Some observations on the cofactor requirement for partially purified DNA ligase from <i>Escherichia coli</i>

Feldberg, Ross S.; Young, H A; Morrice, L.A.F.; Keir, Hamish M.

doi:10.1016/0014-5793(72)80656-2

Cited by 6 publications

(5 citation statements)

References 11 publications

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“…As shown in Fig. 4B, DDPP again inhibited adenylation of S. pneumoniae enzyme by NAD + (lanes 9-12), but failed to inhibit adenylation of human enzyme (lanes [3][4][5][6]. DDPP also failed to inhibit T4 DNA ligase (data not shown).…”

Section: Biochemical Analysis Of S Pneumoniae Dna Ligase and Its Inhmentioning

confidence: 72%

“…In this study, we characterized the NAD + -dependent DNA ligase of S. pneumoniae, which exhibits biochemical properties similar to those of E. coli and M. tuberculosis enzymes [4][5][6]32,33]. We identified a new class of inhibitor, DDPP, a pyrimidopyrimidine derivative.…”

Section: Discussionmentioning

confidence: 99%

“…Several bacterial DNA ligases have been studied biochemically and genetically. Biochemical studies of the Escherichia coli enzyme show that it catalyzes an NAD + ‐dependent DNA ligation reaction [4–6]. Genetic studies show that mutations that inactivate the activity of E. coli DNA ligase are lethal to the cell [5,6].…”

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confidence: 99%

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Identification and characterization of an inhibitor specific to bacterial NAD⁺‐dependent DNA ligases

et al. 2008

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DNA ligase is an enzyme essential for DNA replication, repair and recombination in all organisms [1][2][3]. The enzyme catalyzes the formation of phosphodiester bonds at single-strand breaks in duplex DNA during these physiological processes [1][2][3]. There are two classes of DNA ligases, identified on the basis of their cofactor requirements. Bacterial DNA ligases involved in DNA replication utilize NAD + as a cofactor, whereas mammalian and viral DNA ligases require ATP for activity [1][2][3]. Biochemical studies of bacterial DNA ligase (NAD + -dependent), and viral and human DNA ligases (ATP-dependent) have established that the mechanism of the reactions catalyzed by the two different groups of DNA ligases is similar [1][2][3]. The reaction mechanism consists of three reversible steps: (a) adenylation of the enzyme by transferring the adenylate group from NAD + or ATP to the e-NH 2 group of Lys in the enzyme with the release of nicotinamide + and specifically inhibits enzyme adenylation, but not DNA adenylation or ligation. Labeling studies establish that this molecule inhibits the incorporation of thymidine into DNA and that overexpression of DNA ligase in the cell abolishes this inhibition. Finally, microbiological studies show that this molecule exhibits a broad spectrum of antibacterial activity. Together, this study shows that this small molecule inhibitor identified is specific to bacterial NAD + -dependent DNA ligases, exhibits a broad spectrum of antibacterial activities, and has the potential to be developed into an antibacterial agent.Abbreviations DDPP, 2,4-diamino-7-dimethylamino-pyrimido [4,5-d]pyrimidine; FRET, fluorescence resonance energy transfer; NMN, nicotinamide mononucleotide.

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Section: Biochemical Analysis Of S Pneumoniae Dna Ligase and Its Inhmentioning

confidence: 72%

Section: Discussionmentioning

confidence: 99%

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Identification and characterization of an inhibitor specific to bacterial NAD⁺‐dependent DNA ligases

et al. 2008

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“…These enzymes include those from mesophiles, such as E. coli (11), and thermophilic bacteria, such as Bacillus stearothermophilus (3), T. thermophilus (41), Thermus scotoductus (42), and Rhodothermus marinus (42). The enzyme from T. thermophilus has been reported to show DNA ligase activity at temperatures of up to 85°C, with an optimal reaction temperature of approximately 70°C (41).…”

