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Emile Van Schaftingen - One of the best experts on this subject based on the ideXlab platform.
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mutations responsible for 3 Phosphoserine phosphatase deficiency
European Journal of Human Genetics, 2004Co-Authors: Maria Veigadacunha, Jeanfrancois Collet, J Jaeken, Benoit Prieur, Yves Peeraer, Anja Rabbijns, Emile Van SchaftingenAbstract:We report the identification of the mutations in the only known case of L-3-Phosphoserine phosphatase deficiency, a recessively inherited condition. The two mutations correspond to the replacement of the semiconserved Asp32 residue by an asparagine and of the extremely conserved Met52 by a threonine. The effects of both mutations were studied on the human recombinant enzyme, expressed in Escherichia coli. Met52Thr almost abolished the enzymatic activity, whereas the Asp32Asn mutation caused a 50% decrease in Vmax. In addition, L-serine, which inhibits the conversion of [(14)C] Phosphoserine to serine when catalysed by the wild-type enzyme, had a lesser inhibitory effect on the Asp32Asn mutant, indicating a reduction in the rate of phosphoenzyme hydrolysis. These modifications in the properties of the enzyme are consistent with the modification in the kinetic properties observed in fibroblasts from the patient.
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mechanistic studies of Phosphoserine phosphatase an enzyme related to p type atpases
Journal of Biological Chemistry, 1999Co-Authors: Jeanfrancois Collet, Vincent Stroobant, Emile Van SchaftingenAbstract:Phosphoserine phosphatase belongs to a new class of phosphotransferases forming an acylphosphate during catalysis and sharing three motifs with P-type ATPases and haloacid dehalogenases. The phosphorylated residue was identified as the first aspartate in the first motif (DXDXT) by mass spectrometry analysis of peptides derived from the phosphorylated enzyme treated with NaBH(4) or alkaline [(18)O]H(2)O. Incubation of native Phosphoserine phosphatase with Phosphoserine in [(18)O]H(2)O did not result in (18)O incorporation in residue Asp-20, indicating that the phosphoaspartate is hydrolyzed, as in P-type ATPases, by attack of the phosphorus atom. Mutagenesis studies bearing on conserved residues indicated that four conservative changes either did not affect (S109T) or caused a moderate decrease in activity (G178A, D179E, and D183E). Other mutations inactivated the enzyme by >80% (S109A and G180A) or even by >/=99% (D179N, D183N, K158A, and K158R). Mutations G178A and D179N decreased the affinity for Phosphoserine, suggesting that these residues participate in the binding of the substrate. Mutations of Asp-179 decreased the affinity for Mg(2+), indicating that this residue interacts with the cation. Thus, investigated residues appear to play an important role in the reaction mechanism of Phosphoserine phosphatase, as is known for equivalent residues in P-type ATPases and haloacid dehalogenases.
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human l 3 Phosphoserine phosphatase sequence expression and evidence for a phosphoenzyme intermediate
FEBS Letters, 1997Co-Authors: Jeanfrancois Collet, Isabelle Gerin, Mark H Rider, Maria Veigadacunha, Emile Van SchaftingenAbstract:We report the sequence of the cDNA encoding human L-3-Phosphoserine phosphatase. The encoded polypeptide contains 225 residues and shows 30% sequence identity with the Escherichia coli enzyme. The human protein was expressed in a bacterial expression system and purified. Similar to known L-3-Phosphoserine phosphatases, it catalyzed the Mg2(+)-dependent hydrolysis of L-Phosphoserine and an exchange reaction between L-serine and L-Phosphoserine. In addition we found that the enzyme was phosphorylated upon incubation with L-[32P]Phosphoserine, which indicates that the reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediate. The sensitivity of the phosphoryl-enzyme to alkali and to hydroxylamine suggests that an aspartyl- or a glutamyl-phosphate was formed. The nucleotide sequence of the cDNA described in this article has been deposited in the EMBL data base under accession number Y10275.
