T4 DNA ligase synthesizes dinucleoside polyphosphates

Madrid, Olga; Martı́n, Daniel; Atencia, Eva Ana; Sillero, Antonio; Sillero, Marı́a A. Günther

doi:10.1016/s0014-5793(98)00932-6

Cited by 33 publications

(24 citation statements)

References 39 publications

(49 reference statements)

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“…For the reasons noted above in discussing why high concentrations of ATP were in- hibitory to steady-state ligation, the ADP inhibition cannot plausibly be attributed to sequestration of magnesium (present at 5 mM). The most likely explanation for the ADP inhibition of single-turnover ligation and ATP inhibition of steady-state ligation is that high concentrations of ATP and ADP can act as decoy acceptors for AMP transfer by ligase-adenylate, thereby diverting the ligase from nick joining and toward the synthesis of dinucleoside polyphosphates, as described by Sillero and colleagues (1,4,12). The Sillero lab has also shown that nucleoside triphosphates (NTPs) can act as decoy acceptors for AMP transfer.…”

Section: Resultsmentioning

confidence: 99%

“…Although neither NAD ϩ nor ADP could replace ATP as the nucleotide substrate for nick joining, ADP was uniquely inhibitory to single-turnover ligation by preformed ligase adenylate. Sillero et al (1,4,12) have shown that DNA and RNA ligases can donate their covalently bound adenylates to nonnucleic acid acceptors, particularly to NTPs or nucleoside diphosphates, thereby forming ApppN and AppppN dinucleotide products. The reaction mechanism is presumed to mimic the pyrophosphorolytic reversal of the step 1 ligase adenylylation reaction, which regenerates ATP (26).…”

Section: Discussionmentioning

confidence: 99%

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Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii

Keppetipola

Shuman

2005

J Bacteriol

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Archaea encode a DNA ligase composed of a C-terminal catalytic domain typical of ATP-dependent ligases plus an N-terminal domain similar to that found in eukaryotic cellular and poxvirus DNA ligases. All archaeal DNA ligases characterized to date have ATP-dependent adenylyltransferase and nick-joining activities. However, recent reports of dual-specificity ATP/NAD ؉ ligases in two Thermococcus species and Pyrococcus abyssi and an ATP/ADP ligase in Aeropyrum pernix raise the prospect that certain archaeal enzymes might exemplify an undifferentiated ancestral stage in the evolution of ligase substrate specificity. Here we analyze the biochemical properties of Pyrococcus horikoshii DNA ligase. P. horikoshii ligase catalyzes autoadenylylation and nick sealing in the presence of a divalent cation and ATP; it is unable to utilize NAD ؉ or ADP to promote ligation in lieu of ATP. P. horikoshii ligase is thermophilic in vitro, with optimal adenylyltransferase activity at 90°C and nick-joining activity at 70 to 90°C. P. horikoshii ligase resembles the ligases of Methanobacterium thermautotrophicum and Sulfolobus shibatae in its strict specificity for ATP.DNA ligases are essential components of the DNA replication, repair, and recombination machinery in all domains of the phylogenetic tree: eucarya, archaea, and bacteria. Ligases seal 3Ј OH and 5Ј PO 4 ends via three nucleotidyl transfer reactions (10). First, a lysine nucleophile on the enzyme attacks the ␣-phosphorus of ATP or NAD ϩ , which results in the formation of a covalent ligase-adenylate intermediate and the release of pyrophosphate or nicotinamide mononucleotide. Second, attack by the 5Ј PO 4 on ligase-adenylate results in expulsion of the active-site lysine and formation of an activated DNA-adenylate intermediate. Third, ligase catalyzes the attack of a 3Ј OH on the DNA-adenylate, resulting in the release of AMP and formation of a phosphodiester.DNA ligases are grouped into two families, depending on their requirement for ATP or NAD ϩ in the ligase adenylylation reaction. Whereas NAD ϩ -dependent ligases are found only in bacteria and eukaryotic viruses, ATP-dependent DNA ligases are found in bacteria (and bacteriophages), eucarya (and eukaryotic viruses), and archaea (8,10,21,27). A core ligase module composed of nucleotidyltransferase and OB-fold domains is shared by all known DNA ligases (3,15,16,24). The adenylate-binding pocket is located within the nucleotidyltransferase domain and is composed of five conserved peptide motifs (19). The substrate specificity of NAD ϩ -dependent ligase is dictated by a unique domain that binds the nicotinamide mononucleotide component of the nucleotide substrate (3, 23); the specificity of ATP-dependent ligases is determined, at least in part, by a distinctive motif within the OB-fold domain that coordinates the beta and gamma phosphates of the nucleotide (5,19,22).The archaea are unicellular anucleate organisms with distinctive biosynthetic capacities and an ability to thrive under extreme environmental conditions. The dom...

