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Chen C, Li J, Wang G, Shi M. Accounting for the effect of temperature in clarifying the response of foliar nitrogen isotope ratios to atmospheric nitrogen deposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:1295-1302. [PMID: 28793398 DOI: 10.1016/j.scitotenv.2017.06.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/10/2017] [Accepted: 06/10/2017] [Indexed: 06/07/2023]
Abstract
Atmospheric nitrogen deposition affects nitrogen isotope composition (δ15N) in plants. However, both negative effect and positive effect have been reported. The effects of climate on plant δ15N have not been corrected for in previous studies, this has impeded discovery of a true effect of atmospheric N deposition on plant δ15N. To obtain a more reliable result, it is necessary to correct for the effects of climatic factors. Here, we measured δ15N and N contents of plants and soils in Baiwangshan and Mount Dongling, north China. Atmospheric N deposition in Baiwangshan was much higher than Mount Dongling. Generally, however, foliar N contents showed no difference between the two regions and foliar δ15N was significantly lower in Baiwangshan than Mount Dongling. The corrected foliar δ15N after accounting for a predicted value assumed to vary with temperature was obviously more negative in Baiwangshan than Mount Dongling. Thus, this suggested the necessity of temperature correction in revealing the effect of N deposition on foliar δ15N. Temperature, soil N sources and mycorrhizal fungi could not explain the difference in foliar δ15N between the two regions, this indicated that atmospheric N deposition had a negative effect on plant δ15N. Additionally, this study also showed that the corrected foliar δ15N of bulk data set increased with altitude above 1300m in Mount Dongling, this provided an another evidence for the conclusion that atmospheric N deposition could cause 15N-depletion in plants.
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Affiliation(s)
- Chongjuan Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, Department of Environmental Sciences and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiazhu Li
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, 100091, China
| | - Guoan Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, Department of Environmental Sciences and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Minrui Shi
- Beijing Key Laboratory of Farmland Soil Pollution Prevention-control and Remediation, Department of Environmental Sciences and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
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2
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Gauthier PPG, Lamothe M, Mahé A, Molero G, Nogués S, Hodges M, Tcherkez G. Metabolic origin of δ15 N values in nitrogenous compounds from Brassica napus L. leaves. PLANT, CELL & ENVIRONMENT 2013; 36:128-37. [PMID: 22709428 DOI: 10.1111/j.1365-3040.2012.02561.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nitrogen isotope composition (δ(15) N) in plant organic matter is currently used as a natural tracer of nitrogen acquisition efficiency. However, the δ(15) N value of whole leaf material does not properly reflect the way in which N is assimilated because isotope fractionations along metabolic reactions may cause substantial differences among leaf compounds. In other words, any change in metabolic composition or allocation pattern may cause undesirable variability in leaf δ(15) N. Here, we investigated the δ(15) N in different leaf fractions and individual metabolites from rapeseed (Brassica napus) leaves. We show that there were substantial differences in δ(15) N between nitrogenous compounds (up to 30‰) and the content in ((15) N enriched) nitrate had a clear influence on leaf δ(15) N. Using a simple steady-state model of day metabolism, we suggest that the δ(15) N value in major amino acids was mostly explained by isotope fractionation associated with isotope effects on enzyme-catalysed reactions in primary nitrogen metabolism. δ(15) N values were further influenced by light versus dark conditions and the probable occurrence of alternative biosynthetic pathways. We conclude that both biochemical pathways (that fractionate between isotopes) and nitrogen sources (used for amino acid production) should be considered when interpreting the δ(15) N value of leaf nitrogenous compounds.
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Affiliation(s)
- Paul P G Gauthier
- Institut de Biologie des Plantes, CNRS UMR 8618 Plateforme Métabolisme Métabolome, Université Paris Sud, Orsay Cedex, France.
