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Toci EM, Austin SL, Majumdar A, Woodcock HL, Freel Meyers CL. Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1-Deoxy-d-xylulose-5-phosphate Synthase. Biochemistry 2024; 63:671-687. [PMID: 38393327 PMCID: PMC11015862 DOI: 10.1021/acs.biochem.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The bacterial metabolic enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde-3-phosphate (d-GAP). DXP is an essential bacteria-specific metabolite that feeds into the biosynthesis of isoprenoids, pyridoxal phosphate (PLP), and ThDP. DXPS catalyzes the activation of pyruvate to give the C2α-lactylThDP (LThDP) adduct that is long-lived on DXPS in a closed state in the absence of the cosubstrate. Binding of d-GAP shifts the DXPS-LThDP complex to an open state which coincides with LThDP decarboxylation. This gated mechanism distinguishes DXPS in ThDP enzymology. How LThDP persists on DXPS in the absence of cosubstrate, while other pyruvate decarboxylases readily activate LThDP for decarboxylation, is a long-standing question in the field. We propose that an active site network functions to prevent LThDP activation on DXPS until the cosubstrate binds. Binding of d-GAP coincides with a conformational shift and disrupts the network causing changes in the active site that promote LThDP activation. Here, we show that the substitution of putative network residues, as well as nearby residues believed to contribute to network charge distribution, predictably affects LThDP reactivity. Substitutions predicted to disrupt the network have the effect to activate LThDP for decarboxylation, resulting in CO2 and acetate production. In contrast, a substitution predicted to strengthen the network fails to activate LThDP and has the effect to shift DXPS toward the closed state. Network-disrupting substitutions near the carboxylate of LThDP also have a pronounced effect to shift DXPS to an open state. These results offer initial insights to explain the long-lived LThDP intermediate and its activation through disruption of an active site network, which is unique to DXPS. These findings have important implications for DXPS function in bacteria and its development as an antibacterial target.
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Affiliation(s)
- Eucolona M Toci
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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2
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The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering. Proc Natl Acad Sci U S A 2021; 118:2023348118. [PMID: 33753504 PMCID: PMC8020674 DOI: 10.1073/pnas.2023348118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The continuous replacement of enzymes and other proteins appropriates up to half the maintenance energy budget in microorganisms and plants. High enzyme replacement rates therefore cut the productivity of biosystems ranging from microbial fermentations to crops. However, yardsticks to assess what drives enzyme protein replacement and guidelines on how to reduce it are lacking. Accordingly, we compared enzymes’ life spans across kingdoms using a new yardstick (catalytic cycles until replacement [CCR]) and related CCR to enzyme reaction chemistry. We concluded that 1) many enzymes fail due to collateral damage from the reaction they catalyze, and 2) such damage and its attendant enzyme replacement costs are mitigable by engineering and are therefore promising targets for synthetic biology. Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ∼100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<103 to >107) but different median values (3–4 × 104 in L. lactis and yeast versus 4 × 105 in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.
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Oxygen reactivity with pyridoxal 5'-phosphate enzymes: biochemical implications and functional relevance. Amino Acids 2020; 52:1089-1105. [PMID: 32844248 PMCID: PMC7497351 DOI: 10.1007/s00726-020-02885-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 12/29/2022]
Abstract
The versatility of reactions catalyzed by pyridoxal 5'-phosphate (PLP) enzymes is largely due to the chemistry of their extraordinary catalyst. PLP is necessary for many reactions involving amino acids. Reaction specificity is controlled by the orientation of the external aldimine intermediate that is formed upon addition of the amino acidic substrate to the coenzyme. The breakage of a specific bond of the external aldimine gives rise to a carbanionic intermediate. From this point, the different reaction pathways diverge leading to multiple activities: transamination, decarboxylation, racemization, elimination, and synthesis. A significant novelty appeared approximately 30 years ago when it was reported that some PLP-dependent decarboxylases are able to consume molecular oxygen transforming an amino acid into a carbonyl compound. These side paracatalytic reactions could be particularly relevant for human health, also considering that some of these enzymes are responsible for the synthesis of important neurotransmitters such as γ-aminobutyric acid, dopamine, and serotonin, whose dysregulation under oxidative conditions could have important implications in neurodegenerative states. However, the reactivity of PLP enzymes with dioxygen is not confined to mammals/animals. In fact, some plant PLP decarboxylases have been reported to catalyze oxidative reactions producing carbonyl compounds. Moreover, other recent reports revealed the existence of new oxidase activities catalyzed by new PLP enzymes, MppP, RohP, Ind4, CcbF, PvdN, Cap15, and CuaB. These PLP enzymes belong to the bacterial and fungal kingdoms and are present in organisms synthesizing bioactive compounds. These new PLP activities are not paracatalytic and could only scratch the surface on a wider and unexpected catalytic capability of PLP enzymes.