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Human l‐3‐Phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate
FEBS Letters, 1997Co-Authors: Jeanfrancois Collet, Isabelle Gerin, Mark H Rider, Maria Veiga-da-cunha, Emile Van SchaftingenAbstract:We report the sequence of the cDNA encoding human L-3-Phosphoserine phosphatase. The encoded polypeptide contains 225 residues and shows 30% sequence identity with the Escherichia coli enzyme. The human protein was expressed in a bacterial expression system and purified. Similar to known L-3-Phosphoserine phosphatases, it catalyzed the Mg2(+)-dependent hydrolysis of L-Phosphoserine and an exchange reaction between L-serine and L-Phosphoserine. In addition we found that the enzyme was phosphorylated upon incubation with L-[32P]Phosphoserine, which indicates that the reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediate. The sensitivity of the phosphoryl-enzyme to alkali and to hydroxylamine suggests that an aspartyl- or a glutamyl-phosphate was formed. The nucleotide sequence of the cDNA described in this article has been deposited in the EMBL data base under accession number Y10275.
Jeanfrancois Collet - One of the best experts on this subject based on the ideXlab platform.
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Phosphoserine phosphatase deficiency ina patient withWilliams syndrome
2017Co-Authors: Jeanpierre Fryns, Jeanfrancois Collet, P AllietAbstract:Decreasedserinelevels werefoundin plasmaandcerebrospinal fluid (CSF)ofa boywithpre-andpostnatal growthretardation, moderatepsychomotor retardation, andfacial dysmorphismsuggestive ofWilliams syndrome.Fluorescence in situhybridisation withan elastin gene probeindicated thepresence ofasubmicroscopic 7qI1.23deletion, confirming thisdiagnosis. Furtherinvestigation showedthatthePhosphoserine phosphatase (EC3.1.3.3.) activity inlymphoblasts andfibroblasts amountedtoabout 25% ofnormalvalues. Oralserinenormalised theplasmaandCSFlevels ofthis aminoacidandseemedtohavesomeclinicaleffect. Thesedatasuggest thatthe elastingene and the Phosphoserine phosphatase genemightbeclosely linked. Thisseemsto be thefirst reportof Phosphoserine phosphatase deficiency. (JMed Genet 1997;34:594-596)
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mutations responsible for 3 Phosphoserine phosphatase deficiency
European Journal of Human Genetics, 2004Co-Authors: Maria Veigadacunha, Jeanfrancois Collet, J Jaeken, Benoit Prieur, Yves Peeraer, Anja Rabbijns, Emile Van SchaftingenAbstract:We report the identification of the mutations in the only known case of L-3-Phosphoserine phosphatase deficiency, a recessively inherited condition. The two mutations correspond to the replacement of the semiconserved Asp32 residue by an asparagine and of the extremely conserved Met52 by a threonine. The effects of both mutations were studied on the human recombinant enzyme, expressed in Escherichia coli. Met52Thr almost abolished the enzymatic activity, whereas the Asp32Asn mutation caused a 50% decrease in Vmax. In addition, L-serine, which inhibits the conversion of [(14)C] Phosphoserine to serine when catalysed by the wild-type enzyme, had a lesser inhibitory effect on the Asp32Asn mutant, indicating a reduction in the rate of phosphoenzyme hydrolysis. These modifications in the properties of the enzyme are consistent with the modification in the kinetic properties observed in fibroblasts from the patient.
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mechanistic studies of Phosphoserine phosphatase an enzyme related to p type atpases
Journal of Biological Chemistry, 1999Co-Authors: Jeanfrancois Collet, Vincent Stroobant, Emile Van SchaftingenAbstract:Phosphoserine phosphatase belongs to a new class of phosphotransferases forming an acylphosphate during catalysis and sharing three motifs with P-type ATPases and haloacid dehalogenases. The phosphorylated residue was identified as the first aspartate in the first motif (DXDXT) by mass spectrometry analysis of peptides derived from the phosphorylated enzyme treated with NaBH(4) or alkaline [(18)O]H(2)O. Incubation of native Phosphoserine phosphatase with Phosphoserine in [(18)O]H(2)O did not result in (18)O incorporation in residue Asp-20, indicating that the phosphoaspartate is hydrolyzed, as in P-type ATPases, by attack of the phosphorus atom. Mutagenesis studies bearing on conserved residues indicated that four conservative changes either did not affect (S109T) or caused a moderate decrease in activity (G178A, D179E, and D183E). Other mutations inactivated the enzyme by >80% (S109A and G180A) or even by >/=99% (D179N, D183N, K158A, and K158R). Mutations G178A and D179N decreased the affinity for Phosphoserine, suggesting that these residues participate in the binding of the substrate. Mutations of Asp-179 decreased the affinity for Mg(2+), indicating that this residue interacts with the cation. Thus, investigated residues appear to play an important role in the reaction mechanism of Phosphoserine phosphatase, as is known for equivalent residues in P-type ATPases and haloacid dehalogenases.
