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Benítez-Rangel E, Rodríguez-Hernández A, Velasco-García R. The substrate of the glucose-6-phosphate dehydrogenase of Pseudomonas aeruginosa provides structural stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140331. [PMID: 31760039 DOI: 10.1016/j.bbapap.2019.140331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/22/2019] [Accepted: 11/20/2019] [Indexed: 01/18/2023]
Abstract
In general, eukaryotic glucose-6-phosphate dehydrogenases (G6PDHs) are structurally stabilized by NADP+. Here we show by spectrofluorometric analysis, thermal and urea denaturation, and trypsin proteolysis, that a different mechanism stabilizes the enzyme from Pseudomonas aeruginosa (PaG6PDH) (EC 1.1.1.363). The spectrofluorometric analysis of the emission of 8-anilino-1-naphthalenesulfonic acid (ANS) indicates that this stabilization is the result of a structural change in the enzyme caused by G6P. The similarity between the Kd values determined for the PaG6PDH-G6P complex (78.0 ± 7.9 μM) and the K0.5 values determined for G6P (57.9 ± 2.5 and 104.5 ± 9.3 μM in the NADP+- and NAD+-dependent reactions, respectively) suggests that the structural changes are the result of G6P binding to the active site of PaG6PDH. Modeling of PaG6PDH indicated the residues that potentially bind the ligand. These results and a phylogenetic analysis of the amino acid sequences of forty-four G6PDHs, suggest that the stabilization observed for PaG6PDH could be a characteristic that distinguishes this and other G6PDHs that use NAD+ and NADP+ from those that use NADP+ only or preferentially, such as those found in eukaryotes. This characteristic could be related to the metabolic roles these enzymes play in the organisms to which they belong.
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Affiliation(s)
- Edaena Benítez-Rangel
- Universidad Nacional Autónoma de México, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico
| | - Annia Rodríguez-Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - Roberto Velasco-García
- Universidad Nacional Autónoma de México, Facultad de Estudios Superiores Iztacala, Tlalnepantla, Estado de México 54090, Mexico.
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2
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Özcan E, Selvi SS, Nikerel E, Teusink B, Toksoy Öner E, Çakır T. A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris. Appl Microbiol Biotechnol 2019; 103:3153-3165. [PMID: 30712128 DOI: 10.1007/s00253-019-09630-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 12/14/2018] [Accepted: 01/06/2019] [Indexed: 12/16/2022]
Abstract
Leuconostoc mesenteroides subsp. cremoris is an obligate heterolactic fermentative lactic acid bacterium that is mostly used in industrial dairy fermentations. The phosphoketolase pathway (PKP) is a unique feature of the obligate heterolactic fermentation, which leads to the production of lactate, ethanol, and/or acetate, and the final product profile of PKP highly depends on the energetics and redox state of the organism. Another characteristic of the L. mesenteroides subsp. cremoris is the production of aroma compounds in dairy fermentation, such as in cheese production, through the utilization of citrate. Considering its importance in dairy fermentation, a detailed metabolic characterization of the organism is necessary for its more efficient use in the industry. To this aim, a genome-scale metabolic model of dairy-origin L. mesenteroides subsp. cremoris ATCC 19254 (iLM.c559) was reconstructed to explain the energetics and redox state mechanisms of the organism in full detail. The model includes 559 genes governing 1088 reactions between 1129 metabolites, and the reactions cover citrate utilization and citrate-related flavor metabolism. The model was validated by simulating co-metabolism of glucose and citrate and comparing the in silico results to our experimental results. Model simulations further showed that, in co-metabolism of citrate and glucose, no flavor compounds were produced when citrate could stimulate the formation of biomass. Significant amounts of flavor metabolites (e.g., diacetyl and acetoin) were only produced when citrate could not enhance growth, which suggests that flavor formation only occurs under carbon and ATP excess. The effects of aerobic conditions and different carbon sources on product profiles and growth were also investigated using the reconstructed model. The analyses provided further insights for the growth stimulation and flavor formation mechanisms of the organism.
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Affiliation(s)
- Emrah Özcan
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.,IBSB, Department of Bioengineering, Marmara University, Istanbul, Turkey.,Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU Amsterdam, Amsterdam, The Netherlands
| | - S Selvin Selvi
- IBSB, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Emrah Nikerel
- Genetics and Bioengineering Department, Yeditepe University, Istanbul, Turkey
| | - Bas Teusink
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU Amsterdam, Amsterdam, The Netherlands
| | - Ebru Toksoy Öner
- IBSB, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.