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Hoffarth ER, Rothchild KW, Ryan KS. Emergence of oxygen- and pyridoxal phosphate-dependent reactions. FEBS J 2020; 287:1403-1428. [PMID: 32142210 DOI: 10.1111/febs.15277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/29/2019] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) is an organic cofactor employed by ~ 4% of enzymes. The structure of the PLP cofactor allows for the stabilization of carbanions through resonance. A small number of PLP-dependent enzymes employ molecular oxygen as a cosubstrate. Here, we review the biological roles and possible mechanisms of these enzymes, and we observe that these enzymes are found in multiple protein families, suggesting that reaction with oxygen might have emerged de novo in several protein families and thus could be directed to emerge again through laboratory evolution experiments.
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Affiliation(s)
- Elesha R Hoffarth
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
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5
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Joshi J, Folz JS, Gregory JF, McCarty DR, Fiehn O, Hanson AD. Rethinking the PDH Bypass and GABA Shunt as Thiamin-Deficiency Workarounds. PLANT PHYSIOLOGY 2019; 181:389-393. [PMID: 31409697 PMCID: PMC6776870 DOI: 10.1104/pp.19.00857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 05/18/2023]
Abstract
The PDH bypass and the GABA shunt serve to maintain mainline metabolic fluxes during episodes of organellar thiamin diphosphate deficiency.
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Affiliation(s)
- Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Jacob S Folz
- West Coast Metabolomics Center, University of California Davis, Davis, California 95616
| | - Jesse F Gregory
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida 32611
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, California 95616
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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Hedges JB, Ryan KS. In vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jason B. Hedges
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
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Hedges JB, Ryan KS. In vitro Reconstitution of the Biosynthetic Pathway to the Nitroimidazole Antibiotic Azomycin. Angew Chem Int Ed Engl 2019; 58:11647-11651. [DOI: 10.1002/anie.201903500] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/23/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jason B. Hedges
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
| | - Katherine S. Ryan
- Department of Chemistry University of British Columbia Vancouver British Columbia Canada
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Bunik VI. Redox-Driven Signaling: 2-Oxo Acid Dehydrogenase Complexes as Sensors and Transmitters of Metabolic Imbalance. Antioxid Redox Signal 2019; 30:1911-1947. [PMID: 30187773 DOI: 10.1089/ars.2017.7311] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE This article develops a holistic view on production of reactive oxygen species (ROS) by 2-oxo acid dehydrogenase complexes. Recent Advances: Catalytic and structural properties of the complexes and their components evolved to minimize damaging effects of side reactions, including ROS generation, simultaneously exploiting the reactions for homeostatic signaling. CRITICAL ISSUES Side reactions of the complexes, characterized in vitro, are analyzed in view of protein interactions and conditions in vivo. Quantitative data support prevalence of the forward 2-oxo acid oxidation over the backward NADH oxidation in feeding physiologically significant ROS production by the complexes. Special focus on interactions between the active sites within 2-oxo acid dehydrogenase complexes highlights the central relevance of the complex-bound thiyl radicals in regulation of and signaling by complex-generated ROS. The thiyl radicals arise when dihydrolipoyl residues of the complexes regenerate FADH2 from the flavin semiquinone coproduced with superoxide anion radical in 1e- oxidation of FADH2 by molecular oxygen. FUTURE DIRECTIONS Interaction of 2-oxo acid dehydrogenase complexes with thioredoxins (TRXs), peroxiredoxins, and glutaredoxins mediates scavenging of the thiyl radicals and ROS generated by the complexes, underlying signaling of disproportional availability of 2-oxo acids, CoA, and NAD+ in key metabolic branch points through thiol/disulfide exchange and medically important hypoxia-inducible factor, mammalian target of rapamycin (mTOR), poly (ADP-ribose) polymerase, and sirtuins. High reactivity of the coproduced ROS and thiyl radicals to iron/sulfur clusters and nitric oxide, peroxynitrite reductase activity of peroxiredoxins and transnitrosylating function of thioredoxin, implicate the side reactions of 2-oxo acid dehydrogenase complexes in nitric oxide-dependent signaling and damage.
