1
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Yang D, Gates BC. Analyzing Stabilities of Metal-Organic Frameworks: Correlation of Stability with Node Coordination to Linkers and Degree of Node Metal Hydrolysis. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2024; 128:8551-8559. [PMID: 38835934 PMCID: PMC11145649 DOI: 10.1021/acs.jpcc.4c02105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 06/06/2024]
Abstract
Among the important properties of metal-organic frameworks (MOFs) is stability, which may limit applications, for example, in separations and catalysis. Many MOFs consist of metal oxo cluster nodes connected by carboxylate linkers. Addressing MOF stability, we highlight connections between metal oxo cluster chemistry and MOF node chemistry, including results characterizing Keggin ions and biological clusters. MOF syntheses yield diverse metal oxo cluster node structures, with varying numbers of metal atoms (3-13) and the tendency to form chains. MOF stabilities reflect a balance between the number of node-linker connections and the degree of node hydrolysis. We summarize literature results showing how MOF stability (the temperature of decomposition in air) depends on the degree of hydrolysis/condensation of the node metals, which is correlated to their degree of substitution with linkers. We suggest that this correlation may help guide the discovery of stable new MOFs, and we foresee opportunities for progress in MOF chemistry emerging from progress in metal oxo cluster chemistry.
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Affiliation(s)
- Dong Yang
- Department of Chemical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Bruce C. Gates
- Department of Chemical Engineering, University of California, Davis, Davis, California 95616, United States
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2
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Yang D, Gates BC. Characterization, Structure, and Reactivity of Hydroxyl Groups on Metal-Oxide Cluster Nodes of Metal-Organic Frameworks: Structural Diversity and Keys to Reactivity and Catalysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305611. [PMID: 37660323 DOI: 10.1002/adma.202305611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Among the most stable metal-organic frameworks (MOFs) are those incorporating nodes that are metal oxide clusters with frames such as Zr6 O8 . This review is a summary of the structure, bonding, and reactivity of MOF node hydroxyl groups, emphasizing those bonded to nodes containing aluminum and zirconium ions. Hydroxyl groups are often present on these nodes, sometimes balancing the charges of the metal ions. They arise during MOF syntheses in aqueous media or in post-synthesis treatments. They are identified with infrared and 1 H nuclear magnetic resonance spectroscopies and characterized by their reactivities with polar compounds such as alcohols. Terminal OH, paired µ2 -OH, and aqua groups on nodes are catalytic sites in numerous reactions. Relatively unreactive hydroxyl groups (such as isolated µ2 -OH groups) may replace reactive groups and inhibit catalysis; some node hydroxyl groups (e.g., µ3 -OH) are mere spectators in catalysis. There are similarities between MOF node hydroxyl groups and those on the surfaces of bulk metal oxides, zeolites, and enzymes, but the comparisons are mostly inexact, and much remains to be understood about MOF node hydroxyl group chemistry. It is posited that understanding and controlling this chemistry will lead to tailored MOFs and improved adsorbents and catalysts.
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Affiliation(s)
- Dong Yang
- Department of Chemical Engineering, University of California, Davis, CA, 95616, USA
| | - Bruce C Gates
- Department of Chemical Engineering, University of California, Davis, CA, 95616, USA
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3
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Shen J, Wu G, Pierce BS, Tsai AL, Zhou M. Free ferrous ions sustain activity of mammalian stearoyl-CoA desaturase-1. J Biol Chem 2023:104897. [PMID: 37290533 PMCID: PMC10359943 DOI: 10.1016/j.jbc.2023.104897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/10/2023] Open
Abstract
Mammalian stearoyl-CoA desaturase-1 (SCD1) introduces a double-bond to a saturated long-chain fatty acid in a reaction catalyzed by a diiron center. The diiron center is well-coordinated by conserved histidine residues and is thought to remain with the enzyme. However, we find here that SCD1 progressively loses its activity during catalysis and becomes fully inactive after nine turnovers. Further studies show that the inactivation of SCD1 is due to the loss of an iron (Fe) ion in the diiron center, and that the addition of free ferrous ions (Fe2+) sustains the enzymatic activity. Using SCD1 labeled with Fe isotope, we further show that free Fe2+ is incorporated into the diiron center only during catalysis. We also discover that the diiron center in SCD1 has prominent electron paramagnetic resonance signals in its diferric state, indicative of distinct coupling between the two ferric ions. These results reveal that the diiron center in SCD1 is structurally dynamic during catalysis and that labile Fe2+ in cells could regulate SCD1 activity, and hence lipid metabolism.
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Affiliation(s)
- Jiemin Shen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gang Wu
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA.
| | - Brad S Pierce
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Ah-Lim Tsai
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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4
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Ahn E, Kim B, Park S, Erwin AL, Sung SH, Hovden R, Mosalaganti S, Cho US. Batch Production of High-Quality Graphene Grids for Cryo-EM: Cryo-EM Structure of Methylococcus capsulatus Soluble Methane Monooxygenase Hydroxylase. ACS NANO 2023; 17:6011-6022. [PMID: 36926824 PMCID: PMC10062032 DOI: 10.1021/acsnano.3c00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) has become a widely used tool for determining the protein structure. Despite recent technical advances, sample preparation remains a major bottleneck for several reasons, including protein denaturation at the air-water interface, the presence of preferred orientations, nonuniform ice layers, etc. Graphene, a two-dimensional allotrope of carbon consisting of a single atomic layer, has recently gained attention as a near-ideal support film for cryo-EM that can overcome these challenges because of its superior properties, including mechanical strength and electrical conductivity. Here, we introduce a reliable, easily implemented, and reproducible method to produce 36 graphene-coated grids within 1.5 days. To demonstrate their practical application, we determined the cryo-EM structure of Methylococcus capsulatus soluble methane monooxygenase hydroxylase (sMMOH) at resolutions of 2.9 and 2.5 Å using Quantifoil and graphene-coated grids, respectively. We found that the graphene-coated grid has several advantages, including a smaller amount of protein required and avoiding protein denaturation at the air-water interface. By comparing the cryo-EM structure of sMMOH with its crystal structure, we identified subtle yet significant geometrical changes at the nonheme diiron center, which may better indicate the active site configuration of sMMOH in the resting/oxidized state.
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Affiliation(s)
- Eungjin Ahn
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Byungchul Kim
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Soyoung Park
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Fine Chemistry, Seoul National University
of Science and Technology, Seoul 139-743, Korea
| | - Amanda L. Erwin
- Department
of Cell and Developmental Biology, University
of Michigan, Ann Arbor, Michigan 48109, United
States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Suk Hyun Sung
- Department
of Materials Science and Engineering, University
of Michigan, Ann Arbor, Michigan 48105, United
States
| | - Robert Hovden
- Department
of Materials Science and Engineering, University
of Michigan, Ann Arbor, Michigan 48105, United
States
- Applied
Physics Program, University of Michigan, Ann Arbor, Michigan 48105, United States
| | - Shyamal Mosalaganti
- Department
of Cell and Developmental Biology, University
of Michigan, Ann Arbor, Michigan 48109, United
States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Uhn-Soo Cho
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Shen J, Wu G, Pierce BS, Tsai AL, Zhou M. Free ferrous ions sustain activity of mammalian stearoyl-CoA desaturase-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533000. [PMID: 36993326 PMCID: PMC10055294 DOI: 10.1101/2023.03.17.533000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mammalian stearoyl-CoA desaturase-1 (SCD1) introduces a double-bond to a saturated long-chain fatty acid and the reaction is catalyzed by a diiron center, which is well-coordinated by conserved histidine residues and is thought to remain with enzyme. However, we find that SCD1 progressively loses its activity during catalysis and becomes fully inactive after nine turnovers. Further studies show that the inactivation of SCD1 is due to the loss of an iron (Fe) ion in the diiron center, and that the addition of free ferrous ions (Fe 2+ ) sustains the enzymatic activity. Using SCD1 labeled with Fe isotope, we further show that free Fe 2+ is incorporated into the diiron center only during catalysis. We also discover that the diiron center in SCD1 has prominent electron paramagnetic resonance signals in its diferric state, indicative of distinct coupling between the two ferric ions. These results reveal that the diiron center in SCD1 is structurally dynamic during catalysis and that labile Fe 2+ in cells could regulate SCD1 activity, and hence lipid metabolism.