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3
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Tcherkez G, Mahé A, Hodges M. (12)C/(13)C fractionations in plant primary metabolism. TRENDS IN PLANT SCIENCE 2011; 16:499-506. [PMID: 21705262 DOI: 10.1016/j.tplants.2011.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 05/18/2011] [Accepted: 05/25/2011] [Indexed: 05/13/2023]
Abstract
Natural (13)C abundance is now an unavoidable tool to study ecosystem and plant carbon economies. A growing number of studies take advantage of isotopic fractionation between carbon pools or (13)C abundance in respiratory CO(2) to examine the carbon source of respiration, plant biomass production or organic matter sequestration in soils. (12)C/(13)C isotope effects associated with plant metabolism are thus essential to understand natural isotopic signals. However, isotope effects of enzymes do not influence metabolites separately, but combine to yield a (12)C/(13)C isotopologue redistribution orchestrated by metabolic flux patterns. In this review, we summarise key metabolic isotope effects and integrate them into the corpus of plant primary carbon metabolism.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay cedex, France
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4
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Elucidation of the mechanism of N-demethylation catalyzed by cytochrome P450 monooxygenase is facilitated by exploiting nitrogen-15 heavy isotope effects. Arch Biochem Biophys 2011; 510:35-41. [DOI: 10.1016/j.abb.2011.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/12/2011] [Accepted: 03/14/2011] [Indexed: 11/19/2022]
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5
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Tcherkez G. Natural 15N/ 14N isotope composition in C 3 leaves: are enzymatic isotope effects informative for predicting the 15N-abundance in key metabolites? FUNCTIONAL PLANT BIOLOGY : FPB 2010; 38:1-12. [PMID: 32480857 DOI: 10.1071/fp10091] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 10/24/2010] [Indexed: 06/11/2023]
Abstract
Although nitrogen isotopes are viewed as important tools for understanding plant N acquisition and allocation, the current interpretation of natural 15N-abundances (δ15N values) is often impaired by substantial variability among individuals or between species. Such variability is likely to stem from the fact that 15N-abundance of assimilated N is not preserved during N metabolism and redistribution within the plant; that is, 14N/15N isotope effects associated with N metabolic reactions are certainly responsible for isotopic shifts between organic-N (amino acids) and absorbed inorganic N (nitrate). Therefore, to gain insights into the metabolic origin of 15N-abundance in plants, the present paper reviews enzymatic isotope effects and integrates them into a metabolic model at the leaf level. Using simple steady-state equations which satisfactorily predict the δ15N value of amino acids, it is shown that the sensitivity of δ15N values to both photorespiratory and N-input (reduction by nitrate reductase) rates is quite high. In other words, the variability in δ15N values observed in nature might originate from subtle changes in metabolic fluxes or environment-driven effects, such as stomatal closure that in turn changes v0, the Rubisco-catalysed oxygenation rate.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud 11, 91405 Orsay Cedex, France. Email
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6
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Craine JM, Elmore AJ, Aidar MPM, Bustamante M, Dawson TE, Hobbie EA, Kahmen A, Mack MC, McLauchlan KK, Michelsen A, Nardoto GB, Pardo LH, Peñuelas J, Reich PB, Schuur EAG, Stock WD, Templer PH, Virginia RA, Welker JM, Wright IJ. Global patterns of foliar nitrogen isotopes and their relationships with climate, mycorrhizal fungi, foliar nutrient concentrations, and nitrogen availability. THE NEW PHYTOLOGIST 2009; 183:980-992. [PMID: 19563444 DOI: 10.1111/j.1469-8137.2009.02917.x] [Citation(s) in RCA: 326] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ratios of nitrogen (N) isotopes in leaves could elucidate underlying patterns of N cycling across ecological gradients. To better understand global-scale patterns of N cycling, we compiled data on foliar N isotope ratios (delta(15)N), foliar N concentrations, mycorrhizal type and climate for over 11,000 plants worldwide. Arbuscular mycorrhizal, ectomycorrhizal, and ericoid mycorrhizal plants were depleted in foliar delta(15)N by 2 per thousand, 3.2 per thousand, 5.9 per thousand, respectively, relative to nonmycorrhizal plants. Foliar delta(15)N increased with decreasing mean annual precipitation and with increasing mean annual temperature (MAT) across sites with MAT >or= -0.5 degrees C, but was invariant with MAT across sites with MAT < -0.5 degrees C. In independent landscape-level to regional-level studies, foliar delta(15)N increased with increasing N availability; at the global scale, foliar delta(15)N increased with increasing foliar N concentrations and decreasing foliar phosphorus (P) concentrations. Together, these results suggest that warm, dry ecosystems have the highest N availability, while plants with high N concentrations, on average, occupy sites with higher N availability than plants with low N concentrations. Global-scale comparisons of other components of the N cycle are still required for better mechanistic understanding of the determinants of variation in foliar delta(15)N and ultimately global patterns in N cycling.