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Affiliation(s)
- Victoria I Bunik
- 1 Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,2 Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
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9
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Du YL, Ryan KS. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat Prod Rep 2019; 36:430-457. [DOI: 10.1039/c8np00049b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review reactions catalyzed by pyridoxal phosphate-dependent enzymes, highlighting enzymes reported in the recent natural product biosynthetic literature.
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Affiliation(s)
- Yi-Ling Du
- Institute of Pharmaceutical Biotechnology
- Zhejiang University School of Medicine
- Hangzhou
- China
| | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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DeColli AA, Nemeria NS, Majumdar A, Gerfen GJ, Jordan F, Freel Meyers CL. Oxidative decarboxylation of pyruvate by 1-deoxy-d-xyulose 5-phosphate synthase, a central metabolic enzyme in bacteria. J Biol Chem 2018; 293:10857-10869. [PMID: 29784878 DOI: 10.1074/jbc.ra118.001980] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/17/2018] [Indexed: 01/06/2023] Open
Abstract
The underexploited antibacterial target 1-deoxy-d-xyluose 5-phosphate (DXP) synthase catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP). DXP is an essential intermediate in the biosynthesis of ThDP, pyridoxal phosphate, and isoprenoids in many pathogenic bacteria. DXP synthase catalyzes a distinct mechanism in ThDP decarboxylative enzymology in which the first enzyme-bound pre-decarboxylation intermediate, C2α-lactyl-ThDP (LThDP), is stabilized by DXP synthase in the absence of d-GAP, and d-GAP then induces efficient LThDP decarboxylation. Despite the observed LThDP accumulation and lack of evidence for C2α-carbanion formation in the absence of d-GAP, CO2 is released at appreciable levels under these conditions. Here, seeking to resolve these conflicting observations, we show that DXP synthase catalyzes the oxidative decarboxylation of pyruvate under conditions in which LThDP accumulates. O2-dependent LThDP decarboxylation led to one-electron transfer from the C2α-carbanion/enamine to O2, with intermediate ThDP-enamine radical formation, followed by peracetic acid formation en route to acetate. Thus, LThDP formation and decarboxylation and DXP formation were studied under anaerobic conditions. Our results support a model in which O2-dependent LThDP decarboxylation and peracetic acid formation occur in the absence of d-GAP, decreasing the levels of pyruvate and O2 in solution. The relative pyruvate and O2 concentrations then dictate the extent of LThDP accumulation, and its buildup can be observed when [pyruvate] > [O2]. The finding that O2 acts as a structurally distinct trigger of LThDP decarboxylation supports the hypothesis that a mechanism involving small molecule-dependent LThDP decarboxylation equips DXP synthase for diverse, yet uncharacterized cellular functions.
