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Irons JL, Hodge-Hanson K, Downs DM. RidA Proteins Protect against Metabolic Damage by Reactive Intermediates. Microbiol Mol Biol Rev 2020; 84:e00024-20. [PMID: 32669283 PMCID: PMC7373157 DOI: 10.1128/mmbr.00024-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Rid (YjgF/YER057c/UK114) protein superfamily was first defined by sequence homology with available protein sequences from bacteria, archaea, and eukaryotes (L. Parsons, N. Bonander, E. Eisenstein, M. Gilson, et al., Biochemistry 42:80-89, 2003, https://doi.org/10.1021/bi020541w). The archetypal subfamily, RidA (reactive intermediate deaminase A), is found in all domains of life, with the vast majority of free-living organisms carrying at least one RidA homolog. In over 2 decades, close to 100 reports have implicated Rid family members in cellular processes in prokaryotes, yeast, plants, and mammals. Functional roles have been proposed for Rid enzymes in amino acid biosynthesis, plant root development and nutrient acquisition, cellular respiration, and carcinogenesis. Despite the wealth of literature and over a dozen high-resolution structures of different RidA enzymes, their biochemical function remained elusive for decades. The function of the RidA protein was elucidated in a bacterial model system despite (i) a minimal phenotype of ridA mutants, (ii) the enzyme catalyzing a reaction believed to occur spontaneously, and (iii) confusing literature on the pleiotropic effects of RidA homologs in prokaryotes and eukaryotes. Subsequent work provided the physiological framework to support the RidA paradigm in Salmonella enterica by linking the phenotypes of mutants lacking ridA to the accumulation of the reactive metabolite 2-aminoacrylate (2AA), which damaged metabolic enzymes. Conservation of enamine/imine deaminase activity of RidA enzymes from all domains raises the likelihood that, despite the diverse phenotypes, the consequences when RidA is absent are due to accumulated 2AA (or a similar reactive enamine) and the diversity of metabolic phenotypes can be attributed to differences in metabolic network architecture. The discovery of the RidA paradigm in S. enterica laid a foundation for assessing the role of Rid enzymes in diverse organisms and contributed fundamental lessons on metabolic network evolution and diversity in microbes. This review describes the studies that defined the conserved function of RidA, the paradigm of enamine stress in S. enterica, and emerging studies that explore how this paradigm differs in other organisms. We focus primarily on the RidA subfamily, while remarking on our current understanding of the other Rid subfamilies. Finally, we describe the current status of the field and pose questions that will drive future studies on this widely conserved protein family to provide fundamental new metabolic information.
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Affiliation(s)
- Jessica L Irons
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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Lambrecht JA, Schmitz GE, Downs DM. RidA proteins prevent metabolic damage inflicted by PLP-dependent dehydratases in all domains of life. mBio 2013; 4:e00033-13. [PMID: 23386433 PMCID: PMC3565831 DOI: 10.1128/mbio.00033-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP) is a coenzyme synthesized by all forms of life. Relevant to the work reported here is the mechanism of the PLP-dependent threonine/serine dehydratases, which generate reactive enamine/imine intermediates that are converted to keto acids by members of the RidA family of enzymes. The RidA protein of Salmonella enterica serovar Typhimurium LT2 is the founding member of this broadly conserved family of proteins (formerly known as YjgF/YER057c/UK114). RidA proteins were recently shown to be enamine deaminases. Here we demonstrate the damaging potential of enamines in the absence of RidA proteins. Notably, S. enterica strains lacking RidA have decreased activity of the PLP-dependent transaminase B enzyme IlvE, an enzyme involved in branched-chain amino acid biosynthesis. We reconstituted the threonine/serine dehydratase (IlvA)-dependent inhibition of IlvE in vitro, show that the in vitro system reflects the mechanism of RidA function in vivo, and show that IlvE inhibition is prevented by RidA proteins from all domains of life. We conclude that 2-aminoacrylate (2AA) inhibition represents a new type of metabolic damage, and this finding provides an important physiological context for the role of the ubiquitous RidA family of enamine deaminases in preventing damage by 2AA. IMPORTANCE External stresses that disrupt metabolic components can perturb cellular functions and affect growth. A similar consequence is expected if endogenously generated metabolites are reactive and persist in the cellular environment. Here we show that the metabolic intermediate 2-aminoacrylate (2AA) causes significant cellular damage if allowed to accumulate aberrantly. Furthermore, we show that the widely conserved protein RidA prevents this accumulation by facilitating conversion of 2AA to a stable metabolite. This work demonstrates that the reactive metabolite 2AA, previously considered innocuous in the cell due to a short half-life in aqueous solution, can survive in the cellular environment long enough to cause damage. This work provides insights into the roles and persistence of reactive metabolites in vivo and shows that the RidA family of proteins is able to prevent damage caused by a reactive intermediate that is created as a consequence of PLP-dependent chemistry.