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Phosphoserine phosphatase deficiency in a patient with williams syndrome
Journal of Medical Genetics, 1997Co-Authors: J Jaeken, Jeanfrancois Collet, Michel Detheux, Jeanpierre Fryns, P Alliet, E Van SchaftingenAbstract:Decreased serine levels were found in plasma and cerebrospinal fluid (CSF) of a boy with pre- and postnatal growth retardation, moderate psychomotor retardation, and facial dysmorphism suggestive of Williams syndrome. Fluorescence in situ hybridisation with an elastin gene probe indicated the presence of a submicroscopic 7q11.23 deletion, confirming this diagnosis. Further investigation showed that the Phosphoserine phosphatase (EC 3.1.3.3.) activity in lymphoblasts and fibroblasts amounted to about 25% of normal values. Oral serine normalised the plasma and CSF levels of this amino acid and seemed to have some clinical effect. These data suggest that the elastin gene and the Phosphoserine phosphatase gene might be closely linked. This seems to be the first report of Phosphoserine phosphatase deficiency.
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human l 3 Phosphoserine phosphatase sequence expression and evidence for a phosphoenzyme intermediate
FEBS Letters, 1997Co-Authors: Jeanfrancois Collet, Isabelle Gerin, Mark H Rider, Maria Veigadacunha, Emile Van SchaftingenAbstract:We report the sequence of the cDNA encoding human L-3-Phosphoserine phosphatase. The encoded polypeptide contains 225 residues and shows 30% sequence identity with the Escherichia coli enzyme. The human protein was expressed in a bacterial expression system and purified. Similar to known L-3-Phosphoserine phosphatases, it catalyzed the Mg2(+)-dependent hydrolysis of L-Phosphoserine and an exchange reaction between L-serine and L-Phosphoserine. In addition we found that the enzyme was phosphorylated upon incubation with L-[32P]Phosphoserine, which indicates that the reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediate. The sensitivity of the phosphoryl-enzyme to alkali and to hydroxylamine suggests that an aspartyl- or a glutamyl-phosphate was formed. The nucleotide sequence of the cDNA described in this article has been deposited in the EMBL data base under accession number Y10275.
J Jaeken - One of the best experts on this subject based on the ideXlab platform.
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Phosphoserine aminotransferase deficiency a novel disorder of the serine biosynthesis pathway
American Journal of Human Genetics, 2007Co-Authors: Claire Hart, J Jaeken, Valerie Race, Younes Achouri, Elsa Wiame, Mark Sharrard, S E Olpin, Jennifer Watkinson, James R Bonham, Gert MatthijsAbstract:We present the first two identified cases of Phosphoserine aminotransferase deficiency. This disorder of serine biosynthesis has been identified in two siblings who showed low concentrations of serine and glycine in plasma and cerebrospinal fluid. Clinically, the index patient presented with intractable seizures, acquired microcephaly, hypertonia, and psychomotor retardation and died at age 7 mo despite supplementation with serine (500 mg/kg/d) and glycine (200 mg/kg/d) from age 11 wk. The younger sibling received treatment from birth, which led to a normal outcome at age 3 years. Measurement of Phosphoserine aminotransferase activity in cultured fibroblasts in the index patient was inconclusive, but mutational analysis revealed compound heterozygosity for two mutations in the PSAT1 gene—one frameshift mutation (c.delG107) and one missense mutation (c.299A→C [p.Asp100Ala])—in both siblings. Expression studies of the p.Asp100Ala mutant protein revealed a Vmax of only 15% of that of the wild-type protein.