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Affiliation(s)
| | - Natalia S Nemeria
- the Department of Chemistry, Rutgers University, Newark, New Jersey 07102, and
| | - Ananya Majumdar
- Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Gary J Gerfen
- the Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Frank Jordan
- the Department of Chemistry, Rutgers University, Newark, New Jersey 07102, and
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11
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Hedges JB, Kuatsjah E, Du YL, Eltis LD, Ryan KS. Snapshots of the Catalytic Cycle of an O 2, Pyridoxal Phosphate-Dependent Hydroxylase. ACS Chem Biol 2018; 13:965-974. [PMID: 29466666 DOI: 10.1021/acschembio.8b00039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes that catalyze hydroxylation of unactivated carbons normally contain heme and nonheme iron cofactors. By contrast, how a pyridoxal phosphate (PLP)-dependent enzyme could catalyze such a hydroxylation was unknown. Here, we investigate RohP, a PLP-dependent enzyme that converts l-arginine to ( S)-4-hydroxy-2-ketoarginine. We determine that the RohP reaction consumes oxygen with stoichiometric release of H2O2. To understand this unusual chemistry, we obtain ∼1.5 Å resolution structures that capture intermediates along the catalytic cycle. Our data suggest that RohP carries out a four-electron oxidation and a stereospecific alkene hydration to give the ( S)-configured product. Together with our earlier studies on an O2, PLP-dependent l-arginine oxidase, our work suggests that there is a shared pathway leading to both oxidized and hydroxylated products from l-arginine.
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Affiliation(s)
| | | | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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12
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Bathellier C, Tcherkez G, Lorimer GH, Farquhar GD. Rubisco is not really so bad. PLANT, CELL & ENVIRONMENT 2018; 41:705-716. [PMID: 29359811 DOI: 10.1111/pce.13149] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the most widespread carboxylating enzyme in autotrophic organisms. Its kinetic and structural properties have been intensively studied for more than half a century. Yet important aspects of the catalytic mechanism remain poorly understood, especially the oxygenase reaction. Because of its relatively modest turnover rate (a few catalytic events per second) and the competitive inhibition by oxygen, Rubisco is often viewed as an inefficient catalyst for CO2 fixation. Considerable efforts have been devoted to improving its catalytic efficiency, so far without success. In this review, we re-examine Rubisco's catalytic performance by comparison with other chemically related enzymes. We find that Rubisco is not especially slow. Furthermore, considering both the nature and the complexity of the chemical reaction, its kinetic properties are unremarkable. Although not unique to Rubisco, oxygenation is not systematically observed in enolate and enamine forming enzymes and cannot be considered as an inevitable consequence of the mechanism. It is more likely the result of a compromise between chemical and metabolic imperatives. We argue that a better description of Rubisco mechanism is still required to better understand the link between CO2 and O2 reactivity and the rationale of Rubisco diversification and evolution.
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Affiliation(s)
- Camille Bathellier
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - Guillaume Tcherkez
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
| | - George H Lorimer
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 27042, USA
| | - Graham D Farquhar
- Research School of Biology, College of Science, Australian National University, Canberra, 2601, ACT, Australia
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13
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Han L, Vuksanovic N, Oehm SA, Fenske TG, Schwabacher AW, Silvaggi NR. Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase. Biochemistry 2018; 57:3252-3264. [DOI: 10.1021/acs.biochem.8b00130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lanlan Han
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Nemanja Vuksanovic
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Sarah A. Oehm
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Tyler G. Fenske
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Alan W. Schwabacher
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Nicholas R. Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53201, United States
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Pyridoxal-5'-phosphate as an oxygenase cofactor: Discovery of a carboxamide-forming, α-amino acid monooxygenase-decarboxylase. Proc Natl Acad Sci U S A 2018; 115:974-979. [PMID: 29343643 DOI: 10.1073/pnas.1718667115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Capuramycins are antimycobacterial antibiotics that consist of a modified nucleoside named uridine-5'-carboxamide (CarU). Previous biochemical studies have revealed that CarU is derived from UMP, which is first converted to uridine-5'-aldehyde in a reaction catalyzed by the dioxygenase CapA and subsequently to 5'-C-glycyluridine (GlyU), an unusual β-hydroxy-α-amino acid, in a reaction catalyzed by the pyridoxal-5'-phosphate (PLP)-dependent transaldolase CapH. The remaining steps that are necessary to furnish CarU include decarboxylation, O atom insertion, and oxidation. We demonstrate that Cap15, which has sequence similarity to proteins annotated as bacterial, PLP-dependent l-seryl-tRNA(Sec) selenium transferases, is the sole catalyst responsible for complete conversion of GlyU to CarU. Using a complementary panel of in vitro assays, Cap15 is shown to be dependent upon substrates O2 and (5'S,6'R)-GlyU, the latter of which was unexpected given that (5'S,6'S)-GlyU is the isomeric product of the transaldolase CapH. The two products of Cap15 are identified as the carboxamide-containing CarU and CO2 While known enzymes that catalyze this type of chemistry, namely α-amino acid 2-monooxygenase, utilize flavin adenine dinucleotide as the redox cofactor, Cap15 remarkably requires only PLP. Furthermore, Cap15 does not produce hydrogen peroxide and is shown to directly incorporate a single O atom from O2 into the product CarU and thus is an authentic PLP-dependent monooxygenase. In addition to these unusual discoveries, Cap15 activity is revealed to be dependent upon the inclusion of phosphate. The biochemical characteristics along with initiatory mechanistic studies of Cap15 are reported, which has allowed us to assign Cap15 as a PLP-dependent (5'S,6'R)-GlyU:O2 monooxygenase-decarboxylase.
