partial least square (PLS) mathematical model was constructed. The PLS model correlates the structure of substrates and enzyme activity, namely kinetic properties (k (cat)/K (M)). Therefore, information coming from the PLS analysis goes beyond the simple ability of the enzyme to recognize the substrate, but includes the factors that affect the capacity of the enzyme to reduce the activation energy of the rate determining step of the reaction. The two principal components of the model are able to describe both steric and electronic factors and, more importantly, their interactions. Indeed, interactions of factors appear to affect significantly the ability of SsuD of transforming efficiently a substrate.
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Affiliation(s)
- V Ferrario
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, P.le Europa 1, 34127, Trieste, Italy
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25
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Identification of critical steps governing the two-component alkanesulfonate monooxygenase catalytic mechanism. Biochemistry 2012; 51:6378-87. [PMID: 22775358 DOI: 10.1021/bi300138d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alkanesulfonate monooxygenase enzyme (SsuD) catalyzes the oxygenolytic cleavage of a carbon-sulfur bond from sulfonated substrates. A mechanism involving acid-base catalysis has been proposed for the desulfonation mechanism by SsuD. In the proposed mechanism, base catalysis is involved in abstracting a proton from the alkane peroxyflavin intermediate, while acid catalysis is needed for the protonation of the FMNO(-) intermediate. The pH profiles of k(cat) indicate that catalysis by SsuD requires a group with a pK(a) of 6.6 ± 0.2 to be deprotonated and a second group with a pK(a) of 9.5 ± 0.1 to be protonated. The upper pK(a) value was not present in the pH profiles of k(cat)/K(m). Several conserved amino acid residues (His228, His11, His333, Cys54, and Arg226) have been identified as having potential catalytic importance due to the similar spatial arrangements with close structural and functional relatives of SsuD. Substitutions to these amino acid residues were generated, and the pH dependencies were evaluated and compared to wild-type SsuD. Although a histidine residue was previously proposed to be the active site base, the His variants possessed similar steady-state kinetic parameters as wild-type SsuD. Interestingly, R226A and R226K SsuD variants possessed undetectable activity, and there was no detectable formation of the C4a-(hydro)peroxyflavin intermediate for the Arg226 SsuD variants. Guanidinium rescue with the R226A SsuD variant resulted in the recovery of 1.5% of the wild-type SsuD k(cat) value. These results implicate Arg226 playing a critical role in catalysis and provide essential insights into the mechanistic steps that guide the SsuD desulfonation process.
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26
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Xiong J, Ellis HR. Deletional studies to investigate the functional role of a dynamic loop region of alkanesulfonate monooxygenase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:898-906. [DOI: 10.1016/j.bbapap.2012.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/30/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
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27
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Ellis HR. Mechanism for sulfur acquisition by the alkanesulfonate monooxygenase system. Bioorg Chem 2011; 39:178-84. [DOI: 10.1016/j.bioorg.2011.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 08/01/2011] [Accepted: 08/03/2011] [Indexed: 11/28/2022]
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28
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Carpenter RA, Xiong J, Robbins JM, Ellis HR. Functional Role of a Conserved Arginine Residue Located on a Mobile Loop of Alkanesulfonate Monooxygenase. Biochemistry 2011; 50:6469-77. [DOI: 10.1021/bi200429d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Russell A. Carpenter
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Jingyuan Xiong
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - John M. Robbins
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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Kantz A, Gassner GT. Nature of the reaction intermediates in the flavin adenine dinucleotide-dependent epoxidation mechanism of styrene monooxygenase. Biochemistry 2010; 50:523-32. [PMID: 21166448 DOI: 10.1021/bi101328r] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Styrene monooxygenase (SMO) is a two-component flavoenzyme composed of an NADH-specific flavin reductase (SMOB) and FAD-specific styrene epoxidase (NSMOA). NSMOA binds tightly to reduced FAD and catalyzes the stereospecific addition of one atom of molecular oxygen to the vinyl side chain of styrene in the enantioselective synthesis of S-styrene oxide. In this mechanism, molecular oxygen first reacts with NSMOA(FAD(red)) to yield an FAD C(4a)-peroxide intermediate. This species is nonfluorescent and has an absorbance maximum of 382 nm. Styrene then reacts with the peroxide intermediate with a second-order rate constant of (2.6 ± 0.1) × 10(6) M(-1) s(-1) to yield a fluorescent intermediate with an absorbance maximum of 368 nm. We compute an activation free energy of 8.7 kcal/mol for the oxygenation step, in good agreement with that expected for a peroxide-catalyzed epoxidation, and acid-quenched samples recovered at defined time points in the single-turnover reaction indicate that styrene oxide synthesis is coincident with the formation phase of the fluorescent intermediate. These findings support FAD C(4a)-peroxide being the oxygen atom donor and the identity of the fluorescent intermediate as an FAD C(4a)-hydroxide product of the styrene epoxidation. Overall, four pH-dependent rate constants corresponding to peroxyflavin formation (pK(a) = 7.2), styrene epoxidation (pK(a) = 7.7), styrene oxide dissociation (pK(a) = 8.3), and hydroxyflavin dehydration (pK(a) = 7.6) are needed to fit the single-turnover kinetics.
