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Raboni S, Marchetti M, Faggiano S, Campanini B, Bruno S, Marchesani F, Margiotta M, Mozzarelli A. The Energy Landscape of Human Serine Racemase. Front Mol Biosci 2019; 5:112. [PMID: 30687716 PMCID: PMC6333871 DOI: 10.3389/fmolb.2018.00112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022] Open
Abstract
Human serine racemase is a pyridoxal 5′-phosphate (PLP)-dependent dimeric enzyme that catalyzes the reversible racemization of L-serine and D-serine and their dehydration to pyruvate and ammonia. As D-serine is the co-agonist of the N-methyl-D-aspartate receptors for glutamate, the most abundant excitatory neurotransmitter in the brain, the structure, dynamics, function, regulation and cellular localization of serine racemase have been investigated in detail. Serine racemase belongs to the fold-type II of the PLP-dependent enzyme family and structural models from several orthologs are available. The comparison of structures of serine racemase co-crystallized with or without ligands indicates the presence of at least one open and one closed conformation, suggesting that conformational flexibility plays a relevant role in enzyme regulation. ATP, Mg2+, Ca2+, anions, NADH and protein interactors, as well as the post-translational modifications nitrosylation and phosphorylation, finely tune the racemase and dehydratase activities and their relative reaction rates. Further information on serine racemase structure and dynamics resulted from the search for inhibitors with potential therapeutic applications. The cumulative knowledge on human serine racemase allowed obtaining insights into its conformational landscape and into the mechanisms of cross-talk between the effector binding sites and the active site.
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Affiliation(s)
- Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
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Marchetti M, Bruno S, Campanini B, Bettati S, Peracchi A, Mozzarelli A. Regulation of human serine racemase activity and dynamics by halides, ATP and malonate. Amino Acids 2014; 47:163-73. [PMID: 25331425 DOI: 10.1007/s00726-014-1856-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 02/03/2023]
Abstract
D-Serine is a non-proteinogenic amino acid that acts as a co-agonist of the NMDA receptors in the central nervous system. D-Serine is produced by human serine racemase (hSR), a homodimeric pyridoxal 5'-phosphate (PLP)-dependent enzyme that also catalyzes the physiologically relevant β-elimination of both L- and D-serine to pyruvate and ammonia. After improving the protein purification yield and stability, which had so far limited the biochemical characterization of hSR, we found that the catalytic activity is affected by halides, in the order fluoride > chloride > bromide. On the contrary, iodide elicited a complete inhibition, accompanied by a modulation of the tautomeric equilibrium of the internal aldimine. We also investigated the reciprocal effects of ATP and malonate, an inhibitor that reversibly binds at the active site, 20 Å away from the ATP-binding site. ATP increased ninefold the affinity of hSR for malonate and malonate increased 100-fold that of ATP, confirming an allosteric interaction between the two binding sites. To further investigate this allosteric communication, we probed the active site accessibility by quenching of the coenzyme fluorescence in the absence and presence of ATP. We found that ATP stabilizes a closed conformation of the external aldimine Schiff base, suggesting a possible mechanism for ATP-induced hSR activation.
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Durbecq V, Thia-Toong TL, Charlier D, Villeret V, Roovers M, Wattiez R, Legrain C, Glansdorff N. Aspartate carbamoyltransferase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. Cloning, sequence analysis, enzyme purification and characterization. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 264:233-41. [PMID: 10447693 DOI: 10.1046/j.1432-1327.1999.00619.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genes coding for aspartate carbamoyltransferase (ATCase) in the extremely thermophilic archaeon Sulfolobus acidocaldarius have been cloned by complementation of a pyrBI deletion mutant of Escherichia coli. Sequencing revealed the existence of an enterobacterial-like pyrBI operon encoding a catalytic chain of 299 amino acids (34 kDa) and a regulatory chain of 170 amino acids (17.9 kDa). The deduced amino acid sequences of the pyrB and pyrI genes showed 27.6-50% identity with archaeal and enterobacterial ATCases. The recombinant S. acidocaldarius ATCase was purified to homogeneity, allowing the first detailed studies of an ATCase isolated from a thermophilic organism. The recombinant enzyme displayed the same properties as the ATCase synthesized in the native host. It is highly thermostable and exhibits Michaelian saturation kinetics for carbamoylphosphate (CP) and positive homotropic cooperative interactions for the binding of L-aspartate. Moreover, it is activated by nucleoside triphosphates whereas the catalytic subunits alone are inhibited. The holoenzyme purified from recombinant E. coli cells or present in crude extract of the native host have an Mr of 340 000 as estimated by gel filtration, suggesting that it has a quaternary structure similar to that of E. coli ATCase. Only monomers could be found in extracts of recombinant E. coli or Saccharomyces cerevisiae cells expressing the pyrB gene alone. In the presence of CP these monomers assembled into trimers. The stability of S. acidocaldarius ATCase and the allosteric properties of the enzyme are discussed in function of a modeling study.
