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Knuuti J, Belevich G, Sharma V, Bloch DA, Verkhovskaya M. A single amino acid residue controls ROS production in the respiratory Complex I from Escherichia coli. Mol Microbiol 2013; 90:1190-200. [PMID: 24325249 DOI: 10.1111/mmi.12424] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2013] [Indexed: 01/08/2023]
Abstract
Reactive oxygen species (ROS) production by respiratory Complex I from Escherichia coli was studied in bacterial membrane fragments and in the isolated and purified enzyme, either solubilized or incorporated in proteoliposomes. We found that the replacement of a single amino acid residue in close proximity to the nicotinamide adenine dinucleotide (NADH)-binding catalytic site (E95 in the NuoF subunit) dramatically increases the reactivity of Complex I towards dioxygen (O2 ). In the E95Q variant short-chain ubiquinones exhibit strong artificial one-electron reduction at the catalytic site, also leading to a stronger increase in ROS production. Two mechanisms can contribute to the observed kinetic effects: (a) a change in the reactivity of flavin mononucleotide (FMN) towards dioxygen at the catalytic site, and (b) a change in the population of the ROS-generating state. We propose the existence of two (closed and open) states of the NAD(+) -bound enzyme as one feature of the substrate-binding site of Complex I. The analysis of the kinetic model of ROS production allowed us to propose that the population of Complex I with reduced FMN is always low in the wild-type enzyme even at low ambient redox potentials, minimizing the rate of reaction with O2 in contrast to E95Q variant.
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Affiliation(s)
- Juho Knuuti
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PO Box 65 (Viikinkaari 1), FIN-00014, Helsinki, Finland
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Mansoorabadi SO, Thibodeaux CJ, Liu HW. The diverse roles of flavin coenzymes--nature's most versatile thespians. J Org Chem 2007; 72:6329-42. [PMID: 17580897 PMCID: PMC2519020 DOI: 10.1021/jo0703092] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavin coenzymes play a variety of roles in biological systems. This Perspective highlights the chemical versatility of flavins by reviewing research on five flavoenzymes that have been studied in our laboratory. Each of the enzymes discussed in this review [the acyl-CoA dehydrogenases (ACDs), CDP-6-deoxy-l-threo-d-glycero-4-hexulose-3-dehydrase reductase (E3), CDP-4-aceto-3,6-dideoxygalactose synthase (YerE), UDP-galactopyranose mutase (UGM), and type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2)] utilizes flavin in a distinct role. In particular, the catalytic mechanisms of two of these enzymes, UGM and IDI-2, may involve novel flavin chemistry.
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Affiliation(s)
- Steven O. Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
| | - Christopher J. Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
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Wu Q, Liu YN, Chen H, Molitor EJ, Liu HW. A retro-evolution study of CDP-6-deoxy-D-glycero-L-threo-4-hexulose-3-dehydrase (E1) from Yersinia pseudotuberculosis: implications for C-3 deoxygenation in the biosynthesis of 3,6-dideoxyhexoses. Biochemistry 2007; 46:3759-67. [PMID: 17323931 PMCID: PMC2515278 DOI: 10.1021/bi602352g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CDP-6-deoxy-l-threo-d-glycero-4-hexulose-3-dehydrase (E1), which catalyzes C-3 deoxygenation of CDP-4-keto-6-deoxyglucose in the biosynthesis of 3,6-dideoxyhexoses, shares a modest sequence identity with other B6-dependent enzymes, albeit with two important distinctions. It is a rare example of a B6-dependent enzyme that harbors a [2Fe-2S] cluster, and a highly conserved lysine that serves as an anchor for PLP in most B6-dependent enzymes is replaced by histidine at position 220 in E1. Since alteration of His220 to a lysine residue may produce a putative progenitor of E1, the H220K mutant was constructed and tested for the ability to process the predicted substrate, CDP-4-amino-4,6-dideoxyglucose, using PLP as the coenzyme. Our data showed that H220K-E1 has no dehydrase activity, but can act as a PLP-dependent transaminase. However, the reaction is not catalytic since PLP cannot be regenerated during turnover. Reported herein are the results of this investigation and the implications for the role of His220 in the catalytic mechanism of E1.