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Affiliation(s)
- Joseph M Craine
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Andrew J Elmore
- University of Maryland Center for Environmental Science, Appalachian Laboratory, 301 Braddock Road, Frostburg, MD 21532, USA
| | - Marcos P M Aidar
- Department of Plant Physiology and Biochemistry, Institute of Botany, PB 4005 CEP 01061-970 São Paulo, Brazil
| | | | - Todd E Dawson
- Division of Ecosystem Sciences, Mulford Hall, University of California, Berkeley, CA 94720, USA
- Center for Stable Isotope Biogeochemistry, Department of Integrative Biology, University of California, Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Erik A Hobbie
- Institute for the Study of Earth, Oceans, and Space, Morse Hall, University of New Hampshire, 39 College Road, Durham, NH 03824, USA
| | - Ansgar Kahmen
- Center for Stable Isotope Biogeochemistry, Department of Integrative Biology, University of California, Valley Life Sciences Building, Berkeley, CA 94720, USA
| | - Michelle C Mack
- Department of Botany, University of Florida, PO Box 118526, Gainesville, FL 32611, USA
| | | | - Anders Michelsen
- Department of Terrestrial Ecology, Institute of Biology, Oester Farimagsgade 2D, DK-1353 Copenhagen K, Denmark
| | - Gabriela B Nardoto
- Lab. Ecologia Isotópica - CENA/USP, Universidade de São Paulo, Av. Centenário, 303, Piracicaba SP 13416-000, Brazil
| | - Linda H Pardo
- USDA Forest Service, PO Box 968, Burlington, VT 05402, USA
| | - Josep Peñuelas
- Unitat d'Ecofisiologia CSIC-CREAF-CEAB, Centre de Recerca Ecològica i Aplicacions Forestals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Peter B Reich
- Department of Forest Resources, University of Minnesota, 115 Green Hall, 1530 Cleveland Avenue North, St Paul, MN 55108, USA
| | - Edward A G Schuur
- Department of Botany, University of Florida, PO Box 118526, Gainesville, FL 32611, USA
| | - William D Stock
- Centre for Ecosystem Management, School of Natural Sciences, Edith Cowan University, Joondalup 6027, Western Australia, Australia
| | - Pamela H Templer
- Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA
| | - Ross A Virginia
- Environmental Studies, Dartmouth College, Hanover, NH 03755, USA
| | - Jeffrey M Welker
- Environment and Natural Resources Institute, University of Alaska, 707 A Street, Anchorage, AK 99501, USA
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University 2109, Sydney, Australia
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7
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Molinié R, Kwiecień RA, Paneth P, Hatton W, Lebreton J, Robins RJ. Investigation of the mechanism of nicotine demethylation in Nicotiana through 2H and 15N heavy isotope effects: implication of cytochrome P450 oxidase and hydroxyl ion transfer. Arch Biochem Biophys 2007; 458:175-83. [PMID: 17254540 DOI: 10.1016/j.abb.2006.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 12/12/2006] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
Heavy-atom isotope effects for the N-demethylation of nicotine have been determined in vivo in static-phase biosynthetically incompetent plant cell cultures of Nicotiana species. A (2)H kinetic isotope effect of 0.587 and a (15)N kinetic isotope effect of 1.0028 were obtained. An identical (15)N kinetic isotope effect of 1.0032 was obtained for the nicotine analogue, N-methyl-2-phenylpyrrolidine. The magnitude of the (15)N heavy-atom isotope effect indicates that the fission of the CN bond is not rate limiting for demethylation. The theoretical calculation of heavy-atom isotope effects for a model of the reaction pathway based on cytochrome P450 best fits the measured kinetic isotope effect to the addition of hydroxyl ion to iminium to form N-hydroxymethyl, for which the computed (2)H- and (15)N kinetic isotope effects are 0.689 and 1.0081, respectively. This large inverse (2)H kinetic isotope effect is not compatible with the initial abstraction of the H from the methyl group playing a significant kinetic role in the overall kinetic limitation of the reaction pathway, since computed values for this step (4.54 and 0.9995, respectively) are inconsistent with the experimental data.
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Affiliation(s)
- Roland Molinié
- Laboratory of Isotopic and Electrochemical Analysis of Metabolism (LAIEM), CNRS UMR6006, University of Nantes, 2 rue de la Houssinière, 44322 Nantes, France
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8
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Seila AC, Okuda K, Núñez S, Seila AF, Strobel SA. Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction. Biochemistry 2005; 44:4018-27. [PMID: 15751978 DOI: 10.1021/bi047742f] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ribosome is the macromolecular machine responsible for protein synthesis in all cells. Here, we establish a kinetic framework for the 50S modified fragment reaction that makes it possible to measure the kinetic effects that result from isotopic substitution in either the A or P site of the ribosome. This simplified peptidyl transferase assay follows a rapid equilibrium random mechanism in which the reverse reaction is nonexistent and the forward commitment is negligible. A normal effect (1.009) is observed for (15)N substitution of the incoming nucleophile at both low and high pH. This suggests that the first irreversible step is the formation of the tetrahedral intermediate. The observation of a normal isotope effect that does not change as a function of pH suggests that the ribosome promotes peptide bond formation by a mechanism that differs in its details from an uncatalyzed aminolysis reaction in solution. This implies that the ribosome contributes chemically to catalysis of peptide bond formation.