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Affiliation(s)
- V Durbecq
- Laboratoire de Microbiologie, Université de Libre de Bruxelles, Belgium
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Wales ME, Wild JR. Analysis of structure-function relationships by formation of chimeric enzymes produced by gene fusion. Methods Enzymol 1991; 202:687-706. [PMID: 1784194 DOI: 10.1016/0076-6879(91)02032-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Beck D, Kedzie KM, Wild JR. Comparison of the aspartate transcarbamoylases from Serratia marcescens and Escherichia coli. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84752-x] [Citation(s) in RCA: 8] [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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Masood R, Venkitasubramanian TA. Purification and properties of aspartate transcarbamylase from Mycobacterium smegmatis. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 953:106-13. [PMID: 3342242 DOI: 10.1016/0167-4838(88)90014-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aspartate transcarbamylase (carbamoyl-phosphate: L-aspartate carbamoyltransferase, EC 2.1.3.2) has been purified from Mycobacterium smegmatis TMC 1546 using streptomycin sulphate precipitation, ammonium sulphate precipitation, DE-52 chromatography, second ammonium sulphate precipitation, Sephadex G-200 gel filtration, and aspartate-linked CNBr-activated Sepharose 4B affinity chromatography in successive order. The enzyme was purified 231.6-fold, and the preparation was found to be homogeneous on column chromatography and polyacrylamide gel electrophoresis. The purified enzyme had a molecular weight of 246,000 and was composed of two asymmetrical subunits. The kinetic and regulatory properties of aspartate transcarbamylase from M. smegmatis were also studied. The enzyme was found to be an allosteric in nature with carbamyl phosphate showing positive cooperativity and UMP exhibiting a negative cooperativity. CTP was found to be the most potent inhibitor among nucleotides. Phosphate acted as a non-competitive product inhibitor with respect to aspartate. Succinate and maleate exerted a competitive inhibition when aspartate was the variable substrate.
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Affiliation(s)
- R Masood
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, India
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Wild JR, Johnson JL, Loughrey SJ. ATP-liganded form of aspartate transcarbamoylase, the logical regulatory target for allosteric control in divergent bacterial systems. J Bacteriol 1988; 170:446-8. [PMID: 3275626 PMCID: PMC210664 DOI: 10.1128/jb.170.1.446-448.1988] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In Escherichia coli, the mechanism for regulatory control of aspartate transcarbamoylase is clear; CTP allosterically inhibits catalysis in direct competition with ATP. However, both CTP and ATP may be activators or may have no effect on aspartate transcarbamoylases from other enteric bacteria. A common regulatory logic observed was that the ATP-activated enzymes were rendered less active as the result of competition with CTP, regardless of the independent effects.
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Affiliation(s)
- J R Wild
- Department of Biochemistry and Biophysics, Texas A & M University System, College Station 77843
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Foltermann KF, Beck DA, Wild JR. In vivo formation of hybrid aspartate transcarbamoylases from native subunits of divergent members of the family Enterobacteriaceae. J Bacteriol 1986; 167:285-90. [PMID: 3722124 PMCID: PMC212873 DOI: 10.1128/jb.167.1.285-290.1986] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The genes encoding the catalytic (pyrB) and regulatory (pyrI) polypeptides of aspartate transcarbamoylase (ATCase, EC 2.1.3.2) from several members of the family Enterobacteriaceae appear to be organized as bicistronic operons. The pyrBI gene regions from several enteric sources were cloned into selected plasmid vectors and expressed in Escherichia coli. Subsequently, the catalytic cistrons were subcloned and expressed independently from the regulatory cistrons from several of these sources. The regulatory cistron of E. coli was cloned separately and expressed from lac promoter-operator vectors. By utilizing plasmids from different incompatibility groups, it was possible to express catalytic and regulatory cistrons from different bacterial sources in the same cell. In all cases examined, the regulatory and catalytic polypeptides spontaneously assembled to form stable functional hybrid holoenzymes. This hybrid enzyme formation indicates that the r:c domains of interaction, as well as the dodecameric architecture, are conserved within the Enterobacteriaceae. The catalytic subunits of the hybrid ATCases originated from native enzymes possessing varied responses to allosteric effectors (CTP inhibition, CTP activation, or very slight responses; and ATP activation or no ATP response). However, each of the hybrid ATCases formed with regulatory subunits from E. coli demonstrated ATP activation and CTP inhibition, which suggests that the allosteric control characteristics are determined by the regulatory subunits.