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Affiliation(s)
| | | | | | | | - Hung-wen Liu
- To whom correspondence and reprint requests should be addressed. Phone: 512-232-7811. Fax: 512-471-2746. E-mail:
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Tejero J, Peregrina JR, Martínez-Júlvez M, Gutiérrez A, Gómez-Moreno C, Scrutton NS, Medina M. Catalytic mechanism of hydride transfer between NADP+/H and ferredoxin-NADP+ reductase from Anabaena PCC 7119. Arch Biochem Biophys 2006; 459:79-90. [PMID: 17224127 DOI: 10.1016/j.abb.2006.10.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 10/20/2006] [Accepted: 10/20/2006] [Indexed: 11/15/2022]
Abstract
The mechanism of hydride transfer between Anabaena FNR and NADP+/H was analysed using for the first time stopped-flow photodiode array detection and global analysis deconvolution. The results indicated that the initial spectral changes, occurring within the instrumental dead time upon reaction of FNR with NADP+/H, included not only the initial interaction and complex formation, but also the first subsequent steps of the sequential reactions that involve hydride transfer. Two different charge-transfer complexes formed prior and upon hydride transfer, FNRox-NADPH and FNRrd-NADP+. Detectable amounts of FNRox-NADPH were found at equilibrium, but FNRrd-NADP+ accumulated to a small extent and quickly evolved. The spectral properties of both charge-transfer complexes, for the first time in Anabaena FNR, as well as the corresponding inter-conversion hydride transfer rates were obtained. The need of an adequate initial interaction between NADP+/H and FNR, and subsequent conformational changes, was also established by studying the reactions of two FNR mutants.
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Affiliation(s)
- Jesús Tejero
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, E-50009 Zaragoza, Spain
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Yan F, Munos JW, Liu P, Liu HW. Biosynthesis of fosfomycin, re-examination and re-confirmation of a unique Fe(II)- and NAD(P)H-dependent epoxidation reaction. Biochemistry 2006; 45:11473-81. [PMID: 16981707 PMCID: PMC2515266 DOI: 10.1021/bi060839c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(S)-2-Hydroxypropylphosphonic acid epoxidase (HppE) catalyzes the epoxide ring closure of (S)-HPP to form fosfomycin, a clinically useful antibiotic. Early investigation showed that its activity can be reconstituted with Fe(II), FMN, NADH, and O2 and identified HppE as a new type of mononuclear non-heme iron-dependent oxygenase involving high-valent iron-oxo species in the catalysis. However, a recent study showed that the Zn(II)-reconstituted HppE is active, and HppE exhibits modest affinity for FMN. Thus, a new mechanism is proposed in which the active site-bound Fe2+ or Zn2+ serves as a Lewis acid to activate the 2-OH group of (S)-HPP and the epoxide ring is formed by the attack of the 2-OH group at C-1 coupled with the transfer of the C-1 hydrogen as a hydride ion to the bound FMN. To distinguish between these mechanistic discrepancies, we re-examined the bioautography assay, the basis for the alternative mechanism, and showed that Zn(II) cannot replace Fe(II) in the HppE reaction and NADH is indispensable. Moreover, we demonstrated that the proposed role for FMN as a hydride acceptor is inconsistent with the finding that FMN cannot bind to HppE in the presence of substrate. In addition, using a newly developed HPLC assay, we showed that several non-flavin electron mediators could replace FMN in the HppE-catalyzed epoxidation. Taken together, these results do not support the newly proposed "nucleophilic displacement-hydride transfer" mechanism but are fully consistent with the previously proposed iron-redox mechanism for HppE catalysis, which is unique within the mononuclear non-heme iron enzyme superfamily.