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15
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Bunik VI, Brand MD. Generation of superoxide and hydrogen peroxide by side reactions of mitochondrial 2-oxoacid dehydrogenase complexes in isolation and in cells. Biol Chem 2018; 399:407-420. [DOI: 10.1515/hsz-2017-0284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/03/2018] [Indexed: 01/06/2023]
Abstract
Abstract
Mitochondrial 2-oxoacid dehydrogenase complexes oxidize 2-oxoglutarate, pyruvate, branched-chain 2-oxoacids and 2-oxoadipate to the corresponding acyl-CoAs and reduce NAD+ to NADH. The isolated enzyme complexes generate superoxide anion radical or hydrogen peroxide in defined reactions by leaking electrons to oxygen. Studies using isolated mitochondria in media mimicking cytosol suggest that the 2-oxoacid dehydrogenase complexes contribute little to the production of superoxide or hydrogen peroxide relative to other mitochondrial sites at physiological steady states. However, the contributions may increase under pathological conditions, in accordance with the high maximum capacities of superoxide or hydrogen peroxide-generating reactions of the complexes, established in isolated mitochondria. We assess available data on the use of modulations of enzyme activity to infer superoxide or hydrogen peroxide production from particular 2-oxoacid dehydrogenase complexes in cells, and limitations of such methods to discriminate specific superoxide or hydrogen peroxide sources in vivo.
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Affiliation(s)
- Victoria I. Bunik
- A.N. Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , 119992 Moscow , Russia
| | - Martin D. Brand
- Buck Institute for Research on Aging , 8001 Redwood Blvd. , Novato, CA 94945 , USA
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16
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Tsepkova PM, Artiukhov AV, Boyko AI, Aleshin VA, Mkrtchyan GV, Zvyagintseva MA, Ryabov SI, Ksenofontov AL, Baratova LA, Graf AV, Bunik VI. Thiamine Induces Long-Term Changes in Amino Acid Profiles and Activities of 2-Oxoglutarate and 2-Oxoadipate Dehydrogenases in Rat Brain. BIOCHEMISTRY (MOSCOW) 2017; 82:723-736. [PMID: 28601082 DOI: 10.1134/s0006297917060098] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Molecular mechanisms of long-term changes in brain metabolism after thiamine administration (single i.p. injection, 400 mg/kg) were investigated. Protocols for discrimination of the activities of the thiamine diphosphate (ThDP)-dependent 2-oxoglutarate and 2-oxoadipate dehydrogenases were developed to characterize specific regulation of the multienzyme complexes of the 2-oxoglutarate (OGDHC) and 2-oxoadipate (OADHC) dehydrogenases by thiamine. The thiamine-induced changes depended on the brain-region-specific expression of the ThDP-dependent dehydrogenases. In the cerebral cortex, the original levels of OGDHC and OADHC were relatively high and not increased by thiamine, whereas in the cerebellum thiamine upregulated the OGDHC and OADHC activities, whose original levels were relatively low. The effects of thiamine on each of the complexes were different and associated with metabolic rearrangements, which included (i) the brain-region-specific alterations of glutamine synthase and/or glutamate dehydrogenase and NADP+-dependent malic enzyme, (ii) the brain-region-specific changes of the amino acid profiles, and (iii) decreased levels of a number of amino acids in blood plasma. Along with the assays of enzymatic activities and average levels of amino acids in the blood and brain, the thiamine-induced metabolic rearrangements were assessed by analysis of correlations between the levels of amino acids. The set and parameters of the correlations were tissue-specific, and their responses to the thiamine treatment provided additional information on metabolic changes, compared to that gained from the average levels of amino acids. Taken together, the data suggest that thiamine decreases catabolism of amino acids by means of a complex and long-term regulation of metabolic flux through the tricarboxylic acid cycle, which includes coupled changes in activities of the ThDP-dependent dehydrogenases of 2-oxoglutarate and 2-oxoadipate and adjacent enzymes.