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii

Keppetipola

Shuman

2005

J Bacteriol

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“…p 4 A has been discovered in commercial preparations of ATP and in several biological extracts; it is produced in vitro, apparently as a by‐product, by several ATP‐utilising enzymes (see [21,22] and references therein). To the best of our knowledge, it is the first time that its synthesis by a synthetase of the peptidoglycan metabolism is elicited.…”

Section: Discussionmentioning

confidence: 99%

Formation of adenosine 5′‐tetraphosphate from the acyl phosphate intermediate: a difference between the MurC and MurD synthetases of Escherichia coli

et al. 1999

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The mechanism of the Mur synthetases of peptidoglycan biosynthesis is thought to involve in each case the successive formation of an acyl phosphate and a tetrahedral intermediate. The existence of the acyl phosphates for the MurC and MurD enzymes from Escherichia coli was firmly established by their in situ reduction by sodium borohydride followed by acid hydrolysis, yielding the corresponding amino alcohols. Furthermore, it was found that MurD, but not MurC, catalyses the synthesis of adenosine 5'-tetraphosphate from the acyl phosphate, thereby substantiating its existence and pointing out a difference between the two enzymes.

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“…Less is known about the enzymes responsible for stress-induced increases in Ap4A but within the context of DNA replication and repair, DNA ligases are likely candidates and have been proposed to fulfil this role [2]. These enzymes synthesize Ap4A by transfer of AMP from the enzyme-adenylate intermediate to an ATP acceptor [15,58], an activity that is inhibited by DNA-binding [2]. So far, Lig III is the only mammalian ligase shown to synthesize Ap4A in vitro [2].…”

Section: Enzymology Of Ap4a Generation In Vivomentioning

confidence: 99%

Diadenosine 5′, 5′′′-P1,P4-tetraphosphate (Ap4A) is synthesized in response to DNA damage and inhibits the initiation of DNA replication

et al. 2015

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The level of intracellular diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) increases several fold in mammalian cells treated with non-cytotoxic doses of interstrand DNA-crosslinking agents such as mitomycin C. It is also increased in cells lacking DNA repair proteins including XRCC1, PARP1, APTX and FANCG, while >50-fold increases (up to around 25 μM) are achieved in repair mutants exposed to mitomycin C. Part of this induced Ap4A is converted into novel derivatives, identified as mono- and di-ADP-ribosylated Ap4A. Gene knockout experiments suggest that DNA ligase III is primarily responsible for the synthesis of damage-induced Ap4A and that PARP1 and PARP2 can both catalyze its ADP-ribosylation. Degradative proteins such as aprataxin may also contribute to the increase. Using a cell-free replication system, Ap4A was found to cause a marked inhibition of the initiation of DNA replicons, while elongation was unaffected. Maximum inhibition of 70-80% was achieved with 20 μM Ap4A. Ap3A, Ap5A, Gp4G and ADP-ribosylated Ap4A were without effect. It is proposed that Ap4A acts as an important inducible ligand in the DNA damage response to prevent the replication of damaged DNA.

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T4 DNA ligase synthesizes dinucleoside polyphosphates

Cited by 33 publications

References 39 publications

Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii

Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii

Formation of adenosine 5′‐tetraphosphate from the acyl phosphate intermediate: a difference between the MurC and MurD synthetases of Escherichia coli

Diadenosine 5′, 5′′′-P1,P4-tetraphosphate (Ap4A) is synthesized in response to DNA damage and inhibits the initiation of DNA replication

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