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Affiliation(s)
- Jiemin Shen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gang Wu
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Brad S. Pierce
- Department of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Ah-Lim Tsai
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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6
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Halim NFAA, Ali MSM, Leow ATC, Rahman RNZRA. Membrane fatty acid desaturase: biosynthesis, mechanism, and architecture. Appl Microbiol Biotechnol 2022; 106:5957-5972. [PMID: 36063178 DOI: 10.1007/s00253-022-12142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022]
Abstract
Fatty acid desaturase catalyzes the desaturation reactions by inserting double bonds into the fatty acyl chain, producing unsaturated fatty acids, which play a vital part in the synthesis of polyunsaturated fatty acids. Though soluble fatty acid desaturases have been described extensively in advanced organisms, there are very limited studies of membrane fatty acid desaturases due to their difficulties in producing a sufficient amount of recombinant desaturases. However, the advancement of technology has shown substantial progress towards the development of elucidating crystal structures of membrane fatty acid desaturase, thus, allowing modification of structure to be manipulated. Understanding the structure, mechanism, and biosynthesis of fatty acid desaturase lay a foundation for the potential production of various strategies associated with alteration and modifications of polyunsaturated fatty acids. This manuscript presents the current state of knowledge and understanding about the structure, mechanisms, and biosynthesis of fatty acid desaturase. In addition, the role of unsaturated fatty acid desaturases in health and diseases is also encompassed. This will be useful in understanding the molecular basis and structural protein of fatty acid desaturase that are significant for the advancement of therapeutic strategies associated with the improvement of health status. KEY POINTS: • Current state of knowledge and understanding about the biosynthesis, mechanisms, and structure of fatty acid desaturase. • The role of unsaturated fatty acid desaturase. • The molecular basis and structural protein elucidated the crystal structure of fatty acid desaturase.
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Affiliation(s)
- Nur Farah Anis Abd Halim
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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7
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Guan H, Tung CH, Liu L. Methane Monooxygenase Mimic Asymmetric Oxidation: Self-Assembling μ-Hydroxo, Carboxylate-Bridged Diiron(III)-Catalyzed Enantioselective Dehydrogenation. J Am Chem Soc 2022; 144:5976-5984. [PMID: 35324200 DOI: 10.1021/jacs.2c00638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mimicking naturally occurring metalloenzymes to enrich the diversity of catalytic asymmetric oxidation reactions is a long-standing goal for modern chemistry. Toward this end, a range of methane monooxygenase (MMO) mimic chiral carboxylate-bridged (μ-hydroxo) diiron(III) dimer complexes using salan as basal ligand and sodium aryl carboxylate as additive have been designed and synthesized. The chiral diiron complexes exhibit efficient catalytic reactivity in dehydrogenative kinetic resolution of indolines using environmentally benign hydrogen peroxide as oxidant. In particular, complex C9 bearing sterically encumbered salan ligands and a 2-naphthoate bridge is identified as the optimal catalyst in terms of chiral recognition. Further investigation reveals that this MMO mimic chiral catalyst can be readily generated by self-assembly under the dehydrogenation conditions. The self-assembling catalytic system is applicable to a series of indolines with multiple stereocenters and diverse substituent patterns in high efficiency with a high level of chiral recognition (selectivity factor up to 153). Late-stage dehydrogenative kinetic resolution of bioactive molecules is further examined.
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Affiliation(s)
- Honghao Guan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Lei Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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8
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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9
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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10
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Nachtschatt M, Okada S, Speight R. Integral Membrane Fatty Acid Desaturases: A Review of Biochemical, Structural, and Biotechnological Advances. EUR J LIPID SCI TECH 2020. [DOI: 10.1002/ejlt.202000181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthias Nachtschatt
- Commonwealth Scientific and Industrial Research Organisation Clunies Ross St. Canberra ACT 2601 Australia
- Queensland University of Technology 2 George St. Brisbane QLD 4000 Australia
| | - Shoko Okada
- Commonwealth Scientific and Industrial Research Organisation Clunies Ross St. Canberra ACT 2601 Australia
| | - Robert Speight
- Queensland University of Technology 2 George St. Brisbane QLD 4000 Australia
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11
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Shen J, Wu G, Tsai AL, Zhou M. Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase. J Mol Biol 2020; 432:5152-5161. [PMID: 32470559 PMCID: PMC7483794 DOI: 10.1016/j.jmb.2020.05.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/16/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022]
Abstract
Stearoyl-CoA desaturase 1 (SCD1) is a membrane-embedded metalloenzyme that catalyzes the formation of a double bond on a saturated acyl-CoA. SCD1 has a diiron center and its proper function requires an electron transport chain composed of NADH (or NADPH), cytochrome b5 reductase (b5R), and cytochrome b5 (cyt b5). Since SCD1 is a key regulator in fat metabolism and is required for survival of cancer cells, there is intense interest in targeting SCD1 for various metabolic diseases and cancers. Crystal structures of human and mouse SCD1 were reported recently; however, both proteins have two zinc ions instead of two iron ions in the catalytic center, and as a result, the enzymes are inactive. Here we report a general approach for incorporating iron into heterologously expressed proteins in HEK293 cells. We produced mouse SCD1 that contains a diiron center and visualized its diiron center by solving its crystal structure to 3.5 Å. We assembled the entire electron transport chain using the purified soluble domains of cyt b5 and b5R, and the purified mouse SCD1, and we showed that three proteins coordinate to produce proper products. These results established an in vitro system that allows precise perturbations of the electron transport chain for the understanding of the catalytic mechanism in SCD1.
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Affiliation(s)
- Jiemin Shen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Gang Wu
- Division of Hematology, Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin, Houston, TX 77030, USA
| | - Ah-Lim Tsai
- Division of Hematology, Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin, Houston, TX 77030, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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12
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Kisgeropoulos EC, Griese JJ, Smith ZR, Branca RMM, Schneider CR, Högbom M, Shafaat HS. Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein. J Am Chem Soc 2020; 142:5338-5354. [PMID: 32062969 DOI: 10.1021/jacs.0c00333] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater MnII affinity than FeII affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.