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Properties of hybrid aspartate transcarbamoylase formed with native subunits from divergent bacteria. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90798-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Jyssum S. Pyrimidine biosynthesis in Neisseria meningitidis. 2. Regulation of enzyme synthesis. ACTA PATHOLOGICA, MICROBIOLOGICA, ET IMMUNOLOGICA SCANDINAVICA. SECTION B, MICROBIOLOGY 1983; 91:257-60. [PMID: 6414243 DOI: 10.1111/j.1699-0463.1983.tb00043.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In Neisseria meningitidis aspartate carbamoyltransferase (ACTase), ornithine carbamoyltransferase (OCTase), and carbamoylphosphate synthetase (CPSase) showed incomplete repression by uracil and arginine. De-repression studies with pyrimidine and arginine mutants showed no de-repressed levels of these enzymes.
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Yon RJ, Grayson JE, Chawda A, Butterworth PJ. The quaternary structure of wheat-germ aspartate transcarbamoylase. Biochem J 1982; 203:413-7. [PMID: 7115295 PMCID: PMC1158245 DOI: 10.1042/bj2030413] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
1. The molecular mass of aspartate transcarbamoylase purified from wheat germ was found to be 101kDa by sucrose-density-gradient centrifugation, 103kDa by gel-filtration chromatography and 108kDa by polyacrylamide-gel electrophoresis. A mean value of 104 +/- 11kDa was obtained by pooling several replicate results from each method. 2. Polyacrylamide-gel electrophoresis in the presence of sodium dodecyl sulphate indicated a single size of polypeptide chain of mean molecular mass 37 +/- 4kDa. The ratio of the mean molecular masses of the active and denatured enzymes is 2.8.3. When the active enzyme was covalently cross-linked at a low protein concentration by dimethyl suberimidate, and then examined electrophoretically under denaturing conditions, three size species were observed to predominate, of apparent molecular masses 36, 77 and 106kDa respectively. 4. These results indicate that the intact, fully regulatory enzyme is a simple trimer, slightly larger than the trimeric "catalytic subunit' of the aspartate transcarbamoylase from Escherichia coli [Weber (1968) Nature (London) 218, 1116-1118]. The prevalence of trimeric structures amongst carbamoyl-transferase enzymes is discussed.
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Abstract
Serratia marcescens HY possessed a single carbamylphosphate synthase (CPSase) which was subject to cumulative repression by arginine and a pyrimidine. CPSase did not appear to be a part of a multifunctional enzyme complex as is the case for other enzymes of pyrimidine biosynthesis in this organism. CPSase was purified to homogeneity. The molecular weight of the enzyme was estimated to be 167,000 by sucrose density gradient ultracentrifugation. The double-reciprocal plot for magnesium adenosine triphosphate was linear, yielding a Km value of 2.5 mM. The enzyme utilized either glutamine (Km, 0.1 mM) or NH3 (Km, 10.5 mM) as a nitrogen donor in the reaction. CPSase activity was subject to activation by ornithine and feedback inhibition by uridine monophosphate, as is the case for other enteric bacteria. Carbamate kinase activity, detected in crude extracts of S. marcescens, was shown to be due to a constitutive acetate kinase. The absence of carbamate kinase from S. marcescens HY is consistent with the inability of this organism to utilize arginine as a source of energy under anaerobic conditions.
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Wild JR, Foltermann KF, O'Donovan GA. Regulatory divergence of aspartate transcarbamoylases within the enterobacteriaceae. Arch Biochem Biophys 1980; 201:506-17. [PMID: 7396519 DOI: 10.1016/0003-9861(80)90539-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Wild JR, Belser WL. Pyrimidine biosynthesis in Serratia marcescens: a possible role for nonsequential enzyme interactions in mimicking coordinate gene expression. Biochem Genet 1977; 15:157-72. [PMID: 192191 DOI: 10.1007/bf00484559] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The coordinate expression of four sequential enzymes in the de novo pyrimidine pathway may result from the interaction of the various polypeptides of the pathway in Serratia marcescens rather than represent some unit of transcriptional regulation. These interactions were defined by examining the polypeptide association observed in extracts of parental and mutant strains in a series of pleiotropic pyrimidine auxotrophs. Extracts of pyrE auxotrophs [processing dihydroorotate (DHOase) activity but no orotidine-5'-monophosphate pyrophosphorylase (OMPppase) activity] stimulate OMPppase activity in extracts of pyrC auxotrophs (posessing reduced OMPppase activity but no DHOase activity). Separation by molecular weight on Sephadex G200 has suggested an aggregation between the final two enzymes, OMPppase and OMPdecarboxylase (OMPdecase), and the earlier enzyme, DHOase. The reduction of OMPppase activity in pyrC auxotrophs (encoding either a defective polypeptide or reduced levels) is explained by the lack of adequate levels of DHOase for aggregate formation. Such polypeptide interactions appear to mimic the coordinate formation of polypeptides which are controlled as a unit of regulation. The measurable levels of enzymatic activity vary in a quantitatively identical manner, but the variation does not result directly from the regulation of polypeptide formation.
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