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Geddes BA, Oresnik IJ. Physiology, genetics, and biochemistry of carbon metabolism in the alphaproteobacterium Sinorhizobium meliloti. Can J Microbiol 2014; 60:491-507. [PMID: 25093748 DOI: 10.1139/cjm-2014-0306] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A large proportion of genes within a genome encode proteins that play a role in metabolism. The Alphaproteobacteria are a ubiquitous group of bacteria that play a major role in a number of environments. For well over 50 years, carbon metabolism in Rhizobium has been studied at biochemical and genetic levels. Here, we review the pre- and post-genomics literature of the metabolism of the alphaproteobacterium Sinorhizobium meliloti. This review provides an overview of carbon metabolism that is useful to readers interested in this organism and to those working on other organisms that do not follow other model system paradigms.
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Affiliation(s)
- Barney A Geddes
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Watanabe S, Makino K. Novel modified version of nonphosphorylated sugar metabolism - an alternative l-rhamnose pathway of Sphingomonas sp. FEBS J 2009; 276:1554-67. [DOI: 10.1111/j.1742-4658.2009.06885.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Watanabe S, Saimura M, Makino K. Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism. J Biol Chem 2008; 283:20372-82. [PMID: 18505728 DOI: 10.1074/jbc.m801065200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Entner-Doudoroff (ED) pathway is a classic central pathway of d-glucose metabolism in all three phylogenetic domains. On the other hand, Archaea and/or bacteria possess several modified versions of the ED pathway, in which nonphosphorylated intermediates are involved. Several fungi, including Pichia stipitis and Debaryomyces hansenii, possess an alternative pathway of L-rhamnose metabolism, which is different from the known bacterial pathway. Gene cluster related to this hypothetical pathway was identified by bioinformatic analysis using the metabolic enzymes involved in analogous sugar pathways to the ED pathway. Furthermore, the homologous gene cluster was found not only in many other fungi but also several bacteria, including Azotobacter vinelandii. Four putative metabolic genes, LRA1-4, were cloned, overexpressed in Escherichia coli, and purified. Substrate specificity and kinetic analysis revealed that nonphosphorylated intermediates related to L-rhamnose are significant active substrates for the purified LRA1-4 proteins. Furthermore, L-2-keto-3-deoxyrhamnonate was structurally identified as both reaction products of dehydration by LRA3 and aldol condensation by LRA4. These results suggested that the LRA1-4 genes encode L-rhamnose 1-dehydrogenase, L-rhamnono-gamma-lactonase, L-rhamnonate dehydratase, and L-KDR aldolase, respectively, by which L-rhamnose is converted into pyruvate and L-lactaldehyde through analogous reaction steps to the ED pathway. There was no evolutionary relationship between L-KDR aldolases from fungi and bacteria.
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Affiliation(s)
- Seiya Watanabe
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.
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Yasutake Y, Nishiya Y, Tamura N, Tamura T. Structural Insights into Unique Substrate Selectivity of Thermoplasma acidophilum d-Aldohexose Dehydrogenase. J Mol Biol 2007; 367:1034-46. [PMID: 17300803 DOI: 10.1016/j.jmb.2007.01.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 01/09/2007] [Accepted: 01/10/2007] [Indexed: 11/28/2022]
Abstract
The D-aldohexose dehydrogenase from the thermoacidophilic archaea Thermoplasma acidophilum (AldT) belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and catalyzes the oxidation of several monosaccharides with a preference for NAD(+) rather than NADP(+) as a cofactor. It has been found that AldT is a unique enzyme that exhibits the highest dehydrogenase activity against D-mannose. Here, we describe the crystal structures of AldT in ligand-free form, in complex with NADH, and in complex with the substrate D-mannose, at 2.1 A, 1.65 A, and 1.6 A resolution, respectively. The AldT subunit forms a typical SDR fold with an unexpectedly long C-terminal tail and assembles into an intertwined tetramer. The D-mannose complex structure reveals that Glu84 interacts with the axial C2 hydroxyl group of the bound D-mannose. Structural comparison with Bacillus megaterium glucose dehydrogenase (BmGlcDH) suggests that the conformation of the glutamate side-chain is crucial for discrimination between D-mannose and its C2 epimer D-glucose, and the conformation of the glutamate side-chain depends on the spatial arrangement of nearby hydrophobic residues that do not directly interact with the substrate. Elucidation of the D-mannose recognition mechanism of AldT further provides structural insights into the unique substrate selectivity of AldT. Finally, we show that the extended C-terminal tail completely shuts the substrate-binding pocket of the neighboring subunit both in the presence and absence of substrate. The elaborate inter-subunit interactions between the C-terminal tail and the entrance of the substrate-binding pocket imply that the tail may play a pivotal role in the enzyme activity.
