The Crystal Structure of Pyrococcus furiosus UMP Kinase Provides Insight into Catalysis and Regulation in Microbial Pyrimidine Nucleotide Biosynthesis

Marco-Marı́n, Clara; Gil-Ortiz, F.; Rubio, Vicente

doi:10.1016/j.jmb.2005.07.045

Cited by 53 publications

(78 citation statements)

References 50 publications

(72 reference statements)

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“…The major structural difference among the different AAK family members resides in their N-terminal lobe, which is involved in binding different substrates and formation of different dimer interfaces. On the other hand, the structures of the C-terminal lobe, which is involved in binding the common substrate ATP, are similar (38,41). The structural differences among the NAGKs from different organisms consist mainly of variations in the conformation of the ␤3-␤4 loop, which results in differences in the degree of closure of the active site.…”

Section: Resultsmentioning

confidence: 99%

The Crystal Structure of N-Acetyl-L-glutamate Synthase from Neisseria gonorrhoeae Provides Insights into Mechanisms of Catalysis and Regulation

Shi

Sagar

Jin

et al. 2008

Journal of Biological Chemistry

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Section: Resultsmentioning

confidence: 99%

The Crystal Structure of N-Acetyl-L-glutamate Synthase from Neisseria gonorrhoeae Provides Insights into Mechanisms of Catalysis and Regulation

Shi

Sagar

Jin

et al. 2008

Journal of Biological Chemistry

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“…Phosphoryl transfer. In general, enzymes catalyzing phosphoryl transfer reactions also require two Mg 2ϩ , as demonstrated from studies of Pyrococcus furiosus UMP kinase (PDB code 2bmu) (197), Staphylococcus aureus tagatose 6-phosphate kinase (PDB code 2jg1) (198), Bifidobacterium longum N-acetylhexosamine kinase (PDB code 4wh3) (199), mammalian cyclin-dependent kinase 2 (PDB code 3qhw) (200), or cyclic AMP (cAMP)-dependent protein kinase A (PDB codes 1l3r and 4hpu) (201,202). We shall use protein kinase A for a more detailed description.…”

Section: Substitution Reactions At ␣- ␤- or ␥-Phosphatesmentioning

confidence: 99%

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

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

157

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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“…The fold of bacterial UMPKs is related to that of the hexameric UMPKs of archaeal origin (31,32). Therefore, bacterial and archaeal UMPKs represent a structurally homogeneous family.…”

Section: Differences In Regulatory Mechanisms Betweenmentioning

confidence: 99%

Structural and Functional Characterization of Escherichia coli UMP Kinase in Complex with Its Allosteric Regulator GTP

Meyer

Evrin

Briozzo

et al. 2008

Journal of Biological Chemistry

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Bacterial UMP kinases are essential enzymes involved in the multistep synthesis of UTP. They are hexamers regulated by GTP (allosteric activator) and UTP (inhibitor). We describe here the 2.8 Å crystal structure of Escherichia coli UMP kinase bound to GTP. The GTP-binding site, situated at 15 Å from the UMP-binding site and at 24 Å from the ATP-binding site, is delineated by two contiguous dimers. The overall structure, as compared with those bound to UMP, UDP, or UTP, shows a rearrangement of its quaternary structure: GTP induces an 11°o pening of the UMP kinase dimer, resulting in a tighter dimerdimer interaction. A nucleotide-free UMP kinase dimer has an intermediate opening. Superposition of our structure with that of archaeal UMP kinases, which are also hexamers, shows that a loop appears to hamper any GTP binding in archeal enzymes. This would explain the absence of activating effect of GTP on this group of UMP kinases. Among GTP-binding residues, the Asp-93 is the most conserved in bacterial UMP kinases. In the previously published structures of E. coli UMP kinase, this residue was shown to be involved in hydrogen bonds between the subunits of a dimer. Its substitution by an alanine decreases the cooperativity for UTP binding and suppresses the reversal by GTP of UTP inhibition. This demonstrates that the previously described mutual exclusion of these two nucleotides is mediated by Asp-93.Uridine 5Ј-monophosphate kinases (UMPKs) 4 catalyze the reversible transfer of the ␥-phosphoryl group from ATP to UMP, according to the reaction, Mg⅐ATP ϩ UMP 7 Mg⅐ADP ϩ UDP. The resulting UDP is further phosphorylated by nucleoside diphosphate kinase to UTP, serving as a substrate for RNA polymerase or as a precursor for CTP. UDP can also be reduced by ribonucleoside diphosphate reductase to 2Ј-deoxy-UDP, which serves in the production of dTTP and dCTP used for DNA synthesis.The eukaryotic UMP/CMP kinases phosphorylate with comparable efficiency both UMP and CMP. Conversely, bacteria possess two distinct enzymes, each specific for either UMP or CMP. Bacterial UMPKs exist in solution as stable homohexamers, whereas eukaryotic UMP/CMP kinases are monomers. We previously solved three crystal structures of UMPK from Escherichia coli (UMPKeco) in complex with UMP, UDP, or UTP (1), using an enzyme variant (D159N) with similar stability and kinetic properties (2) but with significantly higher solubility than the wild-type protein. These structures showed that the overall fold of the monomer is different from that of eukaryotic UMP/CMP kinases. Besides, the three-dimensional structure of the UMPKeco hexamer is closely related to all of the other bacterial UMPKs structures deposited in the Protein Data Bank.Bacterial UMPKs are submitted to allosteric activation by GTP and to feedback inhibition by UTP, the major product of the reaction they catalyze (3). This contributes to balance the synthesis of purine versus pyrimidine nucleoside triphosphates. The crystal structure of UMPKeco in complex with UTP showed that the nucleotide, ...

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The Crystal Structure of Pyrococcus furiosus UMP Kinase Provides Insight into Catalysis and Regulation in Microbial Pyrimidine Nucleotide Biosynthesis

Cited by 53 publications

References 50 publications

The Crystal Structure of N-Acetyl-L-glutamate Synthase from Neisseria gonorrhoeae Provides Insights into Mechanisms of Catalysis and Regulation

The Crystal Structure of N-Acetyl-L-glutamate Synthase from Neisseria gonorrhoeae Provides Insights into Mechanisms of Catalysis and Regulation

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

Structural and Functional Characterization of Escherichia coli UMP Kinase in Complex with Its Allosteric Regulator GTP

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