Pcal_1127, a highly stable and efficient ribose-5-phosphate pyrophosphokinase from Pyrobaculum calidifontis

Bibi, Tahira; Perveen, Sumera; Aziz, Iram; Bashir, Qamar; Rashid, Naeem; Imanaka, Tadayuki; Akhtar, Muhammad

doi:10.1007/s00792-016-0869-z

Cited by 8 publications

(7 citation statements)

References 40 publications

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“…Indeed, comparison of amino acid residues involved in the formation of the bent dimer of M. jannaschii with those of T. kodakarensis revealed an almost exact match, suggesting that active T. kodakarensis PRPP synthase may constitute a tetramer similar to that of M. jannaschii PRPP synthase. PRPP synthase from the hyperthermophilic archaeon Pyrobaculum calidifontis has been characterized and shown to resemble that of T. kodakarensis (422). The similarities of the amino acid sequence of T. kodakarensis PRPP synthase with those of M. jannaschii, S. sulfolobus, and T. volcanium are 52 to 58% (identity, 32 to 40%), whereas with B. subtilis PRPP synthase the values are 47% (similarity) and 28% (identity).…”

Section: Archaeal Prpp Synthasesmentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

161

187

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SUMMARY Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.

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Section: Archaeal Prpp Synthasesmentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

161

187

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“…We have been studying various enzymes from the hyperthermophilic archaeon Pyrobaculum calidifontis (24)(25)(26)(27)(28)(29). The genome of P. calidifontis harbors two open reading frames, Pcal_0041 and Pcal_1743, whose products belong to the PfkB family of ribokinases and contain PFK and pyrimidine kinase domains.…”

mentioning

confidence: 99%

A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate

et al. 2018

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The genome of the hyperthermophilic archaeon contains an open reading frame Pcal_0041 annotated as PfkB family ribokinase consisting of phosphofructokinase and pyrimidine kinase domains. Among biochemically characterized enzymes, the Pcal_0041 protein was 37% identical to the phosphofructokinase (Ape_0012) from, which displayed kinase activity towards a broad spectrum of substrates including sugars, sugar phosphates and nucleosides, and 36% identical to a phosphofructokinase from In order to examine the biochemical function of the Pcal_0041 protein, we cloned and expressed the gene and purified the recombinant protein. Although the Pcal_0041 protein contained a putative phosphofructokinase domain, it exhibited only low levels of phosphofructokinase activity. The recombinant enzyme catalyzed the phosphorylation of nucleosides, and to a lower extent, sugars and sugar phosphates. Surprisingly among the substrates tested, highest activity was detected with ribose 1-phosphate (R1P), followed by cytidine and uridine. Catalytic efficiency (/) toward R1P was 11.5 mM s ATP was the most preferred phosphate donor, followed by GTP. Activity measurements with cell-free extracts of indicated the presence of nucleoside phosphorylase activity, which would provide the means to generate R1P from nucleosides. The study suggests that, in addition to the recently identified ADP-dependent ribose-1-phosphate kinase (R1P kinase) in that functions in the pentose bisphosphate pathway, R1P kinase is also present in members of the Crenarchaeota. The discovery of the pentose bisphosphate pathway in has clarified how this archaeon can degrade nucleosides. Homologs of the enzymes of this pathway are present in many members of the Thermococcales, suggesting that this metabolism occurs in these organisms. However this is not the case in other archaea, and degradation mechanisms for nucleosides or ribose 1-phosphate are still unknown. This study reveals an important first step in understanding nucleoside metabolism in Crenarchaeota, and identifies an ATP-dependent ribose-1-phosphate kinase in The enzyme is structurally distinct to previously characterized archaeal members of the ribokinase family and represents a group of proteins found in many crenarchaea.

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“…) although the optimal growth temperature of T. kodakarensis is 85 °C. This result is in contrast to most of the enzymes from hyperthermophiles but similar to ribose‐5‐phosphate pyrophosphokinases from T. kodakarensis and Pyrobaculum calidifontis , and phosphoribosyl diphosphate synthase from S. solfataricus . It should be noted that a protective mechanism of protein stabilization in hyperthermophiles has been suggested involving the secretion of small‐molecule osmolytes in stressful conditions .…”

Section: Resultsmentioning

confidence: 64%

“…The gene encoding Tk TrpD was expressed in Escherichia coli and the recombinant gene product was purified, characterized, crystallized and its crystal structure was determined in free form as well as in the presence of Zn 2+ to 1.9 and 2.4 Å resolutions, respectively. The results would provide a better understanding of the TrpD family of enzymes and help in biotechnological applications to synthesize compounds for use in biochemical assays . Moreover, TrpD has also emerged as a potential candidate for biomedical applications.…”

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confidence: 95%

Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure

et al. 2017

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Anthranilate phosphoribosyltransferase (TrpD) is involved in tryptophan biosynthesis, catalyzing the transfer of a phosphoribosyl group to anthranilate, leading to the generation of phosphoribosyl anthranilate. TrpD belongs to the phosphoribosyltransferase (PRT) superfamily and is the only member of the structural class IV. X‐ray structures of TrpD from seven species have been solved to date. Here, functional and structural characterization of a recombinant TrpD from hyperthermophilic archaeon Thermococcus kodakarensis KOD1 ( Tk TrpD) was carried out. Contrary to previously characterized Mg 2+ ‐dependent TrpD enzymes, Tk TrpD was found to have a unique divalent cation dependency characterized by maximum activity in the presence of Zn 2+ (1580 μmol·min −1 ·mg −1 , the highest reported for any TrpD) followed by Ca 2+ (948 μmol·min −1 ·mg −1 ) and Mg 2+ (711 μmol·min −1 ·mg −1 ). Tk TrpD displayed an unusually low thermostability compared to other previously characterized proteins from T. kodakarensis KOD1. The crystal structure of Tk TrpD was determined in free form and in the presence of Zn 2+ to 1.9 and 2.4 Å resolutions, respectively. Tk TrpD structure displayed the typical PRT fold similar to other class IV PRTs, with a small N‐terminal α‐helical domain and a larger C‐terminal α/β domain. Electron densities for Zn 2+ were identified at the expected zinc‐binding motif, DE(217–218), of the enzyme in each subunit of the dimer. Two additional Zn 2+ were found at a new dimer interface formed in the presence of Zn 2+ . A fifth Zn 2+ was found bound to Glu118 at crystal lattice contacts and a sixth one was ligated with Glu235. Based on the Tk TrpD–Zn 2+ structure, it is suggested that the formation of a new dimer may be responsible for the higher enzyme activity of Tk TrpD in the presence of Zn 2+ ions.

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Pcal_1127, a highly stable and efficient ribose-5-phosphate pyrophosphokinase from Pyrobaculum calidifontis

Cited by 8 publications

References 40 publications

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

A Phosphofructokinase Homolog from Pyrobaculum calidifontis Displays Kinase Activity towards Pyrimidine Nucleosides and Ribose 1-Phosphate

Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure

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