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Affiliation(s)
| | | | | | - Hung-wen Liu
- To whom correspondence should be addressed. Fax: 512-471-2746, E-mail:
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Pongdee R, Liu HW. Elucidation of enzyme mechanisms using fluorinated substrate analogues. Bioorg Chem 2004; 32:393-437. [PMID: 15381404 DOI: 10.1016/j.bioorg.2004.06.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Indexed: 11/24/2022]
Abstract
A great variety of biological reactions that are physiologically important are catalyzed by enzymes. Understanding the reaction course of these enzyme-catalyzed transformations are of significant importance since the insights gained from these experiments may facilitate the design of methods to control or mimic their actions. A common strategy to study enzyme catalyses is to use fluorinated substrate analogues as mechanistic probes, since fluorine is an effective hydroxyl group mimic and can also be used to replace a hydrogen atom. Using fluorinated substrate probes have enabled researchers to obtain crucial information regarding the catalytic mechanism of enzymatic reactions. Many of these compounds are good enzyme inhibitors and have been developed into clinically useful chemotherapeutic agents. This review will discuss some examples of the use of fluorine containing compounds as mechanistic probes/enzyme inhibitors, many of which are selected from our own work.
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Affiliation(s)
- Rongson Pongdee
- Division of Medicinal Chemistry, Department of Chemistry and Biochemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
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Abstract
Carbohydrates are highly abundant biomolecules found extensively in nature. Besides playing important roles in energy storage and supply, they often serve as essential biosynthetic precursors or structural elements needed to sustain all forms of life. A number of unusual sugars that have certain hydroxyl groups replaced by a hydrogen, an amino group, or an alkyl side chain play crucial roles in determining the biological activity of the parent natural products in bacterial lipopolysaccharides or secondary metabolite antibiotics. Recent investigation of the biosynthesis of these monosaccharides has led to the identification of the gene clusters whose protein products facilitate the unusual sugar formation from the ubiquitous NDP-glucose precursors. This review summarizes the mechanistic studies of a few enzymes crucial to the biosynthesis of C-2, C-3, C-4, and C-6 deoxysugars, the characterization and mutagenesis of nucleotidyl transferases that can recognize and couple structural analogs of their natural substrates and the identification of glycosyltransferases with promiscuous substrate specificity. Information gleaned from these studies has allowed pathway engineering, resulting in the creation of new macrolides with unnatural deoxysugar moieties for biological activity screening. This represents a significant progress toward our goal of searching for more potent agents against infectious diseases and malignant tumors.
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Affiliation(s)
- Xuemei M He
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA.
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Abstract
In the past few years, significant progress has been made in our understanding of the biosynthesis of deoxyhexoses. Mechanistic studies have revealed how enzymes can cleave CbondO bonds of a hexose substrate to make unusual sugars. The increasing amount of knowledge about the biosynthesis of deoxysugars may allow the assembly of a repertoire of novel sugar structures through recruitment and collaborative action of genes from a variety of biosynthetic pathways to create diverse secondary metabolites in our search for novel antibiotic/antitumour agents.
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Affiliation(s)
- Xuemei He
- Division of Medicinal Chemistry, College of Pharmacy, Department of Chemistry and Biochemistry, University of Texas, Austin 78712, USA
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Agnihotri G, Liu HW. PLP and PMP Radicals: A New Paradigm in Coenzyme B6 Chemistry. Bioorg Chem 2001; 29:234-57. [PMID: 16256695 DOI: 10.1006/bioo.2001.1211] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2000] [Indexed: 11/22/2022]
Abstract
Enzymes frequently rely on a broad repertoire of cofactors to perform chemically challenging transformations. The B6 coenzymes, composed of pyridoxal 5'-phosphate (PLP) and pyridoxamine 5'-phosphate (PMP), are used by many transaminases, racemases, decarboxylases, and enzymes catalyzing alpha,beta and beta,gamma-eliminations. Despite the variety of reactions catalyzed by B6-dependent enzymes, the mechanism of almost all such enzymes is based on their ability to stabilize high-energy anionic intermediates in their reaction pathways by the pyridinium moiety of PLP/PMP. However, there are two notable exceptions to this model, which are discussed in this article. The first enzyme, lysine 2,3-aminomutase, is a PLP-dependent enzyme that catalyzes the interconversion of L-lysine to L-beta-lysine using a one-electron-based mechanism utilizing a [4Fe-4S] cluster and S-adenosylmethionine. The second enzyme, CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase, is a PMP-dependent enzyme involved in the formation of 3,6-dideoxysugars in bacteria. This enzyme also contains an iron-sulfur cluster and uses a one-electron based mechanism to catalyze removal of a C-3 hydroxy group from a 4-hexulose. In both cases, the participation of free radicals in the reaction pathway has been established, placing these two B6-dependent enzymes in an exclusive class by themselves.
