Identification and characterization of the smbA gene, a suppressor of the mukB null mutant of Escherichia coli

Yamanaka, Kunitoshi; Ogura, Teru; Niki, Hironori; Hiraga, Sota

doi:10.1128/jb.174.23.7517-7526.1992

Cited by 59 publications

(51 citation statements)

References 44 publications

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“…This enzyme has been studied from a variety of bacterial sources (Valentin-Hansen, 1978, Yamanaka et al, 1992, Serina et al, 1995, Serina et al, 1996. The bacterial enzyme is allosterically regulated by both GTP and UTP (Serina et al, 1995).…”

Section: Ump Kinase (Umpk Ec 2744)mentioning

confidence: 99%

Purine and Pyrimidine Nucleotide Synthesis and Metabolism

Moffatt

Ashihara

2002

The Arabidopsis Book

264

249

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Section: Ump Kinase (Umpk Ec 2744)mentioning

confidence: 99%

Purine and Pyrimidine Nucleotide Synthesis and Metabolism

Moffatt

Ashihara

2002

The Arabidopsis Book

264

249

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“…For all bacterial species, UMPK appears as essential for growth (5)(6)(7)(8). Bacterial UMPKs represent a unique target for the design of antibacterial agents as underlined by recently published papers (8,9) and even a patent (10).…”

mentioning

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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“…Catalytic activity of the recombinant A122T variant matches that found in vivo for the dum-1 mutant strain. The residual catalytic activity of the D201N+E241D variant (pyrH1609) corresponds to that of the D201N variant of E. coli (Yamanaka et al, 1992). This latter E. coli mutant and the S. enterica serovar Typhimurium pyrH1609 mutant display a similar phenotype in that both are cold-sensitive.…”

Section: S Enterica Serovar Typhimurium Pyrh Mutantsmentioning

confidence: 93%

“…For catalytic activity, the results obtained with S. enterica serovar Typhimurium confirm that the highly conserved D201 residue is important, as also applies to E. coli. In this respect it is worth mentioning that the D201N 'conservative' substitution first described by Yamanaka et al (1992) and explored enzymically by Bucurenci et al (1998) in E. coli, has a more dramatic effect on protein stability and catalysis than that observed with the newly described D201G variant. In the modelled structure of E. coli UMP kinase, D201 is situated at the N terminus of helix-7, which is predicted to provide residues to the catalytic centre (Labesse et al, 2002).…”

Section: Key Residues Of Bacterial Ump Kinasesmentioning

confidence: 95%

Structure–function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria

et al. 2004

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Bacterial uridine monophosphate (UMP) kinases are essential enzymes encoded by pyrH genes, and conditional-lethal or other pyrH mutants were analysed with respect to structure-function relationships. A set of thermosensitive pyrH mutants from Escherichia coli was generated and studied, along with already described pyrH mutants from Salmonella enterica serovar Typhimurium. It is shown that Arg-11 and Gly-232 are key residues for thermodynamic stability of the enzyme, and that Asp-201 is important for both catalysis and allosteric regulation. A comparison of the amino acid sequence of UMP kinases from several prokaryotes showed that these were conserved residues. Discussion on the enzyme activity level in relation to bacterial viability is also presented.

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Identification and characterization of the smbA gene, a suppressor of the mukB null mutant of Escherichia coli

Cited by 59 publications

References 44 publications

Purine and Pyrimidine Nucleotide Synthesis and Metabolism

Purine and Pyrimidine Nucleotide Synthesis and Metabolism

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

Structure–function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria

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