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Affiliation(s)
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | | | - Rui M M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, SE-171 21 Solna, Sweden
| | | | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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13
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Kutin Y, Kositzki R, Branca RMM, Srinivas V, Lundin D, Haumann M, Högbom M, Cox N, Griese JJ. Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins. J Biol Chem 2019; 294:18372-18386. [PMID: 31591267 DOI: 10.1074/jbc.ra119.010570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/04/2019] [Indexed: 11/06/2022] Open
Abstract
A heterobimetallic Mn/Fe cofactor is present in the R2 subunit of class Ic ribonucleotide reductases (R2c) and in R2-like ligand-binding oxidases (R2lox). Although the protein-derived metal ligands are the same in both groups of proteins, the connectivity of the two metal ions and the chemistry each cofactor performs are different: in R2c, a one-electron oxidant, the Mn/Fe dimer is linked by two oxygen bridges (μ-oxo/μ-hydroxo), whereas in R2lox, a two-electron oxidant, it is linked by a single oxygen bridge (μ-hydroxo) and a fatty acid ligand. Here, we identified a second coordination sphere residue that directs the divergent reactivity of the protein scaffold. We found that the residue that directly precedes the N-terminal carboxylate metal ligand is conserved as a glycine within the R2lox group but not in R2c. Substitution of the glycine with leucine converted the resting-state R2lox cofactor to an R2c-like cofactor, a μ-oxo/μ-hydroxo-bridged MnIII/FeIII dimer. This species has recently been observed as an intermediate of the oxygen activation reaction in WT R2lox, indicating that it is physiologically relevant. Cofactor maturation in R2c and R2lox therefore follows the same pathway, with structural and functional divergence of the two cofactor forms following oxygen activation. We also show that the leucine-substituted variant no longer functions as a two-electron oxidant. Our results reveal that the residue preceding the N-terminal metal ligand directs the cofactor's reactivity toward one- or two-electron redox chemistry, presumably by setting the protonation state of the bridging oxygens and thereby perturbing the redox potential of the Mn ion.
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Affiliation(s)
- Yury Kutin
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Box 1031, SE-171 21 Solna, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia.
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden.
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14
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Osborne CD, Haritos VS. Beneath the surface: Evolution of methane activity in the bacterial multicomponent monooxygenases. Mol Phylogenet Evol 2019; 139:106527. [PMID: 31173882 DOI: 10.1016/j.ympev.2019.106527] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 02/09/2023]
Abstract
The bacterial multicomponent monooxygenase (BMM) family has evolved to oxidise a wide array of hydrocarbon substrates of importance to environmental emissions and biotechnology: foremost amongst these is methane, which requires among the most powerful oxidant in biology to activate. To understand how the BMM evolved methane oxidation activity, we investigated the changes in the enzyme family at different levels: operonic, phylogenetic analysis of the catalytic hydroxylase, subunit or folding factor presence, and sequence-function analysis across the entirety of the BMM phylogeny. Our results show that the BMM evolution of new activities was enabled by incremental increases in oxidative power of the active site, and these occur in multiple branches of the hydroxylase phylogenetic tree. While the hydroxylase primary sequence changes that resulted in increased oxidative power of the enzyme appear to be minor, the principle evolutionary advances enabling methane activity occurred in the other components of the BMM complex and in the recruitment of stability proteins. We propose that enzyme assembly and stabilization factors have independently-evolved multiple times in the BMM family to support enzymes that oxidise increasingly difficult substrates. Herein, we show an important example of evolution of catalytic function where modifications to the active site and substrate accessibility, which are the usual focus of enzyme evolution, are overshadowed by broader scale changes to structural stabilization and non-catalytic unit development. Retracing macroscale changes during enzyme evolution, as demonstrated here, should find ready application to other enzyme systems and in protein design.
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Affiliation(s)
- Craig D Osborne
- Department of Chemical Engineering, Monash University, Wellington Road, Clayton 3800, Australia
| | - Victoria S Haritos
- Department of Chemical Engineering, Monash University, Wellington Road, Clayton 3800, Australia.
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15
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Barman SK, Cano J, Lloret F, Mukherjee R. Single-Molecule-Magnet FeII4FeIII2 and Antiferromagnetic FeIII4 Coordination Clusters. Inorg Chem 2019; 58:8086-8099. [DOI: 10.1021/acs.inorgchem.9b00828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suman K. Barman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
| | - Joan Cano
- Departament de Química, Inorgànica/Instituto de Ciencia Molecular (ICMOL), Universitat de València, Polígono de
la Coma, s/n, 46980 Paterna (València), Spain
| | - Francesc Lloret
- Departament de Química, Inorgànica/Instituto de Ciencia Molecular (ICMOL), Universitat de València, Polígono de
la Coma, s/n, 46980 Paterna (València), Spain
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16
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YAGUCHI R, FURUTACHI H, SHIROTSUKI S, ZHANG X, ISHIKAWA T, AKINE S, TOSHA T, FUJINAMI S, SUZUKI M, KITAGAWA T. Synthesis and Crystal Structure of the Bis(μ-hydroxo)diiron(II) Complex with Tridentate Ligands Having a Sterically Bulky Imidazolyl Group. X-RAY STRUCTURE ANALYSIS ONLINE 2019. [DOI: 10.2116/xraystruct.35.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Reiko YAGUCHI
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Hideki FURUTACHI
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Sanae SHIROTSUKI
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Xi ZHANG
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Takanao ISHIKAWA
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Shigehisa AKINE
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University
| | | | - Shuhei FUJINAMI
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Masatatsu SUZUKI
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Teizo KITAGAWA
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
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17
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Bedin M, Agarwala H, Marx J, Schünemann V, Ott S, Thapper A. Synthesis and properties of a heterobimetallic iron-manganese complex and its comparison with homobimetallic analogues. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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18
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Yu MJ, Chen SL. From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
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19
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Griese JJ, Kositzki R, Haumann M, Högbom M. Assembly of a heterodinuclear Mn/Fe cofactor is coupled to tyrosine-valine ether cross-link formation in the R2-like ligand-binding oxidase. J Biol Inorg Chem 2019; 24:211-221. [PMID: 30689052 PMCID: PMC6399176 DOI: 10.1007/s00775-019-01639-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/18/2019] [Indexed: 11/28/2022]
Abstract
R2-like ligand-binding oxidases (R2lox) assemble a heterodinuclear Mn/Fe cofactor which performs reductive dioxygen (O2) activation, catalyzes formation of a tyrosine-valine ether cross-link in the protein scaffold, and binds a fatty acid in a putative substrate channel. We have previously shown that the N-terminal metal binding site 1 is unspecific for manganese or iron in the absence of O2, but prefers manganese in the presence of O2, whereas the C-terminal site 2 is specific for iron. Here, we analyze the effects of amino acid exchanges in the cofactor environment on cofactor assembly and metalation specificity using X-ray crystallography, X-ray absorption spectroscopy, and metal quantification. We find that exchange of either the cross-linking tyrosine or the valine, regardless of whether the mutation still allows cross-link formation or not, results in unspecific manganese or iron binding at site 1 both in the absence or presence of O2, while site 2 still prefers iron as in the wild-type. In contrast, a mutation that blocks binding of the fatty acid does not affect the metal specificity of either site under anoxic or aerobic conditions, and cross-link formation is still observed. All variants assemble a dinuclear trivalent metal cofactor in the aerobic resting state, independently of cross-link formation. These findings imply that the cross-link residues are required to achieve the preference for manganese in site 1 in the presence of O2. The metalation specificity, therefore, appears to be established during the redox reactions leading to cross-link formation.