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3
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Li Z, Jiang N, Yang K, Zheng J. Cloning, expression, and characterization of a thermostable glucose-6-phosphate dehydrogenase from Thermoanaerobacter tengcongensis. Extremophiles 2016; 20:149-56. [DOI: 10.1007/s00792-016-0808-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/05/2016] [Indexed: 11/25/2022]
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4
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Bianconi ML. Avoiding Buffer Interference in ITC Experiments: A Case Study from the Analysis of Entropy-Driven Reactions of Glucose-6-Phosphate Dehydrogenase. Methods Enzymol 2015; 567:237-56. [PMID: 26794357 DOI: 10.1016/bs.mie.2015.08.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Isothermal titration calorimetry (ITC) is a label-free technique that allows the direct determination of the heat absorbed or released in a reaction. Frequently used to determining binding parameters in biomolecular interactions, it is very useful to address enzyme-catalyzed reactions as both kinetic and thermodynamic parameters can be obtained. Since calorimetry measures the total heat effects of a reaction, it is important to consider the contribution of the heat of protonation/deprotonation that is possibly taking place. Here, we show a case study of the reaction catalyzed by the glucose-6-phosphate dehydrogenase (G6PD) from Leuconostoc mesenteroides. This enzyme is able to use either NAD(+) or NADP(+) as a cofactor. The reactions were done in five buffers of different enthalpy of protonation. Depending on the buffer used, the observed calorimetric enthalpy (ΔH(cal)) of the reaction varied from -22.93 kJ/mol (Tris) to 19.37 kJ/mol (phosphate) for the NADP(+)-linked reaction, and -11.67 kJ/mol (Tris) to 7.32 kcal/mol or 30.63 kJ/mol (phosphate) for the NAD(+) reaction. We will use this system as an example of how to extract proton-independent reaction enthalpies from kinetic data to ensure that the reported accurately represent the intrinsic heat of reaction.
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Affiliation(s)
- M Lucia Bianconi
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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5
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Karra S, Gorski W. Signal Amplification in Enzyme-Based Amperometric Biosensors. Anal Chem 2013; 85:10573-80. [DOI: 10.1021/ac4026994] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sushma Karra
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, United States
| | - Waldemar Gorski
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, United States
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6
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Ravera S, Calzia D, Morelli A, Panfoli I. Oligomerization studies of Leuconostoc mesenteroides G6PD activity after SDS-PAGE and blotting. Mol Biol 2010. [DOI: 10.1134/s002689331003009x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Kirsch M, Talbiersky P, Polkowska J, Bastkowski F, Schaller T, de Groot H, Klärner FG, Schrader T. A mechanism of efficient G6PD inhibition by a molecular clip. Angew Chem Int Ed Engl 2009; 48:2886-90. [PMID: 19283805 DOI: 10.1002/anie.200806175] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Triple duty: A synthetic molecular clip traps nicotinamide adenine dinucleotide phosphate (NADP(+); see picture) as well as occupying both the cofactor- and the substrate-binding site in glucose-6-phosphate (G6P) dehydrogenase. This combination of two inhibition mechanisms makes the clip highly effective and selective for this enzyme over other dehydrogenases.
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Affiliation(s)
- Michael Kirsch
- Institut für Physiologische Chemie, Iniversitätsklinikum Essen, Hufelandstrasse 55, 45122 Essen, Germany
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Kirsch M, Talbiersky P, Polkowska J, Bastkowski F, Schaller T, de Groot H, Klärner FG, Schrader T. A Mechanism of Efficient G6PD Inhibition by a Molecular Clip. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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9
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Gurpilhares DB, Pessoa A, Roberto IC. Glucose-6-phosphate dehydrogenase and xylitol production by Candida guilliermondii FTI 20037 using statistical experimental design. Process Biochem 2006. [DOI: 10.1016/j.procbio.2005.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Pletnev VZ, Weeks CM, Duax WL. Rational proteomics II: electrostatic nature of cofactor preference in the short-chain oxidoreductase (SCOR) enzyme family. Proteins 2005; 57:294-301. [PMID: 15340916 PMCID: PMC1476702 DOI: 10.1002/prot.20205] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The dominant role of long-range electrostatic interatomic interactions in nicotinamide adenine dinucleotide/nicotinamide adenine dinucleotide phosphate (NAD/NADP) cofactor recognition has been shown for enzymes of the short-chain oxidoreductase (SCOR) family. An estimation of cofactor preference based only on the contribution of the electrostatic energy term to the total energy of enzyme-cofactor interaction has been tested for approximately 40 known three-dimensional (3D) crystal complexes and approximately 330 SCOR enzymes, with cofactor preference predicted by the presence of Asp or Arg recognition residues at specific 3D positions in the beta2alpha3 loop (Duax et al., Proteins 2003;53:931-943). The results obtained were found to be consistent with approximately 90% reliable cofactor assignments for those subsets. The procedure was then applied to approximately 170 SCOR enzymes with completely uncertain NAD/NADP dependence, due to the lack of Asp and Arg marker residues. The proposed 3D electrostatic approach for cofactor assignment ("3D_DeltaE(el)") has been implemented in an automatic screening procedure, and together with the use of marker residues proposed earlier (Duax et al., Proteins 2003;53:931-943), increases the level of reliable predictions for the putative SCORs from approximately 70% to approximately 90%. It is expected to be applicable for any NAD/NADP-dependent enzyme subset having at least 25-30% sequence identity, with at least one enzyme of known 3D crystal structure.