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Affiliation(s)
- G Agnihotri
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, USA
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He X, Agnihotri G, Liu Hw HW. Novel enzymatic mechanisms in carbohydrate metabolism. Chem Rev 2000; 100:4615-62. [PMID: 11749360 DOI: 10.1021/cr9902998] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- X He
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712
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Chang CWT, Johnson DA, Bandarian V, Zhou H, LoBrutto R, Reed GH, Liu HW. Characterization of a Unique Coenzyme B6 Radical in the Ascarylose Biosynthetic Pathway. J Am Chem Soc 2000. [DOI: 10.1021/ja0000807] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cheng-Wei T. Chang
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota, 55455 The Institute for Enzyme Research, Graduate School and Department of Biochemistry College of Agricultural and Life Sciences University of Wisconsin, Madison, Wisconsin 53705 Department of Plant Biology Arizona State University, Tempe, Arizona
| | - David A. Johnson
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota, 55455 The Institute for Enzyme Research, Graduate School and Department of Biochemistry College of Agricultural and Life Sciences University of Wisconsin, Madison, Wisconsin 53705 Department of Plant Biology Arizona State University, Tempe, Arizona
| | - Vahe Bandarian
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota, 55455 The Institute for Enzyme Research, Graduate School and Department of Biochemistry College of Agricultural and Life Sciences University of Wisconsin, Madison, Wisconsin 53705 Department of Plant Biology Arizona State University, Tempe, Arizona
| | - Huiqiang Zhou
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota, 55455 The Institute for Enzyme Research, Graduate School and Department of Biochemistry College of Agricultural and Life Sciences University of Wisconsin, Madison, Wisconsin 53705 Department of Plant Biology Arizona State University, Tempe, Arizona
| | - Russell LoBrutto
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota, 55455 The Institute for Enzyme Research, Graduate School and Department of Biochemistry College of Agricultural and Life Sciences University of Wisconsin, Madison, Wisconsin 53705 Department of Plant Biology Arizona State University, Tempe, Arizona
| | - George H. Reed
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota, 55455 The Institute for Enzyme Research, Graduate School and Department of Biochemistry College of Agricultural and Life Sciences University of Wisconsin, Madison, Wisconsin 53705 Department of Plant Biology Arizona State University, Tempe, Arizona
| | - Hung-wen Liu
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota, 55455 The Institute for Enzyme Research, Graduate School and Department of Biochemistry College of Agricultural and Life Sciences University of Wisconsin, Madison, Wisconsin 53705 Department of Plant Biology Arizona State University, Tempe, Arizona
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Abstract
In the past few years, there have been many important advances in our understanding of the biosynthesis of deoxysugars. Mechanistic studies have shed light on how enzymes can cleave C-O bonds, epimerize the configuration of substituents and reduce keto groups to make deoxysugars. Exciting progress has also been made in our comprehension of the genetics of deoxysugar biosynthesis in antibiotics. All this information is important for potential medical and biotechnological applications, such as drug discovery based on combinatorial biology.
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Affiliation(s)
- D A Johnson
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA
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Pieper PA, Yang DY, Zhou HQ, Liu HW. 3-Deoxy-3-fluoropyridoxamine 5‘-Phosphate: Synthesis and Chemical and Biological Properties of a Coenzyme B6 Analog. J Am Chem Soc 1997. [DOI: 10.1021/ja9632668] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patricia A. Pieper
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ding-yah Yang
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Hui-qiang Zhou
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Hung-wen Liu
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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