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Lambrecht JA, Downs DM. Anthranilate phosphoribosyl transferase (TrpD) generates phosphoribosylamine for thiamine synthesis from enamines and phosphoribosyl pyrophosphate. ACS Chem Biol 2013; 8:242-8. [PMID: 23101964 DOI: 10.1021/cb300364k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anthranilate phosphoribosyl transferase (TrpD) has been well characterized for its role in the tryptophan biosynthetic pathway. Here, we characterized a new reaction catalyzed by TrpD that resulted in the formation of the purine/thiamine intermediate metabolite phosphoribosylamine (PRA). The data showed that 4- and 5-carbon enamines served as substrates for TrpD, and the reaction product was predicted to be a phosphoribosyl-enamine adduct. Isotopic labeling data indicated that the TrpD reaction product was hydrolyzed to PRA. Variants of TrpD that were proficient for tryptophan synthesis were unable to support PRA formation in vivo in Salmonella enterica. These protein variants had substitutions at residues that contributed to binding substrates anthranilate or phosphoribosyl pyrophosphate (PRPP). Taken together the data herein identified a new reaction catalyzed by a well-characterized biosynthetic enzyme, and both illustrated the robustness of the metabolic network and identified a role for an enamine that accumulates in the absence of reactive intermediate deaminase RidA.
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Affiliation(s)
- Jennifer A. Lambrecht
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United
States
| | - Diana M. Downs
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United
States
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Lambrecht JA, Flynn JM, Downs DM. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J Biol Chem 2011; 287:3454-61. [PMID: 22094463 DOI: 10.1074/jbc.m111.304477] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The YjgF/YER057c/UK114 family of proteins is conserved in all domains of life, suggesting that the role of these proteins arose early and was maintained throughout evolution. Metabolic consequences of lacking this protein in Salmonella enterica and other organisms have been described, but the biochemical function of YjgF remained unknown. This work provides the first description of a conserved biochemical activity for the YjgF protein family. Our data support the conclusion that YjgF proteins have enamine/imine deaminase activity and accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA). Results from structure-guided mutagenesis experiments suggest that YjgF lacks a catalytic residue and that it facilitates ammonia release by positioning a critical water molecule in the active site. YjgF is renamed RidA (reactive intermediate/imine deaminase A) to reflect the conserved activity of the protein family described here. This study, combined with previous physiological studies on yjgF mutants, suggests that intermediates of pyridoxal 5'-phosphate-mediated reactions may have metabolic consequences in vivo that were previously unappreciated. The conservation of the RidA/YjgF family suggests that reactive enamine/imine metabolites are of concern to all organisms.
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Affiliation(s)
- Jennifer A Lambrecht
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
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Kirschenbaum DM. MOLAR ABSORPTIVITY AND A1%1cm VALUES FOR PROTEINS AT SELECTED WAVELENGTHS OF THE ULTRAVIOLET AND VISIBLE REGION. VI*. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1972.tb03409.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Umbarger HE. Threonine deaminases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 37:349-95. [PMID: 4570068 DOI: 10.1002/9780470122822.ch6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Eisenstein E. Cloning, expression, purification, and characterization of biosynthetic threonine deaminase from Escherichia coli. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)67668-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abstract
Recent reviews dealing with phototrophic bacteria are concerned with bioenergetics, nitrogen fixation and hydrogen metabolism, synthesis of the photosynthetic apparatus and phylogeny/taxonomy. The organic N-metabolism of these phylogenetically diverse bacteria has last been reviewed in 1978. However, amino acid utilization and biosynthesis, ammonia assimilation, purine and pyrimidine metabolism and biosynthesis of delta-aminolevulinic acid as precursor of bacteriochlorophylls and hemes are topics of vital importance. This review focuses on utilization of amino acids as N- and C/N-sources, the pathways of purine and pyrimidine degradation, novel aspects of amino acid biosynthesis (with emphasis on branched-chain amino acids and delta-aminolevulinic acid) and some aspects of ammonia assimilation and glutamate synthesis by purple bacteria, green sulfur bacteria and Chloroflexus aurantiacus.