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confidence: 99%

A DNA Ligase from a Hyperthermophilic Archaeon with Unique Cofactor Specificity

et al. 2000

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A gene encoding DNA ligase (lig Tk ) from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1, has been cloned and sequenced, and its protein product has been characterized. ؉ . This is the first biochemical study of a DNA ligase from a hyperthermophilic archaeon.DNA ligases (EC 6.5.1.1 and EC 6.5.1.2) catalyze the phosphodiester bond formation between adjacent 3Ј-hydroxyl and 5Ј-phosphoryl groups at a single-strand break in doublestranded DNA (22). They are essential enzymes for maintaining the integrity of the genome during DNA replication (24), DNA excision repair (48), and DNA recombination (16). DNA strand breaks are commonly generated as reaction intermediates in these events, and the sealing of these breaks solely depends on the proper function of DNA ligase. Therefore, DNA ligases are indispensable enzymes in all organisms.DNA ligases fall into two groups on the basis of the required cofactor for activity: the group requiring ATP (8) and the group requiring NAD ϩ (43). There is high similarity among the ligases within the ATP-dependent group (19) or NAD ϩ -dependent group (42). ATP-dependent DNA ligase I from humans and Saccharomyces cerevisiae are 42% identical, and NAD ϩ -dependent enzymes from Escherichia coli and Thermus thermophilus are 46% identical. However, enzymes between the two groups show no similarity, with the exception of the KXDG motif, which includes the active-site lysine (19). Furthermore, biochemical investigations have indicated that there is strict specificity towards the respective cofactors. This suggests that the two groups have evolved through completely different pathways.It is now accepted that both ATP-dependent and NAD ϩ -dependent DNA ligases catalyze their reactions through a common mechanism (7). The ligation reaction proceeds through three steps: (i) activation of the enzyme through the covalent addition of AMP to the conserved active-site lysine of the protein, accompanied by the release of PP i or nicotinamide mononucleotide from the cofactor (ATP or NAD ϩ ), (ii) transfer of AMP from the protein to the 5Ј-phosphoryl group of the nick on the DNA, and (iii) phosphodiester bond formation with concomitant release of free AMP from the adenylated DNA intermediate.Biochemical and genetic studies have been performed for DNA ligases from various organisms. It has been shown that eukaryotes (17, 33, 46), viruses (29, 30), and bacteriophages (7,20) harbor ATP-dependent enzymes. Although only a single type of DNA ligase has been reported for viruses and bacteriophages, eukaryotic organisms have multiple enzymes. Five distinct DNA ligases have been reported from mammalian cells (17,33,45,46). ATP-dependent enzymes show a wide range in molecular mass, from 41 kDa (bacteriophage T7) (7) to 102 kDa (human DNA ligase I) (2). This considerable difference in size is mainly due to the diversity of the N-terminal region of each DNA ligase. DNA ligase I from humans includes a regulatory domain of 216 amino acid residues in its N-terminal region, which is dispensable for DNA ligas...

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“…(b) Similar assays at pH 8.0 followed the conversion of covalently closed circular DNA from bacteriophage A from a rapidly sedimenting molecular species into slowly sedimenting single-stranded circular and linear molecules, by centrifugation through alkaline sucrose density gradients. The centrifugation details and the preparation of 3H-labelled covalently closed circular A. DNA by the action of polynucleotide ligase from E. coil on Hershey, circles of A DNA were as described by Feldberg et al (1972).…”

Section: Assay Of Dnaasementioning

confidence: 99%

Deoxyribonucleic acid-dependent ribonucleic acid polymerases from normal and polyoma-transformed BHK-21/C13 cells

Cooper

Keir

1975

Biochemical Journal

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DNA-dependent RNA polymerase (EC 2.7.7.6) ACTIVITIES FROM NORMAL BHK-21/C13 cells and from BHK-21/C13 cells transformed by polyoma virus (PYY cells) were solubilized and fractionated on columns of DEAE-Sephadex. Various properties of the A and B enzymes from the two types of cell were compared. 1. The yields of polymerase relative to the DNA content of the nuclear preparations are similar for both cell types. 2. The ionic-strength optima of polymerases A and B are 12.5 mM and 100mM with respect to (NH4)2SO4 for both cell types. 3. The Mn2+/Mg2+ activity ratio (measured at the respective optimum for each cation) for polymerase A from BHK-21/C13 cells was 1.48 and for the polymerase A from PYY cells was 0.55. The corresponding ratios for polymerase B were 10.11 for BHK-21/C13 cells and 22.75 for PYY cells. 4. Minor differences in the ability of the A polymerases to transcribe native and denatured DNA templates were observed; such differences were not apparent when the B polymerases were compared. 5. All the polymerases were inhibited completely by actinomycin D and by rifampicin AF/013, but not markedly so by rifampicin. Alpha-amanitin inhibited polymerase B but not polymerase A.

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Some observations on the cofactor requirement for partially purified DNA ligase from Escherichia coli

Cited by 6 publications

References 11 publications

Identification and characterization of an inhibitor specific to bacterial NAD⁺‐dependent DNA ligases

Identification and characterization of an inhibitor specific to bacterial NAD⁺‐dependent DNA ligases

A DNA Ligase from a Hyperthermophilic Archaeon with Unique Cofactor Specificity

Deoxyribonucleic acid-dependent ribonucleic acid polymerases from normal and polyoma-transformed BHK-21/C13 cells

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Some observations on the cofactor requirement for partially purified DNA ligase from Escherichia coli

Cited by 6 publications

References 11 publications

Identification and characterization of an inhibitor specific to bacterial NAD+‐dependent DNA ligases

Identification and characterization of an inhibitor specific to bacterial NAD+‐dependent DNA ligases

A DNA Ligase from a Hyperthermophilic Archaeon with Unique Cofactor Specificity

Deoxyribonucleic acid-dependent ribonucleic acid polymerases from normal and polyoma-transformed BHK-21/C13 cells

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Identification and characterization of an inhibitor specific to bacterial NAD⁺‐dependent DNA ligases

Identification and characterization of an inhibitor specific to bacterial NAD⁺‐dependent DNA ligases