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Affiliation(s)
- Amy C Seila
- Department of Molecular Biophysics, Yale University, New Haven, Connecticut 06520-8114, USA
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9
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Reitzer L. Biosynthesis of Glutamate, Aspartate, Asparagine, L-Alanine, and D-Alanine. EcoSal Plus 2004; 1. [PMID: 26443364 DOI: 10.1128/ecosalplus.3.6.1.3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Indexed: 06/05/2023]
Abstract
Glutamate, aspartate, asparagine, L-alanine, and D-alanine are derived from intermediates of central metabolism, mostly the citric acid cycle, in one or two steps. While the pathways are short, the importance and complexity of the functions of these amino acids befit their proximity to central metabolism. Inorganic nitrogen (ammonia) is assimilated into glutamate, which is the major intracellular nitrogen donor. Glutamate is a precursor for arginine, glutamine, proline, and the polyamines. Glutamate degradation is also important for survival in acidic environments, and changes in glutamate concentration accompany changes in osmolarity. Aspartate is a precursor for asparagine, isoleucine, methionine, lysine, threonine, pyrimidines, NAD, and pantothenate; a nitrogen donor for arginine and purine synthesis; and an important metabolic effector controlling the interconversion of C3 and C4 intermediates and the activity of the DcuS-DcuR two-component system. Finally, L- and D-alanine are components of the peptide of peptidoglycan, and L-alanine is an effector of the leucine responsive regulatory protein and an inhibitor of glutamine synthetase (GS). This review summarizes the genes and enzymes of glutamate, aspartate, asparagine, L-alanine, and D-alanine synthesis and the regulators and environmental factors that control the expression of these genes. Glutamate dehydrogenase (GDH) deficient strains of E. coli, K. aerogenes, and S. enterica serovar Typhimurium grow normally in glucose containing (energy-rich) minimal medium but are at a competitive disadvantage in energy limited medium. Glutamate, aspartate, asparagine, L-alanine, and D-alanine have multiple transport systems.
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10
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Schnizer HG, Boehlein SK, Stewart JD, Richards NGJ, Schuster SM. gamma-Glutamyl thioester intermediate in glutaminase reaction catalyzed by Escherichia coli asparagine synthetase B. Methods Enzymol 2003; 354:260-71. [PMID: 12418233 DOI: 10.1016/s0076-6879(02)54022-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Holly G Schnizer
- Department of Biochemistry, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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11
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Hobbie EA, Colpaert JV. Nitrogen availability and colonization by mycorrhizal fungi correlate with nitrogen isotope patterns in plants. THE NEW PHYTOLOGIST 2003; 157:115-126. [PMID: 33873704 DOI: 10.1046/j.1469-8137.2003.00657.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• Nitrogen isotope (δ 15 N) patterns in plants may provide insight into plant N dynamics. Here, two analytical models of N-isotope cycling in plants and mycorrhizal fungi were tested, as dominant plants in many forest ecosystems obtain most of their N through intereactions with mycorrhizal fungi. • Fungi were treated either as a single well-mixed N pool, or as two N pools (one available, plus one not available, for transfer to the host). Models were compared against complete biomass and 15 N budgets from culture studies of nonmycorrhizal and ectomycorrhizal Pinus sylvestris (colonized with Suillus luteus or Thelephora terrestris ) grown exponentially at low and high N supply. • Fungal biomass and N increased at low N relative to high N supply, whereas needle δ 15 N decreased. Needle δ 15 N correlated strongly and negatively with biomass of extraradical hyphae. Our data and models suggest that low plant δ 15 N values in low productivity and N-limited environments result partly from high retention of 15 N-enriched N by mycorrhizal fungi; this retention was driven by increased C flux to fungi under N-limited conditions. The two-pool model of fungal N accounted for greater variability in plant δ 15 N than the one-pool model. • Plant δ 15 N patterns may indicate relative allocation of fixed C from plants to mycorrhizal fungi under some conditions. Studies are needed on whether patterns observed in culture can be applied to interpret field measurements of δ 15 N.
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Affiliation(s)
- Erik A Hobbie
- Max Planck Institute for Biogeochemistry, Postfach 100164, 07701 Jena, Germany
- Present address: Morse Hall, Complex Systems Research Center, University of New Hampshire, Durham, New Hampshire 03824-3525, USA
| | - Jan V Colpaert
- Limburgs Universitair Centrum, Environmental Biology, 3590 Diepenbeek, Belgium
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12
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Werner RA, Schmidt HL. The in vivo nitrogen isotope discrimination among organic plant compounds. PHYTOCHEMISTRY 2002; 61:465-84. [PMID: 12409013 DOI: 10.1016/s0031-9422(02)00204-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The bulk delta 15 N-value of plant (leaf) biomass is determined by that of the inorganic primary nitrogen sources NO(3)(-), NH(4)(+) and N(2), and by isotope discriminations on their uptake or assimilation. NH(4)(+) from these is transferred into "organic N" mainly by the glutamine synthetase reaction. The involved kinetic nitrogen isotope effect does not become manifest, because the turnover is quantitative. From the product glutamine any further conversion proceeds in a "closed system", where kinetic isotope effects become only efficient in connection with metabolic branching. The central and most important corresponding process is the GOGAT-reaction, involved in the de novo nitrogen binding and in recycling processes like the phenylpropanoid biosynthesis and photorespiration. The reaction yields relatively 15N-depleted glutamate and remaining glutamine, source of 15N-enriched amide-N in heteroaromatic compounds. Glutamate provides nitrogen for all amino acids and some other compounds with different 15N-abundances. An isotope equilibration is not connected to transamination; the relative delta 15 N-value of individual amino acids is determined by their metabolic tasks. Relative to the bulk delta 15 N-value of the plant cell, proteins are generally 15N-enriched, secondary products like chlorophyll, lipids, amino sugars and alkaloids are depleted in 15N. Global delta 15 N-values and 15N-patterns of compounds with several N-atoms can be calculated from those of their precursors and isotope discriminations in their biosyntheses.
