Catalytic mechanism of the phospholipase D superfamily proceeds via a covalent phosphohistidine intermediate

Gottlin, Elizabeth B.; Rudolph, Amy E.; Zhao, Yi; Matthews, Harry R.; Dixon, Jack E.

doi:10.1073/pnas.95.16.9202

Cited by 146 publications

(115 citation statements)

References 19 publications

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“…Indeed, mutation of H263 produces a catalytically inactive enzyme, whereas mutating H495, K265, or K497 results in impaired enzymatic activity [22,32]. These results are consistent with studies performed on other members of the PLD family [33][34][35][36][37].…”

Section: Biological Functions and Catalytic Mechanismsupporting

confidence: 80%

Tyrosyl-DNA Phosphodiesterase as a Target for Anticancer Therapy

Dexheimer¹,

Antony²,

Marchand³

et al. 2008

ACAMC

144

203

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Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a recently discovered enzyme that catalyzes the hydrolysis of 3′-phosphotyrosyl bonds. Such linkages form in vivo following the DNA processing activity of topoisomerase I (Top1). For this reason, Tdp1 has been implicated in the repair of irreversible Top1-DNA covalent complexes, which can be generated by either exogenous or endogenous factors. Tdp1 has been regarded as a potential therapeutic co-target of Top1 in that it seemingly counteracts the effects of Top1 inhibitors, such as camptothecin and its clinically used derivatives. Thus, by reducing the repair of Top1-DNA lesions, Tdp1 inhibitors have the potential to augment the anticancer activity of Top1 inhibitors provided there is a presence of genetic abnormalities related to DNA checkpoint and repair pathways. Human Tdp1 can also hydrolyze other 3′-end DNA alterations including 3′-phosphoglycolates and 3′-abasic sites indicating it may function as a general 3′-DNA phosphodiesterase and repair enzyme. The importance of Tdp1 in humans is highlighted by the observation that a recessive mutation in the human TDP1 gene is responsible for the inherited disorder, spinocerebellar ataxia with axonal neuropathy (SCAN1). This review provides a summary of the biochemical and cellular processes performed by Tdp1 as well as the rationale behind the development of Tdp1 inhibitors for anticancer therapy.

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Section: Biological Functions and Catalytic Mechanismsupporting

confidence: 80%

Tyrosyl-DNA Phosphodiesterase as a Target for Anticancer Therapy

Dexheimer¹,

Antony²,

Marchand³

et al. 2008

ACAMC

144

203

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“…This REase can therefore not only cleave DNA at specific phosphodiester bonds, but it can also join together two DNA segments by transferring the 5Ј-phosphate at the site of cleavage to a 3Ј-OH from elsewhere in the DNA. The BfiI REase belongs to the PLD superfamily of enzymes (12), and covalent phosphohistidine intermediates have been demonstrated previously for a number of PLD enzymes, including PLD itself, tyrosyl-DNA PDE, and Nuc (18,20,26). Stereochemical pathways for many endonucleases acting at specific DNA sites have been determined by using DNA substrates in which the scissile phosphate is replaced with a chiral phosphorothioate (PTO) of known configuration (27).…”

Section: Dna Alcoholysis By Bfiimentioning

confidence: 99%

“…They follow a two-step mechanism (18,20): in the first step, they attack the phosphorus to form a covalent phosphohistidine intermediate and release the alcohol; in the second, the intermediate is attacked by either another alcohol or water to yield, respectively, the transesterification or the hydrolysis product (21,22).…”

mentioning

confidence: 99%

Site-specific DNA transesterification catalyzed by a restriction enzyme

Sasnauskas¹,

Connolly

Halford

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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Most restriction endonucleases use Mg 2؉ to hydrolyze phosphodiester bonds at specific DNA sites. We show here that BfiI, a metal-independent restriction enzyme from the phospholipase D superfamily, catalyzes both DNA hydrolysis and transesterification reactions at its recognition site. In the presence of alcohols such as ethanol or glycerol, it attaches the alcohol covalently to the 5 terminus of the cleaved DNA. Under certain conditions, the terminal 3 -OH of one DNA strand can attack the target phosphodiester bond in the other strand to create a DNA hairpin. Transesterification reactions on DNA with phosphorothioate linkages at the target bond proceed with retention of stereoconfiguration at the phosphorus, indicating, uniquely for a restriction enzyme, a twostep mechanism. We propose that BfiI first makes a covalent enzyme-DNA intermediate, and then it resolves it by a nucleophilic attack of water or an alcohol, to yield hydrolysis or transesterification products, respectively.I n the presence of Mg 2ϩ , type II restriction endonucleases (REases) hydrolyze specific phosphodiester bonds in DNA to yield 5Ј-phosphate and 3Ј-hydroxyl termini (1). The stereochemical pathway for phosphodiester hydrolysis by four such enzymes, EcoRI, EcoRV, SfiI, and HpaII (2-4), have been determined. All proceed with inversion of configuration at the scissile phosphate, which implies an odd number of chemical steps in the hydrolytic reaction, and it is most simply accounted for by a direct in-line displacement of the 3Ј-leaving group by water (5-7). High-resolution structures are available for many more REases than have been analyzed stereochemically (1). Their active sites are generally similar, with several carboxylates to act as ligands for Mg 2ϩ in spatially equivalent positions (1). All such enzymes probably act in the same way, by using water to attack the scissile phosphate, to invert its configuration.Endonucleases from the transposase-retroviral integrase family, like MuA or HIV-integrase, catalyze at a single active site two sets of reactions on DNA (4, 8, 9). The first, the endonucleolytic cleavage of the 3Ј end of the transposon or viral DNA, is mechanistically similar to the hydrolysis reactions of REases. The second, termed DNA strand transfer, is a single-step transesterification in which the newly liberated 3Ј-OH group attacks and becomes linked to a phosphate group in the target DNA (9, 10).We ask here whether the BfiI REase can catalyze transesterification reactions in addition to DNA hydrolysis. BfiI cleaves DNA at specified positions downstream from an asymmetric recognition sequence (11). Unlike other REases, it functions without metal ions (12). The N-terminal half of BfiI (13, 14) is similar to Nuc, an EDTA-resistant nuclease from Salmonella typhimurium (15, 16) that belongs to the phospholipase D (PLD) superfamily. The PLD superfamily is a diverse group of proteins that includes phospholipases, phospholipid synthases, bacterial toxins, phosphodiesterases (PDEs), and nucleases (17, 18). The PLD enzymes catal...