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Affiliation(s)
- Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden. .,Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden.
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.
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20
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Reaction of O 2 with a diiron protein generates a mixed-valent Fe 2+/Fe 3+ center and peroxide. Proc Natl Acad Sci U S A 2019; 116:2058-2067. [PMID: 30659147 DOI: 10.1073/pnas.1809913116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The gene encoding the cyanobacterial ferritin SynFtn is up-regulated in response to copper stress. Here, we show that, while SynFtn does not interact directly with copper, it is highly unusual in several ways. First, its catalytic diiron ferroxidase center is unlike those of all other characterized prokaryotic ferritins and instead resembles an animal H-chain ferritin center. Second, as demonstrated by kinetic, spectroscopic, and high-resolution X-ray crystallographic data, reaction of O2 with the di-Fe2+ center results in a direct, one-electron oxidation to a mixed-valent Fe2+/Fe3+ form. Iron-O2 chemistry of this type is currently unknown among the growing family of proteins that bind a diiron site within a four α-helical bundle in general and ferritins in particular. The mixed-valent form, which slowly oxidized to the more usual di-Fe3+ form, is an intermediate that is continually generated during mineralization. Peroxide, rather than superoxide, is shown to be the product of O2 reduction, implying that ferroxidase centers function in pairs via long-range electron transfer through the protein resulting in reduction of O2 bound at only one of the centers. We show that electron transfer is mediated by the transient formation of a radical on Tyr40, which lies ∼4 Å from the diiron center. As well as demonstrating an expansion of the iron-O2 chemistry known to occur in nature, these data are also highly relevant to the question of whether all ferritins mineralize iron via a common mechanism, providing unequivocal proof that they do not.
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21
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22
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Felip-León C, Angulo-Pachón CA, Miravet JF, Galindo F. Self-Assembly Controls Reactivity with Nitric Oxide: Implications for Fluorescence Sensing. ACS OMEGA 2018; 3:15538-15545. [PMID: 31458209 PMCID: PMC6643459 DOI: 10.1021/acsomega.8b01869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/31/2018] [Indexed: 06/10/2023]
Abstract
Three molecules containing the fluorophore 4-amino-1,8-naphthalimide (ANI) and showing different tendencies to self-assembly in aqueous environment have been prepared and fully characterized. The fluorescence emissions of two of these compounds in aqueous solutions are efficiently quenched in the presence of nitric oxide (NO) in aerated medium. Nuclear magnetic resonance and mass spectrometry techniques indicate that NO/O2 induces deamination of the ANI fluorophore, resulting in nonemissive 1,8-naphtalimide derivatives. It is found that the reactivity toward NO/O2 is regulated by the different aggregation modes presented by the molecules in aqueous medium. In this way, the molecules displaying fluorescence response toward NO/O2 are those with weak self-association properties whereas the compound with a high hydrophobic character (self-assembling into large nanoparticles) is insensitive to this species. Ultimately, the results described here could not only set the basis for the design of fluorescent bioprobes for NO/O2 based on ANI derivatives or other monoamino compounds but also could raise awareness about the importance of supramolecular interactions for the design of chemosensors.
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Affiliation(s)
- Carles Felip-León
- Departamento de Química
Inorgánica y Orgánica, Universitat
Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain
| | - César A. Angulo-Pachón
- Departamento de Química
Inorgánica y Orgánica, Universitat
Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain
| | - Juan F. Miravet
- Departamento de Química
Inorgánica y Orgánica, Universitat
Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain
| | - Francisco Galindo
- Departamento de Química
Inorgánica y Orgánica, Universitat
Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain
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23
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Biocatalytic Oxidations of Substrates through Soluble Methane Monooxygenase from Methylosinus sporium 5. Catalysts 2018. [DOI: 10.3390/catal8120582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Methane, an important greenhouse gas, has a 20-fold higher heat capacity than carbon dioxide. Earlier, through advanced spectroscopy and structural studies, the mechanisms underlying the extremely stable C–H activation of soluble methane monooxygenase (sMMO) have been elucidated in Methylosinus trichosporium OB3b and Methylococcus capsulatus Bath. Here, sMMO components—including hydroxylase (MMOH), regulatory (MMOB), and reductase (MMOR)—were expressed and purified from a type II methanotroph, Methylosinus sporium strain 5 (M. sporium 5), to characterize its hydroxylation mechanism. Two molar equivalents of MMOB are necessary to achieve catalytic activities and oxidized a broad range of substrates including alkanes, alkenes, halogens, and aromatics. Optimal activities were observed at pH 7.5 for most substrates possibly because of the electron transfer environment in MMOR. Substitution of MMOB or MMOR from another type II methanotroph, Methylocystis species M, retained specific enzyme activities, demonstrating the successful cross-reactivity of M. sporium 5. These results will provide fundamental information for further enzymatic studies to elucidate sMMO mechanisms.
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24
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Osborne CD, Haritos VS. Horizontal gene transfer of three co-inherited methane monooxygenase systems gave rise to methanotrophy in the Proteobacteria. Mol Phylogenet Evol 2018; 129:171-181. [PMID: 30149053 DOI: 10.1016/j.ympev.2018.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/01/2018] [Accepted: 08/19/2018] [Indexed: 12/22/2022]
Abstract
The critical role that bacterial methanotrophs have in regulating the environmental concentrations of the potent greenhouse gas, methane, under aerobic conditions is dependent on monooxygenase enzymes which oxidise the substrate as both a carbon and energy source. Despite the importance of these organisms, the evolutionary origins of aerobic methane oxidation capability and its relationship to proteobacterial evolution is not well understood. Here we investigated the phylogenetic relationship of proteobacterial methanotrophs with related, non-methanotrophic bacteria using 16S rRNA and the evolution of two forms of methane monooxygenase: membrane bound (pMMO and pXMO) and cytoplasmic (sMMO). Through analysis we have concluded that extant proteobacterial methanotrophs evolved from up to five ancestral species, and that all three methane monooxygenase systems, pMMO, pXMO and sMMO, were likely present in the ancestral species (although pXMO and sMMO are not present in most of the present day methanotrophs). Here we propose that the three monooxygenase systems entered the ancestral species by horizontal gene transfer, with these likely to have pre-existing physiological and metabolic attributes that supported conversion to methanotrophy. Further, we suggest that prior to these enzyme systems developing methane oxidation capabilities, the membrane-bound and cytoplasmic monooxygenases were already both functionally and phylogenetically associated. These results not only suggest that sMMO and pXMO have a far greater role in methanotrophic evolution than previously understood but also implies that the co-inheritance of membrane bound and cytoplasmic monooxygenases have roles additional to that of supporting methanotrophy.
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Affiliation(s)
- Craig D Osborne
- Department of Chemical Engineering, Monash University, Wellington Road, Clayton 3800, Australia
| | - Victoria S Haritos
- Department of Chemical Engineering, Monash University, Wellington Road, Clayton 3800, Australia.