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Affiliation(s)
- P M Tsepkova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.
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Artiukhov AV, Graf AV, Bunik VI. Directed regulation of multienzyme complexes of 2-oxo acid dehydrogenases using phosphonate and phosphinate analogs of 2-oxo acids. BIOCHEMISTRY (MOSCOW) 2016; 81:1498-1521. [DOI: 10.1134/s0006297916120129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Han L, Schwabacher AW, Moran GR, Silvaggi NR. Streptomyces wadayamensis MppP Is a Pyridoxal 5′-Phosphate-Dependent l-Arginine α-Deaminase, γ-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry 2015; 54:7029-40. [DOI: 10.1021/acs.biochem.5b01016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lanlan Han
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Alan W. Schwabacher
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Graham R. Moran
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Nicholas R. Silvaggi
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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Quinlan CL, Goncalves RLS, Hey-Mogensen M, Yadava N, Bunik VI, Brand MD. The 2-oxoacid dehydrogenase complexes in mitochondria can produce superoxide/hydrogen peroxide at much higher rates than complex I. J Biol Chem 2014; 289:8312-25. [PMID: 24515115 DOI: 10.1074/jbc.m113.545301] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Several flavin-dependent enzymes of the mitochondrial matrix utilize NAD(+) or NADH at about the same operating redox potential as the NADH/NAD(+) pool and comprise the NADH/NAD(+) isopotential enzyme group. Complex I (specifically the flavin, site IF) is often regarded as the major source of matrix superoxide/H2O2 production at this redox potential. However, the 2-oxoglutarate dehydrogenase (OGDH), branched-chain 2-oxoacid dehydrogenase (BCKDH), and pyruvate dehydrogenase (PDH) complexes are also capable of considerable superoxide/H2O2 production. To differentiate the superoxide/H2O2-producing capacities of these different mitochondrial sites in situ, we compared the observed rates of H2O2 production over a range of different NAD(P)H reduction levels in isolated skeletal muscle mitochondria under conditions that favored superoxide/H2O2 production from complex I, the OGDH complex, the BCKDH complex, or the PDH complex. The rates from all four complexes increased at higher NAD(P)H/NAD(P)(+) ratios, although the 2-oxoacid dehydrogenase complexes produced superoxide/H2O2 at high rates only when oxidizing their specific 2-oxoacid substrates and not in the reverse reaction from NADH. At optimal conditions for each system, superoxide/H2O2 was produced by the OGDH complex at about twice the rate from the PDH complex, four times the rate from the BCKDH complex, and eight times the rate from site IF of complex I. Depending on the substrates present, the dominant sites of superoxide/H2O2 production at the level of NADH may be the OGDH and PDH complexes, but these activities may often be misattributed to complex I.