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Affiliation(s)
- Vladimir Z Pletnev
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, SUNY at Buffalo, Buffalo, New York 14203, USA
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11
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Pancera SM, da Silva LH, Loh W, Itri R, Pessoa A, Petri DF. The effect of poly(ethylene glycol) on the activity and structure of glucose-6-phosphate dehydrogenase in solution. Colloids Surf B Biointerfaces 2002. [DOI: 10.1016/s0927-7765(02)00011-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Rowland P, Basak AK, Gover S, Levy HR, Adams MJ. The three-dimensional structure of glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides refined at 2.0 A resolution. Structure 1994; 2:1073-87. [PMID: 7881907 DOI: 10.1016/s0969-2126(94)00110-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Glucose 6-phosphate dehydrogenase (G6PD) is the first enzyme of the pentose phosphate pathway. Normally the pathway is synthetic and NADP-dependent, but the Gram-positive bacterium Leuconostoc mesenteroides, which does not have a complete glycolytic pathway, also uses the oxidative enzymes of the pentose phosphate pathway for catabolic reactions, and selects either NAD or NADP depending on the demands for catabolic or anabolic metabolism. RESULTS The structure of G6PD has been determined and refined to 2.0 A resolution. The enzyme is a dimer, each subunit consisting of two domains. The smaller domain is a classic dinucleotide-binding fold, while the larger one is a new beta+ alpha fold, not previously seen, with a predominantly antiparallel nine-stranded beta-sheet. There are significant structural differences in the coenzyme-binding domains of the two subunits, caused by Pro 149 which is cis in one subunit and trans in the other. CONCLUSIONS The structure has allowed us to propose the location of the active site and the coenzyme-binding site, and suggests the role of many of the residues conserved between species. We propose that the conserved Arg46 would interact with both the adenine ring and the 2'-phosphate of NADP. Gln47, which is not conserved, may contribute to the change from NADP to dual coenzyme specificity. His178, in a nine-residue peptide conserved for all known sequences, binds a phosphate in the active site pocket. His240 is the most likely candidate for the base to oxidize the 1-hydroxyl group of the glucose 6-phosphate substrate.
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Affiliation(s)
- P Rowland
- University of Oxford, Laboratory of Molecular Biophysics, UK
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Adams MJ, Basak AK, Gover S, Rowland P, Levy HR. Site-directed mutagenesis to facilitate X-ray structural studies of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase. Protein Sci 1993; 2:859-62. [PMID: 8495203 PMCID: PMC2142489 DOI: 10.1002/pro.5560020515] [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: 01/31/2023]
Affiliation(s)
- M J Adams
- Laboratory of Molecular Biophysics, University of Oxford, United Kingdom
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14
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Plomer JJ, Gafni A. Renaturation of glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides after denaturation in 4 M guanidine hydrochloride: kinetics of aggregation and reactivation. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1163:89-96. [PMID: 8476934 DOI: 10.1016/0167-4838(93)90283-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In 4 M guanidine hydrochloride (GdnHCl), the dimeric enzyme glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides (G6PD) dissociated to subunits and was extensively unfolded. Rapid dilution of this high GdnHCl concentration allowed G6PD to partially renature, as measured by enzyme reactivation, to a level which depended on the conditions employed. The fraction of the enzyme which did not renature aggregated and precipitated out of solution, a process which could not be substantially prevented by stabilizing additives. Based on the enzyme concentration dependence of the reactivation yield and on a comparison of the aggregation and reactivation rates, it was determined that aggregation and reactivation compete kinetically for a partially-folded intermediate only very early in the process, during the rapid GdnHCl-dilution step. The kinetics of G6PD reactivation were sigmoidal, indicating that this process involves more than one rate-limiting reaction. The kinetics depended on enzyme concentration in a higher than first-order manner, indicating that association of subunits is one of the rate-limiting reactions. A renaturation mechanism compatible with these observations is described, which involves a bi-unimolecular (subunit association-folding) reaction sequence, with rate constants equal to 2.19 microM-1 min-1 and 0.140 min-1, respectively. This mechanism involves an inactive, dimeric, G6PD-folding intermediate, a species whose existence has recently been established by equilibrium denaturation experiments (Plomer, J.J. and Gafni, A. (1992) Biochim. Biophys. Acta 1122, 234-242).