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25
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26
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Griese JJ, Branca RMM, Srinivas V, Högbom M. Ether cross-link formation in the R2-like ligand-binding oxidase. J Biol Inorg Chem 2018; 23:879-886. [PMID: 29946980 PMCID: PMC6060897 DOI: 10.1007/s00775-018-1583-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
Abstract
R2-like ligand-binding oxidases contain a dinuclear metal cofactor which can consist either of two iron ions or one manganese and one iron ion, but the heterodinuclear Mn/Fe cofactor is the preferred assembly in the presence of MnII and FeII in vitro. We have previously shown that both types of cofactor are capable of catalyzing formation of a tyrosine–valine ether cross-link in the protein scaffold. Here we demonstrate that Mn/Fe centers catalyze cross-link formation more efficiently than Fe/Fe centers, indicating that the heterodinuclear cofactor is the biologically relevant one. We further explore the chemical potential of the Mn/Fe cofactor by introducing mutations at the cross-linking valine residue. We find that cross-link formation is possible also to the tertiary beta-carbon in an isoleucine, but not to the secondary beta-carbon or tertiary gamma-carbon in a leucine, nor to the primary beta-carbon of an alanine. These results illustrate that the reactivity of the cofactor is highly specific and directed.
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Affiliation(s)
- Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden. .,Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden.
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 21, Solna, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.
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27
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Shakeel T, Gupta M, Fatma Z, Kumar R, Kumar R, Singh R, Sharma M, Jade D, Gupta D, Fatma T, Yazdani SS. A consensus-guided approach yields a heat-stable alkane-producing enzyme and identifies residues promoting thermostability. J Biol Chem 2018; 293:9148-9161. [PMID: 29632075 PMCID: PMC6005442 DOI: 10.1074/jbc.ra117.000639] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/06/2018] [Indexed: 01/02/2023] Open
Abstract
Aldehyde-deformylating oxygenase (ADO) is an essential enzyme for production of long-chain alkanes as drop-in biofuels, which are compatible with existing fuel systems. The most active ADOs are present in mesophilic cyanobacteria, especially Nostoc punctiforme Given the potential applications of thermostable enzymes in biorefineries, here we generated a thermostable (Cts)-ADO based on a consensus of ADO sequences from several thermophilic cyanobacterial strains. Using an in silico design pipeline and a metagenome library containing 41 hot-spring microbial communities, we created Cts-ADO. Cts-ADO displayed a 3.8-fold increase in pentadecane production on raising the temperature from 30 to 42 °C, whereas ADO from N. punctiforme (Np-ADO) exhibited a 1.7-fold decline. 3D structure modeling and molecular dynamics simulations of Cts- and Np-ADO at different temperatures revealed differences between the two enzymes in residues clustered on exposed loops of these variants, which affected the conformation of helices involved in forming the ADO catalytic core. In Cts-ADO, this conformational change promoted ligand binding to its preferred iron, Fe2, in the di-iron cluster at higher temperature, but the reverse was observed in Np-ADO. Detailed mapping of residues conferring Cts-ADO thermostability identified four amino acids, which we substituted individually and together in Np-ADO. Among these substitution variants, A161E was remarkably similar to Cts-ADO in terms of activity optima, kinetic parameters, and structure at higher temperature. A161E was located in loop L6, which connects helices H5 and H6, and supported ligand binding to Fe2 at higher temperatures, thereby promoting optimal activity at these temperatures and explaining the increased thermostability of Cts-ADO.
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Affiliation(s)
- Tabinda Shakeel
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Mayank Gupta
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Zia Fatma
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | | | | | - Rahul Singh
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Medha Sharma
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | | | | | - Tasneem Fatma
- the Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Syed Shams Yazdani
- From the Microbial Engineering Group, .,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
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28
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Garba L, Mohamad Yussoff MA, Abd Halim KB, Ishak SNH, Mohamad Ali MS, Oslan SN, Raja Abd Rahman RNZ. Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8. PeerJ 2018; 6:e4347. [PMID: 29576935 PMCID: PMC5863719 DOI: 10.7717/peerj.4347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/19/2018] [Indexed: 01/02/2023] Open
Abstract
Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacterial membrane fatty acid desaturases are not available, relevant information about the enzymes are derived from their amino acid sequences, site-directed mutagenesis and domain swapping in similar membrane-bound desaturases. The cold-tolerant Pseudomonas sp. AMS8 was found to produce high amount of monounsaturated fatty acids at low temperature. Subsequently, an active Δ9-fatty acid desaturase was isolated and functionally expressed in Escherichia coli. In this paper we report homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8 for the first time to the best of our knowledge. Three dimensional structure of the enzyme was built using MODELLER version 9.18 using a suitable template. The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. The structure was subjected to energy minimization and checked for correctness using Ramachandran plots and ERRAT, which showed a good quality model of 91.6 and 65.0%, respectively. The protein model was used to preform MD simulation and docking of palmitic acid using CHARMM36 force field in GROMACS Version 5 and Autodock tool Version 4.2, respectively. The docking simulation with the lowest binding energy, -6.8 kcal/mol had a number of residues in close contact with the docked palmitic acid namely, Ile26, Tyr95, Val179, Gly180, Pro64, Glu203, His34, His206, His71, Arg182, Thr85, Lys98 and His177. Interestingly, among the binding residues are His34, His71 and His206 from the first, second, and third conserved histidine motif, respectively, which constitute the active site of the enzyme. The results obtained are in compliance with the in vivo activity of the Δ9-fatty acid desaturase on the membrane phospholipids.
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Affiliation(s)
- Lawal Garba
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Science, Gombe State University, Gombe, Gombe State, Nigeria
| | - Mohamad Ariff Mohamad Yussoff
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang Darul Makmur, Malaysia
| | - Khairul Bariyyah Abd Halim
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang Darul Makmur, Malaysia
| | - Siti Nor Hasmah Ishak
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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29
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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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30
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E. Bjorck C, D. Dobson P, Pandhal J. Biotechnological conversion of methane to methanol: evaluation of progress and potential. AIMS BIOENGINEERING 2018. [DOI: 10.3934/bioeng.2018.1.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Mondal D, Bhattacharya K. Synthesis and structural characterization of a hemiacetal and aldehyde bound diiron(III) complex with two different coordination numbers: A product by oxidative cleavage of carbon nitrogen single bond. INORG CHEM COMMUN 2017. [DOI: 10.1016/j.inoche.2017.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Miller EK, Trivelas NE, Maugeri PT, Blaesi EJ, Shafaat HS. Time-Resolved Investigations of Heterobimetallic Cofactor Assembly in R2lox Reveal Distinct Mn/Fe Intermediates. Biochemistry 2017; 56:3369-3379. [PMID: 28574263 DOI: 10.1021/acs.biochem.7b00403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assembly mechanism of the Mn/Fe ligand-binding oxidases (R2lox), a family of proteins that are homologous to the nonheme diiron carboxylate enzymes, has been investigated using time-resolved techniques. Multiple heterobimetallic intermediates that exhibit unique spectral features, including visible absorption bands and exceptionally broad electron paramagnetic resonance signatures, are observed through optical and magnetic resonance spectroscopies. On the basis of comparison to known diiron species and model compounds, the spectra have been attributed to (μ-peroxo)-MnIII/FeIII and high-valent Mn/Fe species. Global spectral analysis coupled with isotopic substitution and kinetic modeling reveals elementary rate constants for the assembly of Mn/Fe R2lox under aerobic conditions. A complete reaction mechanism for cofactor maturation that is consistent with experimental data has been developed. These results suggest that the Mn/Fe cofactor can perform direct C-H bond abstraction, demonstrating the potential for potent chemical reactivity that remains unexplored.