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Affiliation(s)
- Roland A Werner
- Max-Planck-Institut für Biogeochemie, Postfach 10 01 64, D-07701, Jena, Germany.
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13
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Schnizer HG, Boehlein SK, Stewart JD, Richards NG, Schuster SM. Formation and isolation of a covalent intermediate during the glutaminase reaction of a class II amidotransferase. Biochemistry 1999; 38:3677-82. [PMID: 10090755 DOI: 10.1021/bi981450v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incubation of Escherichia coli asparagine synthetase B (AS-B) with [14C]-L-glutamine gives a covalent adduct that can be isolated. Radiolabeled protein is not observed (i) when the wild-type enzyme is incubated with 6-diazo-5-oxo-L-norleucine (DON) prior to reaction with [14C]glutamine or (ii) when the C1A AS-B mutant is incubated with [14C]-L-glutamine. Both of these alterations eliminate the ability of the enzyme to utilize glutamine but do not affect ammonia-dependent asparagine synthesis. Formation of the covalent adduct therefore depends on the presence of the N-terminal active site cysteine, which has been shown to be essential for glutamine-dependent activity in this and other class II amidotransferases. The amount of covalent adduct exhibits saturation behavior with increasing concentrations of L-glutamine. The maximum observed quantity of this intermediate is consistent with its involvement on the main pathway of glutamine hydrolysis. The chemical properties of the isolable covalent adduct are consistent with those anticipated for the gamma-glutamyl thioester that has been proposed as an intermediate in the AS-B-catalyzed conversion of glutamine to glutamate. The covalent adduct is acid-stable but is labile under alkaline conditions. On the basis of the measured rates of formation and breakdown of this intermediate, it is kinetically competent to participate in the normal catalytic mechanism. These studies represent the first description of a thioester intermediate for any class II amidotransferase and represent an important step in gaining further insight into the kinetic and chemical mechanisms of AS-B.
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Affiliation(s)
- H G Schnizer
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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14
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Boehlein SK, Stewart JD, Walworth ES, Thirumoorthy R, Richards NG, Schuster SM. Kinetic mechanism of Escherichia coli asparagine synthetase B. Biochemistry 1998; 37:13230-8. [PMID: 9748330 DOI: 10.1021/bi981058h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Escherichia coli asparagine synthetase B (AS-B) catalyzes the synthesis of asparagine from aspartate, glutamine, and ATP. A combination of kinetic, isotopic-labeling, and stoichiometry studies have been performed to define the nature of nitrogen transfer mediated by AS-B. The results of initial rate studies were consistent with initial binding and hydrolysis of glutamine to glutamate plus enzyme-bound ammonia. The initial velocity results were equally consistent with initial binding of ATP and aspartate prior to glutamine binding. However, product inhibition studies were only consistent with the latter pathway. Moreover, isotope-trapping studies confirmed that the enzyme-ATP-aspartate complex was kinetically competent. Studies using 18O-labeled aspartate were consistent with formation of a beta-aspartyl-AMP intermediate, and stoichiometry studies revealed that 1 equiv of this intermediate formed on the enzyme in the absence of a nitrogen source. Taken together, our results are most consistent with initial formation of beta -aspartyl-AMP intermediate prior to glutamine binding. This sequence leaves open many possibilities for the chemical mechanism of nitrogen transfer.