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Affiliation(s)
- J H Klemme
- Institut für Mikrobiologie der Universität Bonn, FRG
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Amino acid metabolism in the thermophilic phototroph, Chloroflexus aurantiacus: properties and metabolic role of two l-threonine (l-serine) dehydratases. Arch Microbiol 1988. [DOI: 10.1007/bf00422013] [Citation(s) in RCA: 2] [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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Finkelnburg B, Klemme JH. Homoserine kinase from the phototrophic bacteriumRhodospirillum rubrumis not sensitive to feedback inhibition by l-threonine. FEMS Microbiol Lett 1987. [DOI: 10.1111/j.1574-6968.1987.tb02522.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Occurrence of two l-threonine (l-serine) dehydratases in the thermophile Chloroflexus aurantiacus. Arch Microbiol 1986. [DOI: 10.1007/bf00410950] [Citation(s) in RCA: 4] [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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Bode R, Schult I, Birnbaum D. Purification and some properties of threonine dehydratase fromCandida maltosa. J Basic Microbiol 1986. [DOI: 10.1002/jobm.3620260802] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Prasad PV, Rao NA. Purification and regulation of aspartate transcarbamylase from germinated mung bean (Vigna radiata) seedlings. J Biosci 1984. [DOI: 10.1007/bf02702645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lakshman M, Shenoy BC, Rao MRR. Purification and properties of diaminopimelate decarboxylase ofMicrococcus glutamicus. J Biosci 1981. [DOI: 10.1007/bf02702651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Datta P, Bhadra R. Biodegradative threonine dehydratase. Reduction of ferricyanide by an intermediate of the enzyme-catalyzed reaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 91:527-32. [PMID: 365527 DOI: 10.1111/j.1432-1033.1978.tb12706.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The threonine-dependent reduction of ferricyanide catalyzed by the purified biodegradative threonine dehydratase of Escherichia coli has been studied. The rate of production of 2-oxobutyrate in the presence of ferricyanide was lower than that found in the absence of ferricyanide. The concentrations of threonine required for half-maximal effects for the reduction of ferricyanide and, in the presence of the dye, for 2-oxobutyrate production, were 3 mM and 9mM, respectively. Reduction of ferricyanide was accompanied by evolution of CO2, and even within a very short incubation time with the enzyme, the ratio of ferricyanide reduced over CO2 evolved was approximately 7. Stopping the enzyme activity after a brief exposure to threonine at pH 9.7 resulted in the accumulation of an intermediate (with a half-life of 4 min at 25 degrees C) which formed an adduct with N-ethylmaleimide; the accumulated intermediate, in the absence of N-ethylmaleimide, reduced ferricyanide with concomitant evolution of CO2. We conclude from these results that 2-aminocrotonate is the intermediate which serves as a source of reducing equivalent for ferricyanide, and nonstoichiometric amount of ferricyanide reduction may be attributed to some secondary reactions of ferricyanide with compounds derived from the oxidation product of 2-aminocrotonate.
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Ahmed SI, Bollon AP, Rogers SJ, Magee PT. Purification and properties of threonine deaminase from Saccharomyces cerevisiae. Biochimie 1976; 58:225-32. [PMID: 782558 DOI: 10.1016/s0300-9084(76)80374-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Threonine deaminase (L-theonine hydro-lyase (deaminating), E.C. 4.2.1.16) has been purified to homogeneity from extracts of Saccharomyces cerevisiae. When purified 1200-fold, the enzyme is homogeneous by the criterion of sodium dodecyl sulfate-polyacrylamide electrophoresis. The reduced and alkylated protein has a molecular weight of approximately 50,000 daltons, one-fourth the value determined previously for the intact enzyme. The purified enzyme exhibits homotropic effects with the substrate; these effects are descresed in the presence of DL-allothreonine, a competitive inhibitor. Half-maximal velocity is achieved at 34 mM L-threonine in the absence of other effectors. L-isoleucine both stimulates at low (0.01-0.05 mM) concentrations and inhibits at high (0.1-1.0 mM) concentrations. Valine activates the enzyme in the absence of isoleucine ; in the presence of isoleucine it reverses inhibition.