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Affiliation(s)
| | | | | | - Elizabeth J Blaesi
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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33
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Ross MO, Rosenzweig AC. A tale of two methane monooxygenases. J Biol Inorg Chem 2017; 22:307-319. [PMID: 27878395 PMCID: PMC5352483 DOI: 10.1007/s00775-016-1419-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.
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Affiliation(s)
- Matthew O Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
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34
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Identification of residues important for the activity of aldehyde-deformylating oxygenase through investigation into the structure-activity relationship. BMC Biotechnol 2017; 17:31. [PMID: 28302170 PMCID: PMC5356278 DOI: 10.1186/s12896-017-0351-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 03/08/2017] [Indexed: 12/24/2022] Open
Abstract
Background Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in the biosynthetic pathway of fatty alk(a/e)nes in cyanobacteria. However, cADO (cyanobacterial ADO) showed extreme low activity with the kcat value below 1 min−1, which would limit its application in biofuel production. To identify the activity related key residues of cADO is urgently required. Results The amino acid residues which might affect cADO activity were identified based on the crystal structures and sequence alignment of cADOs, including the residues close to the di-iron center (Tyr39, Arg62, Gln110, Tyr122, Asp143 of cADO-1593), the protein surface (Trp 178 of cADO-1593), and those involved in two important hydrogen bonds (Gln49, Asn123 of cADO-1593, and Asp49, Asn123 of cADO-sll0208) and in the oligopeptide whose conformation changed in the absence of the di-iron center (Leu146, Asn149, Phe150 of cADO-1593, and Thr146, Leu148, Tyr150 of cADO-sll0208). The variants of cADO-1593 from Synechococcus elongatus PCC7942 and cADO-sll0208 from Synechocystis sp. PCC6803 were constructed, overexpressed, purified and kinetically characterized. The kcat values of L146T, Q49H/N123H/F150Y and W178R of cADO-1593 and L148R of cADO-sll0208 were increased by more than two-fold, whereas that of R62A dropped by 91.1%. N123H, Y39F and D143A of cADO-1593, and Y150F of cADO-sll0208 reduced activities by ≤ 20%. Conclusions Some important amino acids, which exerted some effects on cADO activity, were identified. Several enzyme variants exhibited greatly reduced activity, while the kcat values of several mutants are more than two-fold higher than the wild type. This study presents the report on the relationship between amino acid residues and enzyme activity of cADOs, and the information will provide a guide for enhancement of cADO activity through protein engineering. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0351-8) contains supplementary material, which is available to authorized users.
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35
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Wang VCC, Maji S, Chen PPY, Lee HK, Yu SSF, Chan SI. Alkane Oxidation: Methane Monooxygenases, Related Enzymes, and Their Biomimetics. Chem Rev 2017; 117:8574-8621. [PMID: 28206744 DOI: 10.1021/acs.chemrev.6b00624] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methane monooxygenases (MMOs) mediate the facile conversion of methane into methanol in methanotrophic bacteria with high efficiency under ambient conditions. Because the selective oxidation of methane is extremely challenging, there is considerable interest in understanding how these enzymes carry out this difficult chemistry. The impetus of these efforts is to learn from the microbes to develop a biomimetic catalyst to accomplish the same chemical transformation. Here, we review the progress made over the past two to three decades toward delineating the structures and functions of the catalytic sites in two MMOs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO). sMMO is a water-soluble three-component protein complex consisting of a hydroxylase with a nonheme diiron catalytic site; pMMO is a membrane-bound metalloenzyme with a unique tricopper cluster as the site of hydroxylation. The metal cluster in each of these MMOs harnesses O2 to functionalize the C-H bond using different chemistry. We highlight some of the common basic principles that they share. Finally, the development of functional models of the catalytic sites of MMOs is described. These efforts have culminated in the first successful biomimetic catalyst capable of efficient methane oxidation without overoxidation at room temperature.
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Affiliation(s)
- Vincent C-C Wang
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Suman Maji
- School of Chemical Engineering and Physical Sciences, Lovely Professional University , Jalandhar-Delhi G. T. Road (NH-1), Phagwara, Punjab India 144411
| | - Peter P-Y Chen
- Department of Chemistry, National Chung Hsing University , 250 Kuo Kuang Road, Taichung 402, Taiwan
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Sunney I Chan
- Institute of Chemistry, Academia Sinica , 128, Section 2, Academia Road, Nankang, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University , No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Noyes Laboratory, 127-72, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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36
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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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37
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Rokob TA. Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase. J Am Chem Soc 2016; 138:14623-14638. [PMID: 27682344 DOI: 10.1021/jacs.6b06987] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxygenation of aromatic rings using O2 is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenzyme A epoxidase, BoxB. The calculations revealed four possible pathways for attacking the aromatic ring: (a) electrophilic (2e-) attack by a bis(μ-oxo)-diiron(IV) species (Q pathway); (b) electrophilic (2e-) attack via the σ* orbital of a μ-η2:η2-peroxo-diiron(III) intermediate (Pσ* pathway); (c) radical (1e-) attack via the π*-orbital of a superoxo-diiron(II,III) species (Pπ* pathway); (d) radical (1e-) attack of a partially quenched bis(μ-oxo)-diiron(IV) intermediate (Q' pathway). The results allowed earlier work of de Visser on olefin epoxidation by diiron complexes and QM-cluster studies of Liao and Siegbahn on BoxB to be put into a broader perspective. Parallels with epoxidation using organic peracids were also examined. Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.
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Affiliation(s)
- Tibor András Rokob
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar Tudósok körútja 2, 1117 Budapest, Hungary
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38
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Lawton TJ, Rosenzweig AC. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion. J Am Chem Soc 2016; 138:9327-40. [PMID: 27366961 PMCID: PMC5242187 DOI: 10.1021/jacs.6b04568] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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39
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Li M, Guo W, Chen X. A novel NADPH-dependent reductase of Sulfobacillus acidophilus TPY phenol hydroxylase: expression, characterization, and functional analysis. Appl Microbiol Biotechnol 2016; 100:10417-10428. [PMID: 27376793 DOI: 10.1007/s00253-016-7704-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
The reductase component (MhpP) of the Sulfobacillus acidophilus TPY multicomponent phenol hydroxylase exhibits only 40 % similarity to Pseudomonas sp. strain CF600 phenol hydroxylase reductase. Amino acid sequence alignment analysis revealed that four cysteine residues (Cys-X 4 -Cys-X 2 -Cys-X 29-35 -Cys) are conserved in the N terminus of MhpP for [2Fe-2S] cluster binding, and two other motifs (RXYS and GXXS/T) are conserved in the C terminus for binding the isoalloxazine and phosphate groups of flavin adenine dinucleotide (FAD). Two motifs (S/T-R and yXCGp) responsible for binding to reduce nicotinamide adenine dinucleotide phosphate (NADPH) are also conserved in MhpP, although some residues differ. To confirm the function of this reductase, MhpP was heterologously expressed in Escherichia coli BL21(DE3) and purified. UV-visible spectroscopy and electron paramagnetic resonance spectroscopy revealed that MhpP contains a [2Fe-2S] cluster. MhpP mutants in which the four cysteine residues were substituted via site-directed mutagenesis lost the ability to bind the [2Fe-2S] cluster, resulting in a decrease in enzyme-specific oxidation of NADPH. Thin-layer chromatography revealed that MhpP contains FAD. Substrate specificity analyses confirmed that MhpP uses NADPH rather than NADH as an electron donor. MhpP oxidizes NADPH using cytochrome c, potassium ferricyanide, or nitro blue tetrazolium as an electron acceptor, with a specific activity of 1.7 ± 0.36, 0.78 ± 0.13, and 0.16 ± 0.06 U/mg, respectively. Thus, S. acidophilus TPY MhpP is a novel NADPH-dependent reductase component of phenol hydroxylase that utilizes FAD and a [2Fe-2S] cluster as cofactors.