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mutations responsible for 3 Phosphoserine phosphatase deficiency
European Journal of Human Genetics, 2004Co-Authors: Maria Veigadacunha, Jeanfrancois Collet, J Jaeken, Benoit Prieur, Yves Peeraer, Anja Rabbijns, Emile Van SchaftingenAbstract:We report the identification of the mutations in the only known case of L-3-Phosphoserine phosphatase deficiency, a recessively inherited condition. The two mutations correspond to the replacement of the semiconserved Asp32 residue by an asparagine and of the extremely conserved Met52 by a threonine. The effects of both mutations were studied on the human recombinant enzyme, expressed in Escherichia coli. Met52Thr almost abolished the enzymatic activity, whereas the Asp32Asn mutation caused a 50% decrease in Vmax. In addition, L-serine, which inhibits the conversion of [(14)C] Phosphoserine to serine when catalysed by the wild-type enzyme, had a lesser inhibitory effect on the Asp32Asn mutant, indicating a reduction in the rate of phosphoenzyme hydrolysis. These modifications in the properties of the enzyme are consistent with the modification in the kinetic properties observed in fibroblasts from the patient.
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Phosphoserine phosphatase deficiency in a patient with williams syndrome
Journal of Medical Genetics, 1997Co-Authors: J Jaeken, Jeanfrancois Collet, Michel Detheux, Jeanpierre Fryns, P Alliet, E Van SchaftingenAbstract:Decreased serine levels were found in plasma and cerebrospinal fluid (CSF) of a boy with pre- and postnatal growth retardation, moderate psychomotor retardation, and facial dysmorphism suggestive of Williams syndrome. Fluorescence in situ hybridisation with an elastin gene probe indicated the presence of a submicroscopic 7q11.23 deletion, confirming this diagnosis. Further investigation showed that the Phosphoserine phosphatase (EC 3.1.3.3.) activity in lymphoblasts and fibroblasts amounted to about 25% of normal values. Oral serine normalised the plasma and CSF levels of this amino acid and seemed to have some clinical effect. These data suggest that the elastin gene and the Phosphoserine phosphatase gene might be closely linked. This seems to be the first report of Phosphoserine phosphatase deficiency.
Anastassios C. Papageorgiou - One of the best experts on this subject based on the ideXlab platform.
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Structural Basis of L-Phosphoserine Binding to Bacillus Alcalophilus Phosphoserine Aminotransferase
Acta Crystallographica Section D-biological Crystallography, 2013Co-Authors: Pradeep Battula, Anatoly P. Dubnovitsky, Anastassios C. PapageorgiouAbstract:Phosphoserine aminotransferase is a vitamin B6-dependent enzyme that catalyzes the reversible conversion of 3-phosphohydroxypyruvate to l-Phosphoserine using glutamate as an amine donor. In an effort to gain insight into the substrate-recognition mechanism of the enzyme, crystal structures of Bacillus alcalophilus Phosphoserine aminotransferase in the presence or absence of l-Phosphoserine were determined to resolutions of 1.5 and 1.6 A, respectively. Local conformational changes induced upon substrate binding were identified. However, in contrast to other aminotransferases, no domain or subunit movements were observed. Two Arg residues (Arg42 and Arg328) and two His residues (His41 and His327) were found to form a tight binding site for the phosphate group of l-Phosphoserine. Comparison with Escherichia coli Phosphoserine aminotransferase in complex with the substrate analogue α-methylglutamate revealed more extensive structural changes in the case of l-Phosphoserine binding. Based on the structural analysis, the flexibility of Arg328 is proposed to be critical for substrate recognition.
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enzyme adaptation to alkaline ph atomic resolution 1 08 a structure of Phosphoserine aminotransferase from bacillus alcalophilus
Protein Science, 2009Co-Authors: Anatoly P. Dubnovitsky, Evangelia G Kapetaniou, Anastassios C. PapageorgiouAbstract:The crystal structure of the vitamin B6-dependent enzyme Phosphoserine aminotransferase from the obligatory alkaliphile Bacillus alcalophilus has been determined at 1.08 A resolution. The model was refined to an R-factor of 11.7% (Rfree = 13.9%). The enzyme displays a narrow pH optimum of enzymatic activity at pH 9.0. The final structure was compared to the previously reported structure of the mesophilic Phosphoserine aminotransferase from Escherichia coli and to that of Phosphoserine aminotransferase from a facultative alkaliphile, Bacillus circulans subsp. alkalophilus. All three enzymes are homodimers with each monomer comprising a two-domain architecture. Despite the high structural similarity, the alkaliphilic representatives possess a set of distinctive structural features. Two residues directly interacting with pyridoxal-5′-phosphate are replaced, and an additional hydrogen bond to the O3′ atom of the cofactor is present in alkaliphilic Phosphoserine aminotransferases. The number of hydrogen bonds and hydrophobic interactions at the dimer interface is increased. Hydrophobic interactions between the two domains in the monomers are enhanced. Moreover, the number of negatively charged amino acid residues increases on the solvent-accessible molecular surface and fewer hydrophobic residues are exposed to the solvent. Further, the total amount of ion pairs and ion networks is significantly reduced in the Bacillus enzymes, while the total number of hydrogen bonds is increased. The mesophilic enzyme from Escherichia coli contains two additional β-strands in a surface loop with a third β-strand being shorter in the structure. The identified structural features are proposed to be possible factors implicated in the alkaline adaptation of Phosphoserine aminotransferase.