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Affiliation(s)
- S K Boehlein
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville 32610, USA
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15
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Bachmann BO, Li R, Townsend CA. beta-Lactam synthetase: a new biosynthetic enzyme. Proc Natl Acad Sci U S A 1998; 95:9082-6. [PMID: 9689037 PMCID: PMC21295 DOI: 10.1073/pnas.95.16.9082] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/1998] [Accepted: 06/04/1998] [Indexed: 02/08/2023] Open
Abstract
The principal cause of bacterial resistance to penicillin and other beta-lactam antibiotics is the acquisition of plasmid-encoded beta-lactamases, enzymes that catalyze hydrolysis of the beta-lactam bond and render these antibiotics inactive. Clavulanic acid is a potent inhibitor of beta-lactamases and has proven clinically effective in combating resistant infections. Although clavulanic acid and penicillin share marked structural similarities, the biosyntheses of their bicyclic nuclei are wholly dissimilar. In contrast to the efficient iron-mediated oxidative cyclization of a tripeptide to isopenicillin N, the critical beta-lactam ring of clavulanic acid is demonstrated to form by intramolecular closure catalyzed by a new type of ATP/Mg2+-dependent enzyme, a beta-lactam synthetase (beta-LS). Insertional inactivation of its encoding gene in wild-type Streptomyces clavuligerus resulted in complete loss of clavulanic acid production and the accumulation of N2-(carboxyethyl)-L-arginine (CEA). Chemical complementation of this blocked mutant with authentic deoxyguanidinoproclavaminic acid (DGPC), the expected product of the beta-LS, restored clavulanic acid synthesis. Finally, overexpression of this gene gave the beta-LS, which was shown to mediate the conversion of CEA to DGPC in the presence of ATP/Mg2+. Primary amino acid sequence comparisons suggest that this mode of beta-lactam formation could be more widely spread in nature and mechanistically related to asparagine synthesis.
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Affiliation(s)
- B O Bachmann
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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16
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Xu T, Werner RM, Lee KC, Fettinger JC, Davis JT, Coward JK. Synthesis and Evaluation of Tripeptides Containing Asparagine Analogues as Potential Substrates or Inhibitors of Oligosaccharyltransferase. J Org Chem 1998. [DOI: 10.1021/jo9802123] [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)
- Tong Xu
- Department of Chemistry, Interdepartmental Program of Medicinal Chemistry, and College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - R. Marshall Werner
- Department of Chemistry, Interdepartmental Program of Medicinal Chemistry, and College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Kwun-Chi Lee
- Department of Chemistry, Interdepartmental Program of Medicinal Chemistry, and College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - James C. Fettinger
- Department of Chemistry, Interdepartmental Program of Medicinal Chemistry, and College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Jeffery T. Davis
- Department of Chemistry, Interdepartmental Program of Medicinal Chemistry, and College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - James K. Coward
- Department of Chemistry, Interdepartmental Program of Medicinal Chemistry, and College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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17
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Richards NG, Schuster SM. Mechanistic issues in asparagine synthetase catalysis. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 1998; 72:145-98. [PMID: 9559053 DOI: 10.1002/9780470123188.ch5] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The enzymatic synthesis of asparagine is an ATP-dependent process that utilizes the nitrogen atom derived from either glutamine or ammonia. Despite a long history of kinetic and mechanistic investigation, there is no universally accepted catalytic mechanism for this seemingly straightforward carboxyl group activating enzyme, especially as regards those steps immediately preceding amide bond formation. This chapter considers four issues dealing with the mechanism: (a) the structural organization of the active site(s) partaking in glutamine utilization and aspartate activation; (b) the relationship of asparagine synthetase to other amidotransferases; (c) the way in which ATP is used to activate the beta-carboxyl group; and (d) the detailed mechanism by which nitrogen is transferred.
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Affiliation(s)
- N G Richards
- Department of Chemistry, University of Florida, Gainesville 32611, USA
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18
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Zalkin H, Smith JL. Enzymes utilizing glutamine as an amide donor. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 1998; 72:87-144. [PMID: 9559052 DOI: 10.1002/9780470123188.ch4] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amide nitrogen from glutamine is a major source of nitrogen atoms incorporated biosynthetically into other amino acids, purine and pyrimidine bases, amino-sugars, and coenzymes. A family comprised of at least sixteen amidotransferases are known to catalyze amide nitrogen transfer from glutamine to their acceptor substrates. Recent fine structural advances, largely as a result of X-ray crystallography, now provide structure-based mechanisms that help to explain fundamental aspects of the catalytic and regulatory interactions of several of these aminotransferases. This chapter provides an overview of this recent progress made on the characterization of amidotransferase structure and mechanism.
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19
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Muchmore CR, Krahn JM, Kim JH, Zalkin H, Smith JL. Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Protein Sci 1998; 7:39-51. [PMID: 9514258 PMCID: PMC2143822 DOI: 10.1002/pro.5560070104] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Crystal structures of glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase from Escherichia coli have been determined to 2.0-A resolution in the absence of ligands, and to 2.5-A resolution with the feedback inhibitor AMP bound to the PRPP catalytic site. Glutamine PRPP amidotransferase (GPATase) employs separate catalytic domains to abstract nitrogen from the amide of glutamine and to transfer nitrogen to the acceptor substrate PRPP. The unliganded and AMP-bound structures, which are essentially identical, are interpreted as the inhibited form of the enzyme because the two active sites are disconnected and the PRPP active site is solvent exposed. The structures were compared with a previously reported 3.0-A structure of the homologous Bacillus subtilis enzyme (Smith JL et al., 1994, Science 264:1427-1433). The comparison indicates a pattern of conservation of peptide structures involved with catalysis and variability in enzyme regulatory functions. Control of glutaminase activity, communication between the active sites, and regulation by feedback inhibitors are addressed differently by E. coli and B. subtilis GPATases. The E. coli enzyme is a prototype for the metal-free GPATases, whereas the B. subtilis enzyme represents the metal-containing enzymes. The structure of the E. coli enzyme suggests that a common ancestor of the two enzyme subfamilies may have included an Fe-S cluster.