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Affiliation(s)
- Meng Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Daxue Road 184, Xiamen, 361005, People's Republic of China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, People's Republic of China
| | - Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Daxue Road 184, Xiamen, 361005, People's Republic of China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, People's Republic of China
| | - Xinhua Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Daxue Road 184, Xiamen, 361005, People's Republic of China. .,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, People's Republic of China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.
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40
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Engelmann X, Monte-Pérez I, Ray K. Oxidationsreaktionen mit bioinspirierten einkernigen Nicht-Häm-Oxidometallkomplexen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600507] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xenia Engelmann
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Inés Monte-Pérez
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Kallol Ray
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
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41
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Engelmann X, Monte-Pérez I, Ray K. Oxidation Reactions with Bioinspired Mononuclear Non-Heme Metal-Oxo Complexes. Angew Chem Int Ed Engl 2016; 55:7632-49. [DOI: 10.1002/anie.201600507] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 03/15/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Xenia Engelmann
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Inés Monte-Pérez
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Kallol Ray
- Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Strasse 2 12489 Berlin Germany
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42
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Kutin Y, Srinivas V, Fritz M, Kositzki R, Shafaat HS, Birrell J, Bill E, Haumann M, Lubitz W, Högbom M, Griese JJ, Cox N. Divergent assembly mechanisms of the manganese/iron cofactors in R2lox and R2c proteins. J Inorg Biochem 2016; 162:164-177. [PMID: 27138102 DOI: 10.1016/j.jinorgbio.2016.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/04/2016] [Accepted: 04/12/2016] [Indexed: 01/22/2023]
Abstract
A manganese/iron cofactor which performs multi-electron oxidative chemistry is found in two classes of ferritin-like proteins, the small subunit (R2) of class Ic ribonucleotide reductase (R2c) and the R2-like ligand-binding oxidase (R2lox). It is unclear how a heterodimeric Mn/Fe metallocofactor is assembled in these two related proteins as opposed to a homodimeric Fe/Fe cofactor, especially considering the structural similarity and proximity of the two metal-binding sites in both protein scaffolds and the similar first coordination sphere ligand preferences of MnII and FeII. Using EPR and Mössbauer spectroscopies as well as X-ray anomalous dispersion, we examined metal loading and cofactor activation of both proteins in vitro (in solution). We find divergent cofactor assembly mechanisms for the two systems. In both cases, excess MnII promotes heterobimetallic cofactor assembly. In the absence of FeII, R2c cooperatively binds MnII at both metal sites, whereas R2lox does not readily bind MnII at either site. Heterometallic cofactor assembly is favored at substoichiometric FeII concentrations in R2lox. FeII and MnII likely bind to the protein in a stepwise fashion, with FeII binding to site 2 initiating cofactor assembly. In R2c, however, heterometallic assembly is presumably achieved by the displacement of MnII by FeII at site 2. The divergent metal loading mechanisms are correlated with the putative in vivo functions of R2c and R2lox, and most likely with the intracellular MnII/FeII concentrations in the host organisms from which they were isolated.
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Affiliation(s)
- Yuri Kutin
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Matthieu Fritz
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Hannah S Shafaat
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - James Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Department of Chemistry, Stanford University, Stanford, CA 94305, United States.
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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Sekino M, Furutachi H, Tasaki K, Ishikawa T, Mori S, Fujinami S, Akine S, Sakata Y, Nomura T, Ogura T, Kitagawa T, Suzuki M. New mechanistic insight into intramolecular arene hydroxylation initiated by (μ-1,2-peroxo)diiron(III) complexes with dinucleating ligands. Dalton Trans 2016; 45:469-73. [PMID: 26646073 DOI: 10.1039/c5dt04088d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(μ-1,2-Peroxo)diiron(iii) complexes (-R) with dinucleating ligands (R-L) generated from the reaction of bis(μ-hydroxo)diiron(ii) complexes [Fe2(R-L)(OH)2](2+) (-R) with dioxygen in acetone at -20 °C provide a diiron-centred electrophilic oxidant, presumably diiron(iv)-oxo species, which is involved in aromatic ligand hydroxylation.
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Affiliation(s)
- Mio Sekino
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Hideki Furutachi
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Kyosuke Tasaki
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Takanao Ishikawa
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Shigeki Mori
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Shuhei Fujinami
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Shigehisa Akine
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Yoko Sakata
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Takashi Nomura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Masatatsu Suzuki
- Department of Chemistry and Biochemistry, Graduate Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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44
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Lee SJ. Hydroxylation of methane through component interactions in soluble methane monooxygenases. J Microbiol 2016; 54:277-82. [DOI: 10.1007/s12275-016-5642-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 10/22/2022]
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45
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Da Silva JCS, Pennifold RCR, Harvey JN, Rocha WR. A radical rebound mechanism for the methane oxidation reaction promoted by the dicopper center of a pMMO enzyme: a computational perspective. Dalton Trans 2016; 45:2492-504. [DOI: 10.1039/c5dt02638e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Hydrogen Atom Transfer (HAT) promoted by a triplet state of the bis-oxoCu2(iii) core generates a new radical rebound mechanism for the hydroxylation of methane catalyzed by the binuclear copper site of a pMMO enzyme.
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Affiliation(s)
- Júlio C. S. Da Silva
- BioMat: Biomaterial Modeling Group
- Departamento de Química Fundamental
- CCEN
- Universidade Federal de Pernambuco
- Cidade Universitária
| | | | | | - Willian R. Rocha
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular
- Departamento de Química
- ICEX
- Universidade Federal de Minas Gerais
- Belo Horizonte
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46
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Bao L, Li JJ, Jia C, Li M, Lu X. Structure-oriented substrate specificity engineering of aldehyde-deformylating oxygenase towards aldehydes carbon chain length. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:185. [PMID: 27588038 PMCID: PMC5007808 DOI: 10.1186/s13068-016-0596-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 08/19/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Aldehyde-deformylating oxygenase (ADO) is an important enzyme involved in the biosynthetic pathway of fatty alk(a/e)nes in cyanobacteria. However, ADO exhibits quite low chain-length specificity with respect to the substrates ranging from C4 to C18 aldehydes, which is not suitable for producing fuels with different properties or different chain lengths. RESULTS Based on the crystal structures of cADOs (cyanobacterial ADO) with substrate analogs bound, some amino acids affecting the substrate specificity of cADO were identified, including the amino acids close to the aldehyde group and the hydrophobic tail of the substrate and those along the substrate channel. Using site-directed mutagenesis, selected amino acids were replaced with bulky ones introducing steric hindrance to the binding pocket via large functional groups. All mutants were overexpressed, purified and kinetically characterized. All mutants, except F87Y, displayed dramatically reduced activity towards C14,16,18 aldehydes. Notably, the substrate preferences of some mutants towards different chain-length substrates were enhanced: I24Y for n-heptanal, I27F for n-decanal and n-dodecanal, V28F for n-dodecanal, F87Y for n-decanal, C70F for n-hexanal, A118F for n-butanal, A121F for C4,6,7 aldehydes, V184F for n-dodecanal and n-decanal, M193Y for C6-10 aldehydes and L198F for C7-10 aldehydes. The impact of the engineered cADO mutants on the change of the hydrocarbon profile was demonstrated by co-expressing acyl-ACP thioesterase BTE, fadD and V184F in E. coli, showing that n-undecane was the main fatty alkane. CONCLUSIONS Some amino acids, which can control the chain-length selectivity of substrates of cADO, were identified. The substrate specificities of cADO were successfully changed through structure-guided protein engineering, and some mutants displayed different chain-length preference. The in vivo experiments of V184F in genetically engineered E. coli proved the importance of engineered cADOs on the distribution of the fatty alkane profile. The results would be helpful for the production of fatty alk(a/e)nes in cyanobacteria with different properties.