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Affiliation(s)
- Casey L Quinlan
- From The Buck Institute for Research on Aging, Novato, California 94945
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Bunik VI, Tylicki A, Lukashev NV. Thiamin diphosphate-dependent enzymes: from enzymology to metabolic regulation, drug design and disease models. FEBS J 2013; 280:6412-42. [PMID: 24004353 DOI: 10.1111/febs.12512] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/29/2013] [Accepted: 08/21/2013] [Indexed: 02/06/2023]
Abstract
Bringing a knowledge of enzymology into research in vivo and in situ is of great importance in understanding systems biology and metabolic regulation. The central metabolic significance of thiamin (vitamin B1 ) and its diphosphorylated derivative (thiamin diphosphate; ThDP), and the fundamental differences in the ThDP-dependent enzymes of metabolic networks in mammals versus plants, fungi and bacteria, or in health versus disease, suggest that these enzymes are promising targets for biotechnological and medical applications. Here, the in vivo action of known regulators of ThDP-dependent enzymes, such as synthetic structural analogs of the enzyme substrates and thiamin, is analyzed in light of the enzymological data accumulated during half a century of research. Mimicking the enzyme-specific catalytic intermediates, the phosphonate analogs of 2-oxo acids selectively inhibit particular ThDP-dependent enzymes. Because of their selectivity, use of these compounds in cellular and animal models of ThDP-dependent enzyme malfunctions improves the validity of the model and its predictive power when compared with the nonselective and enzymatically less characterized oxythiamin and pyrithiamin. In vitro studies of the interaction of thiamin analogs and their biological derivatives with potential in vivo targets are necessary to identify and attenuate the analog selectivity. For both the substrate and thiamin synthetic analogs, in vitro reactivities with potential targets are highly relevant in vivo. However, effective concentrations in vivo are often higher than in vitro studies would suggest. The significance of specific inihibition of the ThDP-dependent enzymes for the development of herbicides, antibiotics, anticancer and neuroprotective strategies is discussed.
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Affiliation(s)
- Victoria I Bunik
- A.N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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21
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Graf A, Trofimova L, Loshinskaja A, Mkrtchyan G, Strokina A, Lovat M, Tylicky A, Strumilo S, Bettendorff L, Bunik VI. Up-regulation of 2-oxoglutarate dehydrogenase as a stress response. Int J Biochem Cell Biol 2012; 45:175-89. [PMID: 22814169 DOI: 10.1016/j.biocel.2012.07.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 06/28/2012] [Accepted: 07/01/2012] [Indexed: 01/08/2023]
Abstract
2-Oxoglutarate dehydrogenase multienzyme complex (OGDHC) operates at a metabolic cross-road, mediating Ca(2+)- and ADP-dependent signals in mitochondria. Here, we test our hypothesis that OGDHC plays a major role in the neurotransmitter metabolism and associated stress response. This possibility was assessed using succinyl phosphonate (SP), a highly specific and efficient in vivo inhibitor of OGDHC. Animals exposed to toxicants (SP, ethanol or MnCl(2)), trauma or acute hypoxia showed intrinsic up-regulation of OGDHC in brain and heart. The known mechanism of the SP action as OGDHC inhibitor pointed to the up-regulation triggered by the enzyme impairment. The animal behavior and skeletal muscle or heart performance were tested to correlate physiology with the OGDHC regulation and associated changes in the glutamate and cellular energy status. The SP-treated animals exhibited interdependent changes in the brain OGDHC activity, glutamate level and cardiac autonomic balance, suggesting the neurotransmitter role of glutamate to be involved in the changed heart performance. Energy insufficiency after OGDHC inhibition was detectable neither in animals up to 25 mg/kg SP, nor in cell culture during 24 h incubation with 0.1 mM SP. However, in animals subjected to acute ethanol intoxication SP did evoke energy deficit, decreasing muscular strength and locomotion and increasing the narcotic sleep duration. This correlated with the SP-induced decrease in NAD(P)H levels of the ethanol-exposed neurons. Thus, we show the existence of natural mechanisms to up-regulate mammalian OGDHC in response to stress, with both the glutamate neurotransmission and energy production potentially involved in the OGDHC impact on physiological performance. This article is part of a Directed Issue entitled: Bioenergetic dysfunction, adaptation and therapy.
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Affiliation(s)
- Anastasia Graf
- Department of Physiology of Biology Faculty of Lomonosov Moscow State University, Leninskije Gory 1, 119992 Moscow, Russian Federation.
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