Yoko Chiba - One of the best experts on this subject based on the ideXlab platform.
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Discovery and analysis of a novel type of the serine biosynthetic enzyme Phosphoserine phosphatase in Thermus thermophilus
FEBS Journal, 2018Co-Authors: Yoko Chiba, Ayako Yoshida, Shigeru Shimamura, Masafumi Kameya, Takeo Tomita, Makoto Nishiyama, Ken TakaiAbstract:Studying the diversity of extant metabolisms and enzymes, especially those involved in the biosynthesis of primary metabolites including amino acids, is important to shed light on the evolution of life. Many organisms synthesize serine from Phosphoserine via a reaction catalyzed by Phosphoserine phosphatase (PSP). Two types of PSP, belonging to distinct protein superfamilies, have been reported. Genomic analyses have revealed that the thermophilic bacterium Thermus thermophilus lacks both homologs while still having the ability to synthesize serine. Here, we purified a protein from T. thermophilus which we biochemically identified as a PSP. A knockout mutant of the responsible gene (TT_C1695) was constructed, which showed serine auxotrophy. These results indicated the involvement of this gene in serine biosynthesis in T. thermophilus. TT_C1695 was originally annotated as a protein with unknown function belonging to the haloacid dehalogenase-like hydrolase (HAD) superfamily. The HAD superfamily, which comprises phosphatases against a variety of substrates, includes also the classical PSP as a member. However, the amino acid sequence of the TT_C1695 was more similar to phosphatases acting on non-Phosphoserine substrates than classical PSP; therefore, a BLASTP search and phylogenetic analysis failed to predict TT_C1695 as a PSP. Our results strongly suggest that the T. thermophilus PSP and classical PSP evolved specificity for Phosphoserine independently. ENZYMES: Phosphoserine phosphatase (PSP; EC 3.1.3.3); serine hydroxymethyltransferase (EC 2.1.2.1); 3-phosphoglycerate dehydrogenase (EC 1.1.1.95); 3-Phosphoserine aminotransferase (EC 2.6.1.52).
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structural units important for activity of a novel type Phosphoserine phosphatase from hydrogenobacter thermophilus tk 6 revealed by crystal structure analysis
Journal of Biological Chemistry, 2013Co-Authors: Yoko Chiba, Hiroyuki Arai, Yasuo Igarashi, Shoichiro Horita, Jun Ohtsuka, Koji Nagata, Masaru Tanokura, Masaharu IshiiAbstract:Novel-type serine-synthesizing enzymes, termed metal-independent Phosphoserine phosphatases (iPSPs), were recently identified and characterized from Hydrogenobacter thermophilus, a chemolithoautotrophic bacterium belonging to the order Aquificales. iPSPs are cofactor-dependent phosphoglycerate mutase (dPGM)-like phosphatases that have significant amino acid sequence similarity to dPGMs but lack phosphoglycerate mutase activity. Genes coding dPGM-like phosphatases have been identified in a broad range of organisms; however, predicting the function of the corresponding proteins based on sequence information alone is difficult due to their diverse substrate preferences. Here, we determined the crystal structure of iPSP1 from H. thermophilus in the apo-form and in complex with its substrate l-Phosphoserine to find structural units important for its phosphatase activity toward l-Phosphoserine. Structural and biochemical characterization of iPSP1 revealed that the side chains of His85 and C-terminal region characteristic of iPSP1 are responsible for the PSP activity. The importance of these structural units for PSP activity was confirmed by high PSP activity observed in two novel dPGM-like proteins from Cyanobacteria and Chloroflexus in which the two structural units were conserved. We anticipate that our present findings will facilitate understanding of the serine biosynthesis pathways of organisms that lack gene(s) encoding conventional PSPs, as the structural information revealed here will help to identify iPSP from sequence databases.