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Affiliation(s)
- C R Muchmore
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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20
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Xu T, Coward JK. 13C- and 15N-labeled peptide substrates as mechanistic probes of oligosaccharyltransferase. Biochemistry 1997; 36:14683-9. [PMID: 9398187 DOI: 10.1021/bi9719511] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The carboxamide moiety that links the carbohydrate and protein moieties in N-linked glycoproteins has been unambiguously determined to arise intact from asparagine by the use of chemically synthesized Bz-[4-13C, 15N]Asn-Leu-Thr-NH2 as an oligosaccharyltransferase (OST) substrate. Bz-[4-13C]Asn-Leu-Thr-NH2 was also synthesized and used to evaluate a proposed mechanism of OST catalysis similar to that of glutamine-dependent amidotransferases using 15NH4OAc as a potential external nucleophile. Analysis of NMR and MS spectra of the isotopically labeled peptides and the resulting biosynthesized glycopeptides indicates that free 15NH3 is not lost from the doubly labeled substrate during catalysis nor can exogenous 15NH3 intercept any of several postulated enzyme-bound species. These results indicate that OST-catalyzed glycosylation does not follow a mechanism involving the transient generation of exchangeable "NH3". Thus, in contrast to several glutamine-dependent amidotransferases, OST catalysis does not lead to transient scission of the asparagine beta-carboxamide C-N bond. Together with previously published results, these data argue against nucleophilic activation of the asparagine beta-carboxamide moiety being the underlying chemical mechanism for OST-catalyzed glycosylation of peptides.
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Affiliation(s)
- T Xu
- Department of Chemistry, University of Michigan, Ann Arbor 48109, USA
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21
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Krahn JM, Kim JH, Burns MR, Parry RJ, Zalkin H, Smith JL. Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry 1997; 36:11061-8. [PMID: 9333323 DOI: 10.1021/bi9714114] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Activation of gluatmine phosphoribosylpyrophosphate (RPPP) amidotransferase (GPATase) by binding of a PRPP substrate analog results in the formation of a 20 A channel connecting the active site for glutamine hydrolysis in one domain with the PRPP site in a second domain. This solvent-inaccessible channel permits transfer of the NH3 intermediate between the two active sites. Tunneling of NH3 may be a common mechanism for glutamine amidotransferase-catalyzed nitrogen transfer and for coordination of catalysis at two distinct active sites in complex enzymes. The 2.4 A crystal structure of the active conformer of GPATase also provides the first description of an intact active site for the phosphoribosyltransferase (PRTase) family of nucleotide synthesis and salvage enzymes. Chemical assistance to catalysis is provided primarily by the substrate and secondarily by the enzyme in the proposed structure-based mechanism. Different catalytic and inhibitory modes of divalent cation binding to the PRTase active site are revealed in the active conformer of the enzyme and in a feedback-inhibited GMP complex.
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Affiliation(s)
- J M Krahn
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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22
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Boehlein SK, Walworth ES, Schuster SM. Identification of cysteine-523 in the aspartate binding site of Escherichia coli asparagine synthetase B. Biochemistry 1997; 36:10168-77. [PMID: 9254614 DOI: 10.1021/bi970494l] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The site-directed chemical modifier [p-(fluorosulfonyl)benzoyl]adenosine (5'-FSBA) inactivates Escherichia coli asparagine synthetase B activity following pseudo-first-order kinetics, with ATP providing specific protection, with a Kd of 12 microM. The 5'-FSBA modification appears to be covalent, even though a nonstoichiometric amount (less than 10%) of radiolabeled 5'-FSBA was associated with a totally inactivated enzyme. However, the inactivation by 5'-FSBA could be reversed upon the addition of dithiothreitol. These results are indicative of 5'-FSBA-induced disulfide bond formation, which requires the presence of at least two cysteine residues in the proximity of the ATP binding site. Identification of the critical cysteine residue was accomplished by sequential replacement of each cysteine in the protein by site-directed mutagenesis. Cys 523 was identified as the key residue involved in the formation of the 5'-FSBA-induced disulfide bond. Detailed kinetic analyses and comparison with similar enzymes, suggest that this cysteine residue, while in close proximity to the ATP binding site, is actually involved in aspartate binding in asparagine synthetase B.