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Affiliation(s)
- J J Plomer
- Institute of Gerontology, University of Michigan, Ann Arbor 48109
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15
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Levy HR, Cook C. Purification and properties of NADP-linked glucose-6-phosphate dehydrogenase from Acetobacter hansenii (Acetobacter xylinum). Arch Biochem Biophys 1991; 291:161-7. [PMID: 1929428 DOI: 10.1016/0003-9861(91)90119-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The NADP-linked glucose-6-phosphate dehydrogenase from Acetobacter hansenii (formerly known as Acetobacter xylinum) has been purified to apparent homogeneity. The sequence of the 10 N-terminal amino acids was determined. The subunit molecular weight of the enzyme is 53,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; gel filtration studies under nondenaturing conditions revealed that the molecular weight of the enzyme is 200,000 to 220,000 at pH 6.5 and 9.5, suggesting that the native enzyme is a tetramer. Specificity studies at both pH 6.5 and 9.5 demonstrated that the enzyme is a typical NADP-preferring glucose-6-phosphate dehydrogenase. The enzyme's catalytic activity increases with increasing pH, kcat being approximately 4 times greater at pH 9.5 than at pH 6.7 and the Km for NADP+ being 3 times lower at the higher pH; but the Km for glucose 6-phosphate is nearly 20 times higher at pH 9.5 than at pH 6.7, suggesting that the enzyme is catalytically more efficient at the lower pH. At pH 6.7, initial velocity measurements, product inhibition by NADPH, and inhibition by glucosamine 6-phosphate yielded results that were consistent with a steady-state random mechanism. At pH 9.5, steady-state kinetic analyses suggested that the mechanism is ordered, with coenzyme binding first, but nonlinear double-reciprocal plots were observed in the presence of NADPH when glucose 6-phosphate was varied and a complete kinetic analysis was not undertaken. Among several nucleotides and potential inhibitory ligands examined, only 2',5'-ADP inhibited the enzyme significantly.
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Affiliation(s)
- H R Levy
- Department of Biology, Syracuse University, New York 13244
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Leyland ML, Kelly DJ. Purification and characterization of a monomeric isocitrate dehydrogenase with dual coenzyme specificity from the photosynthetic bacterium Rhodomicrobium vannielii. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 202:85-93. [PMID: 1935983 DOI: 10.1111/j.1432-1033.1991.tb16347.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An isocitrate dehydrogenase able to function with either NADP or NAD as coenzyme was purified to homogeneity from cell-free extracts of the purple photosynthetic eubacterium Rhodomicrobium vannielii using a rapid two-step procedure involving dye-ligand affinity chromatography. The enzyme was obtained in 60% yield with specific activities of 23 U.mg protein-1 (NADP-linked reaction) and 18.5 U.mg protein-1 (NAD-linked reaction). The purified enzyme was monomeric and migrated with an approximate Mr of 75,000-80,000 on both SDS/PAGE and non-denaturing PAGE. Affinity constants (Km values) of 2.5 microM for NADP and 0.77 mM for NAD and values for kcat/Km of 981,200 min-1.mM-1 (NADP) and 2455 min-1.mM-1 (NAD) indicated a greater specificity for NADP compared to NAD. A number of metabolites were examined for possible differential regulatory effects on the NADP- and NAD-linked reactions, using a dual-wavelength assay. Oxaloacetate was found to be an effective inhibitor of both reactions and the enzyme was also sensitive to concerted inhibition by glyoxylate and oxaloacetate. The amino-acid composition and the identity of 39 residues at the N-terminus were determined and compared to other isocitrate dehydrogenases. The results suggested a relationship between the Rm. vannielii enzyme and the monomeric isocitrate dehydrogenase isoenzyme II from Vibrio ABE-1.
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Affiliation(s)
- M L Leyland
- Robert Hill Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, England
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17
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Cloning of the gene and amino acid sequence for glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)98798-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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18
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Interaction of Leuconostoc mesenteroides glucose-6-phosphate dehydrogenase with pyridoxal 5‘-diphospho-5‘-adenosine. Affinity labeling of Lys-21 and Lys-343. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)67631-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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