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“…One is the intermediary phosphorylation of enzymes [5][6][7][8][9][10], of which nucleoside diphosphate kinase is a particularly well-studied example. The other is the reversible protein histidine phosphorylation by protein kinases and phosphatases [3,11].…”

mentioning

confidence: 99%

Identification and characterization of a mammalian 14‐kDa phosphohistidine phosphatase

Pettersson

et al. 2002

European Journal of Biochemistry

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Protein histidine phosphorylation in eukaryotes has been sparsely studied compared to protein serine/threonine and tyrosine phosphorylation. In an attempt to rectify this by probing porcine liver cytosol with the phosphohistidinecontaining peptide succinyl-Ala-His(P)-Pro-Phe-p-nitroanilide (phosphopeptide I), we observed a phosphatase activity that was insensitive towards okadaic acid and EDTA. This suggested the existence of a phosphohistidine phosphatase different from protein phosphatase 1, 2A and 2C. A 1000-fold purification to apparent homogeneity gave a 14-kDa phosphatase with a specific activity of 3 lmolAEmin )1 AEmg )1 at pH 7.5 with 7 lM phosphopeptide I as substrate. Partial amino-acid sequence determination of the purified porcine enzyme by MS revealed similarity with a human sequence representing a human chromosome 9 gene of hitherto unknown function. Molecular cloning from a human embryonic kidney cell cDNAlibrary followed by expression and purification, yielded a protein with a molecular mass of 13 700 Da, and an EDTA-insensitive phosphohistidine phosphatase activity of 9 lmolAEmin )1 AEmg )1 towards phosphopeptide I. No detectable activity was obtained towards a set of phosphoserine-, phosphothreonine-, and phosphotyrosine peptides. Northern blot analysis indicated that the human phosphohistidine phosphatase mRNA was present preferentially in heart and skeletal muscle. These results provide a new tool for studying eukaryotic histidine phosphorylation/dephosphorylation.Keywords: dephosphorylation; N-phosphorylation; phosphoamidase; phosphopeptide; protein histidine phosphatase.Boyer and coworkers detected protein-bound phosphohistidine in rat-liver mitochondrial succinyl-CoA synthetase almost 40 years ago [1,2]. Despite the long time interval and the fact that phosphohistidine represents a substantial fraction of eukaryotic protein-bound phosphate [3], only a few phosphohistidine-containing proteins have been detected compared to the large number of eukaryotic proteins phosphorylated on serine, threonine and tyrosine residues. One reason for this difference may be that the N-bound phosphate of phosphohistidine easily escapes detection by common analytical procedures, due to its lability under acidic conditions, e.g. during fixation and staining of gels after SDS/PAGE [4].The studies on eukaryotic protein histidine phosphorylation and dephosphorylation have dealt with essentially two aspects. One is the intermediary phosphorylation of enzymes [5][6][7][8][9][10], of which nucleoside diphosphate kinase is a particularly well-studied example. The other is the reversible protein histidine phosphorylation by protein kinases and phosphatases [3,11]. An important contribution to the latter field was the purification of a yeast protein histidine kinase in 1991 [12]. Access to this enzyme also made possible the preparation of 32 P-labelled histone H4, which was later used as substrate in the search for phosphohistidine phosphatases. Using such an approach, the catalytic subunits of the well-studied serine/...

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Catalytic mechanism of the phospholipase D superfamily proceeds via a covalent phosphohistidine intermediate

Cited by 146 publications

References 19 publications

Tyrosyl-DNA Phosphodiesterase as a Target for Anticancer Therapy

Tyrosyl-DNA Phosphodiesterase as a Target for Anticancer Therapy

Site-specific DNA transesterification catalyzed by a restriction enzyme

Identification and characterization of a mammalian 14‐kDa phosphohistidine phosphatase

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