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discovery and analysis of cofactor dependent phosphoglycerate mutase homologs as novel Phosphoserine phosphatases in hydrogenobacter thermophilus
Journal of Biological Chemistry, 2012Co-Authors: Yoko Chiba, Kenro Oshima, Hiroyuki Arai, Masaharu Ishii, Yasuo IgarashiAbstract:Abstract Phosphoserine phosphatase (PSP) catalyzes the dephosphorylation of Phosphoserine to serine and inorganic phosphate. PSPs, which have been found in all three domains of life, belong to the haloacid dehalogenase-like hydrolase superfamily. However, certain organisms, particularly bacteria, lack a classical PSP gene, although they appear to possess a functional Phosphoserine synthetic pathway. The apparent lack of a PSP ortholog in Hydrogenobacter thermophilus, an obligately chemolithoautotrophic and thermophilic bacterium, represented a missing link in serine anabolism because our previous study suggested that serine should be synthesized from Phosphoserine. Here, we detected PSP activity in cell-free extracts of H. thermophilus and purified two proteins with PSP activity. Surprisingly, these proteins belonged to the histidine phosphatase superfamily and had been annotated as cofactor-dependent phosphoglycerate mutase (dPGM). However, because they possessed neither mutase activity nor the residues important for the activity, we defined these proteins as novel-type PSPs. Considering the strict substrate specificity toward l-Phosphoserine, kinetic parameters, and PSP activity levels in cell-free extracts, these proteins were strongly suggested to function as PSPs in vivo. We also detected PSP activity from “dPGM-like” proteins of Thermus thermophilus and Arabidopsis thaliana, suggesting that PSP activity catalyzed by dPGM-like proteins may be distributed among a broad range of organisms. In fact, a number of bacterial genera, including Firmicutes and Cyanobacteria, were proposed to be strong candidates for possessing this novel type of PSP. These findings will help to identify the missing link in serine anabolism.
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Discovery and Analysis of Cofactor-dependent Phosphoglycerate Mutase Homologs as Novel Phosphoserine
2012Co-Authors: Yoko Chiba, Kenro Oshima, Hiroyuki Arai, Masaharu Ishii, Yasuo Igarashi, Fromthe ‡ DepartmentofbiotechnologyandAbstract:Phosphoserine phosphatase (PSP) catalyzes the dephosphorylation of Phosphoserine to serine and inorganic phosphate. PSPs, which have been found in all three domains of life, belong to the haloacid dehalogenase-like hydrolase superfamily. However, certain organisms, particularly bacteria, lack a classical PSP gene, although they appear to possess a functional Phosphoserine synthetic pathway. The apparent lack of a PSP ortholog in Hydrogenobacter thermophilus, an obligately chemolithoautotrophic and thermophilic bacterium, represented a missing link in serine anabolism because our previous study suggested that serine should be synthesized from Phosphoserine. Here, we detected PSP activity in cell-free extracts of H. thermophilus and purified two proteins with PSP activity. Surprisingly, these proteins belonged to the histidine phosphatase superfamily and had been annotated as cofactor-dependent phosphoglycerate mutase (dPGM). However, because they possessed neither mutase activity nor the residues important for the activity, we defined these proteins as novel-type PSPs. Considering the strict substrate specificity toward L-Phosphoserine, kinetic parameters, and PSP activity levels in cell-free extracts, these proteins were strongly suggested to function as PSPs in vivo. We also detected PSP activity from “dPGM-like” proteins of Thermus thermophilus and Arabidopsis thaliana, suggesting that PSP activity catalyzed by dPGM-like proteins may be distributed among a broad range of organisms. In fact, a number of bacterial genera, including Firmicutes and Cyanobacteria, were proposed to be strong candidates for possessing this novel type of PSP. These findings will help to identify the missing link in serine anabolism.