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Affiliation(s)
- Yoshiaki Yasutake
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, Toyohira-ku, Sapporo 062-8517, Japan
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Watanabe S, Shimada N, Tajima K, Kodaki T, Makino K. Identification and Characterization of l-Arabonate Dehydratase, l-2-Keto-3-deoxyarabonate Dehydratase, and l-Arabinolactonase Involved in an Alternative Pathway of l-Arabinose Metabolism. J Biol Chem 2006; 281:33521-36. [PMID: 16950779 DOI: 10.1074/jbc.m606727200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623 and Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888). We here report the remaining three enzymes, L-arabonate dehydratase, L-2-keto-3-deoxyarabonate (L-KDA) dehydratase, and L-arabinolactonase. N-terminal amino acid sequences of L-arabonate dehydratase and L-KDA dehydratase purified from A. brasiliense cells corresponded to those of AraC and AraD genes, which form a single transcriptional unit together with the L-arabinose-1-dehydrogenase gene. Furthermore, the L-arabinolactonase gene (AraB) was also identified as a component of the gene cluster. Genetic characterization of the alternative L-arabinose pathway suggested a significant evolutional relationship with the known sugar metabolic pathways, including the Entner-Doudoroff (ED) pathway and the several modified versions. L-arabonate dehydratase belongs to the ILVD/EDD family and spectrophotometric and electron paramagnetic resonance analysis revealed it to contain a [4Fe-4S](2+) cluster. Site-directed mutagenesis identified three cysteine ligands essential for cluster coordination. L-KDA dehydratase was sequentially similar to DHDPS/NAL family proteins. D-2-Keto-3-deoxygluconate aldolase, a member of the DHDPS/NAL family, catalyzes the equivalent reaction to L-KDA aldolase involved in another alternative L-arabinose pathway, probably associating a unique evolutional event between the two alternative L-arabinose pathways by mutation(s) of a common ancestral enzyme. Site-directed mutagenesis revealed a unique catalytic amino acid residue in L-KDA dehydratase, which may be a candidate for such a natural mutation.
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Affiliation(s)
- Seiya Watanabe
- Faculty of Engineering, Kyoto University, Kyotodaigaku-katsura, Saikyo-ku, Kyoto 615-8530, Japan
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Nishiya Y, Tamura N, Tamura T. Analysis of bacterial glucose dehydrogenase homologs from thermoacidophilic archaeon Thermoplasma acidophilum: finding and characterization of aldohexose dehydrogenase. Biosci Biotechnol Biochem 2005; 68:2451-6. [PMID: 15618614 DOI: 10.1271/bbb.68.2451] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The NADP(+)-preferring glucose dehydrogenase from thermoacidophilic archaeon Thermoplasma acidophilum has been characterized, and its crystal structure has been determined (Structure, 2:385-393, 1994). Its sequence and structure are not homologous to bacterial NAD(P)(+)-dependent glucose dehydrogenases, and its molecular weight is also quite defferent. On the other hand, three functionally unknown genes with homologies to bacterial NAD(P)(+)-dependent glucose dehydrogenases have been sequenced as part of the T. acidophilum genome project (gene names: Ta0191, Ta0747, and Ta0754 respectively). We expressed two genes of three, Ta0191 and Ta0754, in Escherichia coli, and purified the gene products to homogeneity. Dehydrogenase activities were thereby detected from the purified proteins. The Ta0754 gene product exhibited aldohexose dehydrogenase activity, and the Ta0191 gene product exhibited weak 2-deoxyglucose dehydrogenase activity. No aldohexose dehydrogenase gene has been isolated, while the enzyme was reported in 1968. This is the first report of the gene and primary structure. The purified Ta0754 gene product, designated AldT, was characterized. The enzyme AldT effectively catalyzed the oxidation of various aldohexoses, especially D-mannose. Lower activities on D-2-deoxyglucose, D-xylose, D-glucose, and D-fucose were detected although no activities were shown on other aldohexoses or additional sugars. As a cofactor, NAD(+) was much more suitable for the activity than NADP(+). The NAD(+)-preferring dehydrogenase most effectively reacting to D-mannose is for the first time. AldT was most active at pH 10 and above 70 degrees C, and completely stable up to 60 degrees C after incubation for 15 min. Other enzymatic properties were also investigated.