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Affiliation(s)
- S K Boehlein
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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23
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Boehlein SK, Rosa-Rodriguez JG, Schuster SM, Richards NGJ. Catalytic Activity of the N-Terminal Domain of Escherichia coli Asparagine Synthetase B Can Be Reengineered by Single-Point Mutation. J Am Chem Soc 1997. [DOI: 10.1021/ja9613668] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susan K. Boehlein
- Contribution from the Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, and Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32611
| | - José G. Rosa-Rodriguez
- Contribution from the Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, and Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32611
| | - Sheldon M. Schuster
- Contribution from the Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, and Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32611
| | - Nigel G. J. Richards
- Contribution from the Department of Chemistry, University of Florida, Gainesville, Florida 32611, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, and Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32611
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24
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Boehlein SK, Walworth ES, Richards NG, Schuster SM. Mutagenesis and chemical rescue indicate residues involved in beta-aspartyl-AMP formation by Escherichia coli asparagine synthetase B. J Biol Chem 1997; 272:12384-92. [PMID: 9139684 DOI: 10.1074/jbc.272.19.12384] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Site-directed mutagenesis and kinetic studies have been employed to identify amino acid residues involved in aspartate binding and transition state stabilization during the formation of beta-aspartyl-AMP in the reaction mechanism of Escherichia coli asparagine synthetase B (AS-B). Three conserved amino acids in the segment defined by residues 317-330 appear particularly crucial for enzymatic activity. For example, when Arg-325 is replaced by alanine or lysine, the resulting mutant enzymes possess no detectable asparagine synthetase activity. The catalytic activity of the R325A AS-B mutant can, however, be restored to about 1/6 of that of wild-type AS-B by the addition of guanidinium HCl (GdmHCl). Detailed kinetic analysis of the rescued activity suggests that Arg-325 is involved in stabilization of a pentacovalent intermediate leading to the formation beta-aspartyl-AMP. This rescue experiment is the second example in which the function of a critical arginine residue that has been substituted by mutagenesis is restored by GdmHCl. Mutation of Thr-322 and Thr-323 also produces enzymes with altered kinetic properties, suggesting that these threonines are involved in aspartate binding and/or stabilization of intermediates en route to beta-aspartyl-AMP. These experiments are the first to identify residues outside of the N-terminal glutamine amide transfer domain that have any functional role in asparagine synthesis.
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Affiliation(s)
- S K Boehlein
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
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25
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Boehlein SK, Schuster SM, Richards NG. Glutamic acid gamma-monohydroxamate and hydroxylamine are alternate substrates for Escherichia coli asparagine synthetase B. Biochemistry 1996; 35:3031-7. [PMID: 8608142 DOI: 10.1021/bi952505l] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Escherichia coli asparagine synthetase B (AS-B) catalyzes the synthesis of asparagine from aspartic acid and glutamine in an ATP-dependent reaction. The ability of this enzyme to employ hydroxylamine and L-glutamic acid gamma-monohydroxamate (LGH) as alternative substrates in place of ammonia and L-glutamine, respectively, has been investigated. The enzyme is able to function as an amidohydrolase, liberating hydroxylamine from LGH with high catalytic efficiency, as measured by k(cat)/K(M). In addition, the kinetic parameters determined for hydroxylamine in AS-B synthetase activity are very similar to those of ammonia. Nitrogen transfer from LGH to yield aspartic acid beta-monohydroxamate is also catalyzed by AS-B. While such an observation has been made for a few members of the trpG amidotransferase family, our results appear to be the first demonstration that nitrogen transfer can occur from glutamine analogs in a purF amidotransferase. However, k(cat)/K(M) for the ATP-dependent transfer of hydroxylamine from LGH to aspartic acid is reduced 3-fold relative to that for glutamine-dependent asparagine synthesis. Further, the AS-B mutant in which asparagine is replaced by alanine (N74A) can also use hydroxylamine as an alternate substrate to ammonia and catalyze the hydrolysis of LGH. The catalytic efficiencies (k(cat)/K(M)) of nitrogen transfer from LGH and L-glutamine to beta-aspartyl-AMP are almost identical for the N74A AS-B mutant. These observations support the proposal that Asn-74 plays a role in catalyzing glutamine-dependent nitrogen transfer. We interpret our kinetic data as further evidence against ammonia-mediated nitrogen transfer from glutamine in the purF amidotransferase AS-B. These results are consistent with two alternate chemical mechanisms that have been proposed for this reaction [Boehlein, S. K., Richards, N. G. J., Walworth, E. S., & Schuster, S. M. (1994) J. Biol. Chem. 269, 26789-26795].
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Affiliation(s)
- S K Boehlein
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, 32610, USA
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