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Shizuta Y, Hayaishi O. Regulation of biodegradative threonine deaminase. CURRENT TOPICS IN CELLULAR REGULATION 1976; 11:99-146. [PMID: 187387 DOI: 10.1016/b978-0-12-152811-9.50010-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kagan ZS, Dorozhko AI, Kovaleva SV, Yakovleva LI. Studies of homogeneous "biosynthetic" L-threonine dehydratase from Escherichia coli K-12. Some kinetic properties and molecular multiplicity. BIOCHIMICA ET BIOPHYSICA ACTA 1975; 403:208-20. [PMID: 240428 DOI: 10.1016/0005-2744(75)90023-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
"Biosynthetic" L-threonine dehydratase (EC 4.2.1.16) was purified to a homogeneous state with 29% yield of total activity from Escherichia coli K-12. The homogeneity of the enzyme was shown by polyacrylamide gel disc electrophoresis in the presence of dodecyl sulphate. The enzyme consisted of equal subunits having a molecular weight of about 57 000. The polyacrylamide gel disc electrophoresis has shown that the native enzyme consisted of a set of oligomeric forms. The multiplicity of molecular organization of the enzyme was reflected in complicated kinetic behaviour: at pH greater than 9 on the plots of initial reaction rate (v) versus initial substrate concentration ([S]o) there were four inflexion points (two intermediate plateaux), the position and deepness of which depended on enzyme concentration. At pH 8.3 on the v versus [S]o plots appeared two inflexion points (one intermediate plateu), the position of which practically did not depend on enzyme concentration in the reaction mixture, but strongly depended on the enzyme concentration in the stock solution. Repeated polyacrylamide gel disc electrophoresis of several oligomeric forms, isolated by the first electrophoresis, has shown that the oligomeric forms underwent a slow polymerization. It was suggested that "biosynthetic" L-threonine dehydratase from E. coli K-12 is a set of multiple oligomeric forms, having different kinetic parameters. Probably, each form of the enzyme has a "simple" kinetics characterized by hyperbolic or sigmoidal shape of v versus [S]o plots. The rate of equilibrium installation between the oligomeric forms was small in comparison with the enzyme reaction velocity, that lead to the complex kinetic curves, appearing as a result of summing up of the kinetics inherent to theindividual forms.
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Decedue CJ, Hofler JG, Burns RO. Threonine deaminase from Salmonella typhimurium. Relationship between regulatory sites. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41846-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Higa EH, Ramaley RF. Purification and properties of threonine deaminase from the X-1 isolate of the genus Thermus. J Bacteriol 1973; 114:556-62. [PMID: 4706189 PMCID: PMC251809 DOI: 10.1128/jb.114.2.556-562.1973] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Threonine deaminase (l-threonine dehydratase EC 4.2.1.16) has been partially purified from a new extreme thermophilic bacterium, Thermus X-1, which is similar to T. aquaticus YT-1. The threonine deaminase of strain X-1 has a maximal rate of reaction at 85 to 90 C and is more thermostable than the threonine deaminase from mesophilic bacteria. The enzyme has an apparent molecular weight of 100,000 to 115,000, a K(m) for l-threonine of 14 mM, a pH optimum of 8.0, and like other threonine deaminases also catalyzes the deamination of serine. However the Thermus X-1 threonine deaminase does not show a strong feedback inhibition by isoleucine. It is suggested that the regulation of the biosynthesis of isoleucine in this extreme theromophile may resemble that reported in Rodospirillum rubrum.
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Kagan ZS, Dorozhko AI. pH-dependent intermediate plateaux in the kinetics of the reaction catalyzed by "biosynthetic" L-threonine dehydratase of Escherichia coli K-12. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 302:110-28. [PMID: 4571178 DOI: 10.1016/0005-2744(73)90014-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Karassevitch Y, Robichon-Szulmajster H. Reversible dissociation of threonine deaminase in an ilvl mutant of Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1972; 117:113-23. [PMID: 4561422 DOI: 10.1007/bf00267608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Feldberg RS, Datta P. Cold inactivation of L-threonine deaminase from Rhodospirillum rubrum. Involvement of hydrophobic interactions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 21:447-54. [PMID: 5569610 DOI: 10.1111/j.1432-1033.1971.tb01491.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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