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Affiliation(s)
- Luyao Bao
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jian-Jun Li
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, China
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North 2nd Street, Haidian District, Beijing, 100190 China
| | - Chenjun Jia
- University of Chinese Academy of Sciences, Beijing, 100049 China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101 China
| | - Mei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101 China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
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Kerber WD, Goheen JT, Perez KA, Siegler MA. Enhanced Stability of the FeII/MnII State in a Synthetic Model of Heterobimetallic Cofactor Assembly. Inorg Chem 2015; 55:848-57. [DOI: 10.1021/acs.inorgchem.5b02322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- William D. Kerber
- Department
of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Joshua T. Goheen
- Department
of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Kaitlyn A. Perez
- Department
of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Maxime A. Siegler
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Griese JJ, Kositzki R, Schrapers P, Branca RMM, Nordström A, Lehtiö J, Haumann M, Högbom M. Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor. J Biol Chem 2015; 290:25254-72. [PMID: 26324712 PMCID: PMC4646176 DOI: 10.1074/jbc.m115.675223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 08/24/2015] [Indexed: 12/31/2022] Open
Abstract
Two recently discovered groups of prokaryotic di-metal carboxylate proteins harbor a heterodinuclear Mn/Fe cofactor. These are the class Ic ribonucleotide reductase R2 proteins and a group of oxidases that are found predominantly in pathogens and extremophiles, called R2-like ligand-binding oxidases (R2lox). We have recently shown that the Mn/Fe cofactor of R2lox self-assembles from Mn(II) and Fe(II) in vitro and catalyzes formation of a tyrosine-valine ether cross-link in the protein scaffold (Griese, J. J., Roos, K., Cox, N., Shafaat, H. S., Branca, R. M., Lehtiö, J., Gräslund, A., Lubitz, W., Siegbahn, P. E., and Högbom, M. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 17189-17194). Here, we present a detailed structural analysis of R2lox in the nonactivated, reduced, and oxidized resting Mn/Fe- and Fe/Fe-bound states, as well as the nonactivated Mn/Mn-bound state. X-ray crystallography and x-ray absorption spectroscopy demonstrate that the active site ligand configuration of R2lox is essentially the same regardless of cofactor composition. Both the Mn/Fe and the diiron cofactor activate oxygen and catalyze formation of the ether cross-link, whereas the dimanganese cluster does not. The structures delineate likely routes for gated oxygen and substrate access to the active site that are controlled by the redox state of the cofactor. These results suggest that oxygen activation proceeds via similar mechanisms at the Mn/Fe and Fe/Fe center and that R2lox proteins might utilize either cofactor in vivo based on metal availability.
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Affiliation(s)
- Julia J Griese
- From the Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ramona Kositzki
- the Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Peer Schrapers
- the Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Rui M M Branca
- the Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, SE-171 21 Solna, Sweden, and
| | - Anders Nordström
- the Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Janne Lehtiö
- the Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, SE-171 21 Solna, Sweden, and
| | - Michael Haumann
- the Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Martin Högbom
- From the Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden,
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Dey SK, Mukherjee A. Investigation of 3d-transition metal acetates in the oxidation of substituted dioxolene and phenols. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcata.2015.06.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang W, Liang AD, Lippard SJ. Coupling Oxygen Consumption with Hydrocarbon Oxidation in Bacterial Multicomponent Monooxygenases. Acc Chem Res 2015; 48:2632-9. [PMID: 26293615 PMCID: PMC4624108 DOI: 10.1021/acs.accounts.5b00312] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A fundamental goal in catalysis is the coupling of multiple reactions to yield a desired product. Enzymes have evolved elegant approaches to address this grand challenge. A salient example is the biological conversion of methane to methanol catalyzed by soluble methane monooxygenase (sMMO), a member of the bacterial multicomponent monooxygenase (BMM) superfamily. sMMO is a dynamic protein complex of three components: a hydroxylase, a reductase, and a regulatory protein. The active site, a carboxylate-rich non-heme diiron center, is buried inside the 251 kDa hydroxylase component. The enzyme processes four substrates: O2, protons, electrons, and methane. To couple O2 activation to methane oxidation, timely control of substrate access to the active site is critical. Recent studies of sMMO, as well as its homologues in the BMM superfamily, have begun to unravel the mechanism. The emerging and unifying picture reveals that each substrate gains access to the active site along a specific pathway through the hydroxylase. Electrons and protons are delivered via a three-amino-acid pore located adjacent to the diiron center; O2 migrates via a series of hydrophobic cavities; and hydrocarbon substrates reach the active site through a channel or linked set of cavities. The gating of these pathways mediates entry of each substrate to the diiron active site in a timed sequence and is coordinated by dynamic interactions with the other component proteins. The result is coupling of dioxygen consumption with hydrocarbon oxidation, avoiding unproductive oxidation of the reductant rather than the desired hydrocarbon. To initiate catalysis, the reductase delivers two electrons to the diiron(III) center by binding over the pore of the hydroxylase. The regulatory component then displaces the reductase, docking onto the same surface of the hydroxylase. Formation of the hydroxylase-regulatory component complex (i) induces conformational changes of pore residues that may bring protons to the active site; (ii) connects hydrophobic cavities in the hydroxylase leading from the exterior to the diiron active site, providing a pathway for O2 and methane, in the case of sMMO, to the reduced diiron center for O2 activation and substrate hydroxylation; (iii) closes the pore, as well as a channel in the case of four-component BMM enzymes, restricting proton access to the diiron center during formation of "Fe2O2" intermediates required for hydrocarbon oxidation; and (iv) inhibits undesired electron transfer to the Fe2O2 intermediates by blocking reductase binding during O2 activation. This mechanism is quite different from that adopted by cytochromes P450, a large class of heme-containing monooxygenases that catalyze reactions very similar to those catalyzed by the BMM enzymes. Understanding the timed enzyme control of substrate access has implications for designing artificial catalysts. To achieve multiple turnovers and tight coupling, synthetic models must also control substrate access, a major challenge considering that nature requires large, multimeric, dynamic protein complexes to accomplish this feat.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexandria D. 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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