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Affiliation(s)
- Auric Kantz
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
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Ruangchan N, Tongsook C, Sucharitakul J, Chaiyen P. pH-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase. J Biol Chem 2010; 286:223-33. [PMID: 21030590 DOI: 10.1074/jbc.m110.163881] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
p-Hydroxyphenylacetate (HPA) 3-hydroxylase (HPAH) catalyzes the hydroxylation of HPA at the ortho-position to yield 3,4-dihydroxyphenylacetate. The enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (C(2)). C(2) catalyzes the hydroxylation of HPA using oxygen and reduced FMN as co-substrates. To date, the effects of pH on the oxygenation of the two-component monooxygenases have never been reported. Here, we report the reaction kinetics of C(2)·FMNH(-) with oxygen at various pH values investigated by stopped-flow and rapid quenched-flow techniques. In the absence of HPA, the rate constant for the formation of C4a-hydroperoxy-FMN (∼1.1 × 10(6) m(-1)s(-1)) was unaffected at pH 6.2-9.9, which indicated that the pK(a) of the enzyme-bound reduced FMN was less than 6.2. The rate constant for the following H(2)O(2) elimination step increased with higher pH, which is consistent with a pK(a) of >9.4. In the presence of HPA, the rate constants for the formation of C4a-hydroperoxy-FMN (∼4.8 × 10(4) m(-1)s(-1)) and the ensuing hydroxylation step (15-17 s(-1)) were not significantly affected by the pH. In contrast, the following steps of C4a-hydroxy-FMN dehydration to form oxidized FMN occurred through two pathways that were dependent on the pH of the reaction. One pathway, dominant at low pH, allowed the detection of a C4a-hydroxy-FMN intermediate, whereas the pathway dominant at high pH produced oxidized FMN without an apparent accumulation of the intermediate. However, both pathways efficiently catalyzed hydroxylation without generating significant amounts of wasteful H(2)O(2) at pH 6.2-9.9. The decreased accumulation of the intermediate at higher pH was due to the greater rates of C4a-hydroxy-FMN decay caused by the abolishment of substrate inhibition in the dehydration step at high pH.
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Affiliation(s)
- Nantidaporn Ruangchan
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
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Ellis HR. The FMN-dependent two-component monooxygenase systems. Arch Biochem Biophys 2010; 497:1-12. [PMID: 20193654 DOI: 10.1016/j.abb.2010.02.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/13/2010] [Accepted: 02/16/2010] [Indexed: 11/19/2022]
Abstract
The FMN-dependent two-component monooxygenase systems catalyze a diverse range of reactions. These two-component systems are composed of an FMN reductase enzyme and a monooxygenase enzyme that catalyze the oxidation of various substrates. The role of the reductase is to supply reduced flavin to the monooxygenase enzyme, while the monooxygenase enzyme utilizes the reduced flavin to activate molecular oxygen. Unlike flavoproteins with a tightly or covalently bound prosthetic group, these enzymes catalyze the reductive and oxidative half-reaction on two separate enzymes. An interesting feature of these enzymes is their ability to transfer reduced flavin from the reductase to the monooxygenase enzyme. This review covers the reported mechanistic and structural properties of these enzyme systems, and evaluates the mechanism of flavin transfer.
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Affiliation(s)
- Holly R Ellis
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
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Catalytic role of a conserved cysteine residue in the desulfonation reaction by the alkanesulfonate monooxygenase enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:97-105. [DOI: 10.1016/j.bbapap.2009.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 09/08/2009] [Accepted: 09/11/2009] [Indexed: 11/19/2022]
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