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Affiliation(s)
- Yoshiaki Nishiya
- Department of Biochemistry, Toyobo Co. Ltd., 17-9 Koami-cho, Nihonbashi, Chuo-ku, Tokyo 103-8530, Japan.
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Abstract
Fucose is a deoxyhexose that is present in a wide variety of organisms. In mammals, fucose-containing glycans have important roles in blood transfusion reactions, selectin-mediated leukocyte-endothelial adhesion, host-microbe interactions, and numerous ontogenic events, including signaling events by the Notch receptor family. Alterations in the expression of fucosylated oligosaccharides have also been observed in several pathological processes, including cancer and atherosclerosis. Fucose deficiency is accompanied by a complex set of phenotypes both in humans with leukocyte adhesion deficiency type II (LAD II; also known as congenital disorder of glycosylation type IIc) and in a recently generated strain of mice with a conditional defect in fucosylated glycan expression. Fucosylated glycans are constructed by fucosyltransferases, which require the substrate GDP-fucose. Two pathways for the synthesis of GDP-fucose operate in mammalian cells, the GDP-mannose-dependent de novo pathway and the free fucose-dependent salvage pathway. In this review, we focus on the biological functions of mammalian fucosylated glycans and the biosynthetic processes leading to formation of the fucosylated glycan precursor GDP-fucose.
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Affiliation(s)
- Daniel J Becker
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, MSRB I, room 3510, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-0650, USA.
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Facilitated diffusion of 6-deoxy-d-glucose by the oxidative yeast, Kluyveromyces lactis. Arch Microbiol 1981. [DOI: 10.1007/bf00527078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kobayashi Y, Horikoshi K. Purification and properties of NAD+-dependent maltose dehydrogenase produced by alkalophilic Corynebacterium sp. No. 93-1. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 614:256-65. [PMID: 7407192 DOI: 10.1016/0005-2744(80)90215-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
NAD+-dependent maltose dehydrogenase was purified about 250-fold from the cell free extract of an alkalophilic Corynebacterium sp. No. 93-1. The purified enzyme was homogeneous on polyacrylamide gel electrophoresis, sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis and ultracentrifugation. The molecular weight of the enzyme was determined to be 40 000 +/- 2000 by gel filtration and SDS-polyacrylamide gel electrophoresis. The enzyme appeared to be a single peptide chain. The isoelectric point was pH 4.50. The optimal pH was 10.2. The enzyme was stable over the range of pH 6 to 10. NAD+-dependent maltose dehydrogenase showed very wide substrate specificity on monosaccharides, disaccharides and trisaccharides. Among these substrates, maltose was the most reactive. Also, the enzyme showed oxidative activity on maltotetraose and maltopentaose. The Km values at pH 10 were 2.1 mM for maltose and 0.15 mM for NAD+. It was conjectured that the primary product of this reaction was maltono-delta-lactone and its was hydrolyzed non-enzymatically to maltobionic acid. p-Chloromercuribenzoic acid, Hg2+ and Ag2+ completely inhibited the activity, and HADH also showed competitive inhibition on the activity.
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Sasajima KI, Sinskey AJ. Oxidation of L-glucose by a Pseudomonad. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 571:120-6. [PMID: 40609 DOI: 10.1016/0005-2744(79)90232-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new enzyme, D-threo-aldolse dehydrogenase (2S,3R-aldose dehydrogenase), found in Pseudomonas caryophylli, was capable of oxidizing L-glucose L-xylose, D-arabinose, and L-fucose in the presence of NAD+. The enzyme was synthesized constitutively and purified about 120-fold from D-glucose-grown cells. The Km values for L-glucose, L-xylose, D-arabinose, and L-fucose were 1.5 . 10(-2), 4.5 . 10(-3), 2.8 . 10(-3), and 2.1 . 10(-3), respectively. D-glucose and other aldoses inhibited the enzyme reaction; this inhibition was competitive with L-glucose as substrate and D-glucose as inhibitor. The optimum pH for the enzyme reaction was 10; the molecular weight of the enzyme was determined by gel filtration to be 7 . 10(4).
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Chan JY, Nwokoro NA, Schachter H. L-Fucose metabolism in mammals. The conversion of L-fucose to two moles of L-lactate, of L-galactose to L-lactate and glycerate, and of D-arabinose to L-lactate and glycollate. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50284-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Donald A, Sibley D, Lyons D, Dahms A. D-Galactonate dehydrase. Purification and properties. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)37776-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Beyer EM. alpha-D-Fucosidase activity of human and pig kidney: a property of alpha-D-galactosidase. Arch Biochem Biophys 1977; 182:335-42. [PMID: 18995 DOI: 10.1016/0003-9861(77)90314-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Rigo LU, Nakano M, Veiga LA, Feingold DS. L-Rhamnose dehydrogenase of pullularia pullulans. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 445:286-93. [PMID: 8142 DOI: 10.1016/0005-2744(76)90083-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Growth of Pullularia pullulans on L-rhamnose induces formation of L-rhamnofuranose dehydrogenase, whichreversibly converts L-rhamnofuranose to L-rhamnono-gamma-lactone with the concomitant reduction of NAD, but not of NADP. The dehydrogenase was purified 100-fold by MnCl(2) treatment...
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Lessmann D, Schimz KL, Kurz G. D-glucose-6-phosphate dehydrogenase (Entner-Doudoroff enzyme) from Pseudomonas fluorescens. Purification, properties and regulation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 59:545-59. [PMID: 1257 DOI: 10.1111/j.1432-1033.1975.tb02481.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
1. The existence of two different D-glucose-6-phosphate dehydrogenases in Pseudomonas fluorescens has been demonstrated. Based on their different specificity and their different metabolic regulation one enzyme is appointed to the Entner-Doudoroff pathway and the other to the hexose monophosphate pathway. 2. A procedure is described for the isolation of that D-glucose-6-phosphate dehydrogenase which forms part of the Entner-Doudoroff pathway (Entner-Doudoroff enzyme). A 950-fold purification was achieved with an overall yield of 44%. The final preparation, having a specific activity of about 300 mumol NADH formed per min per mg protein, was shown to be homogeneous. 3. The molecular weight of the Entner-Doudoroff enzyme has been determined to be 220000 by gel permeation chromatography, and that of the other enzyme (Zwischenferment) has been shown to be 265000. 4. The pI of the Entner-Doudoroff enzyme has been shown to be 5.24 and that of the Zwischenferment 4.27. The Entner-Doudoroff enzyme is stable in the range of pH 6 to 10.5 and shows its maximal activity at pH 8.9. 5. The Entner-Doudoroff enzyme showed specificity for NAD+ as well as for NADP+ and exhibited homotropic effects for D-glucose 6-phosphate. It is inhibited by ATP which acts as a negative allosteric effector. Other nucleoside triphosphates as well as ADP are also inhibitory. 6. The enzyme catalyzes the transfer of the axial hydrogen at carbon-1 of beta-D-glucopyranose 6-phosphate to the si face of carbon-4 of the nicotinamide ring and must be classified as B-side stereospecific dehydrogenase.
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Nwokoro NA, Schachter H. L-fucose metabolism in mammals. Kinetic studies on pork liver 2-keto-3-deoxy-L-fuconate:NAD+ oxidoreductase. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41048-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Anderson RL, Dahms AS. L-arabino-aldose dehydrogenase. Methods Enzymol 1975; 41:150-3. [PMID: 236433 DOI: 10.1016/s0076-6879(75)41037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Dahms AS. 3-Deoxy-D-pentulosonic acid aldolase and its role in a new pathway of D-xylose degradation. Biochem Biophys Res Commun 1974; 60:1433-9. [PMID: 4423285 DOI: 10.1016/0006-291x(74)90358-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Ueberschär KH, Blachnitzky EO, Kurz G. Reaction mechanism of D-galactose dehydrogenases from Pseudomonas saccharophila and Pseudomonas fluorescens. Formation and rearrangemnt of aldono-1,5-lactones. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 48:389-405. [PMID: 4217278 DOI: 10.1111/j.1432-1033.1974.tb03780.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Blachnitzky EO, Wengenmayer F, Kurz G. D-Galactose dehydrogenase from Pseudomonas fluorescens. Purification, properties and structure. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 47:235-50. [PMID: 4153311 DOI: 10.1111/j.1432-1033.1974.tb03687.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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