Cobalt(III) complex-promoted hydrolysis of phosphate diesters: comparison in reactivity of rigid cis-diaquo(tetraaza)cobalt(III) complexes

The 2.15-Å resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca 2؉ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an innersphere water molecule to the phosphate group located 3 to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-S P phosphoryl oxygen on the adjacent 3 phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile.Recently determined crystal structures of type II restriction endonucleases have produced a wealth of information on the basis for target site sequence selectivity (1-6). However, these structures do not resolve the detailed structural mechanism of catalysis. Although acidic and basic groups in the active sites can be identified, and in some cases divalent-metal binding sites delineated, a convincing picture clarifying the way in which the attacking hydroxide ion is generated, and the leaving group stabilized, has not been elucidated for any of the enzymes.EcoRV endonuclease is a homodimer of 244 aa per monomer. It cleaves the duplex sequence 5Ј-GATATC at the central TA step in a blunt-ended fashion (7). As in all type II enzymes, phosphoryl transfer proceeds via attack of a hydroxide ion nucleophile on the scissile phosphorus, generating products containing a 5Ј phosphate group. This reaction occurs by in-line displacement through a pentacovalent transition state, with inversion of stereochemistry at phosphorus and an absolute requirement for divalent metal cations (8, 9). Highresolution crystallographic analyses of EcoRV show that the scissile phosphates of the DNA are located adjacent to the carboxylates of Asp-90 and Asp-74, and that a divalent metal ion bridges the enzyme and DNA at this position (2, 3). Although this metal could stabilize the additional negative charge that develops in the transition state, it is not correctly positioned to generate the attacking hydroxide ion. Thus, speculative mechanisms in which the nucleophile arises from dissociation of a metal-ligated water have invoked significant rearrangements of the DNA from its observed conformation in the crystal structures (2, 10).An alternative mechanism involving substrate-assisted catalysis by the adjacent 3Ј-phosphate of the DNA also has been proposed (11,12). In support of this mechanis...

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“…-fold rate enhancement provided by EcoRV relative to the uncatalyzed hydrolytic cleavage of DNA phosphate diesters (34).…”

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confidence: 99%

Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases

Horton

Newberry

Perona

1998

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

108

151

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“…Molecular Designing. Molecular designing was based upon the x-ray crystallographic structure of distamycin A (compound 1) complexed in the minor groove of d(CGCAAATT-TGCG)2 (17). As shown by this x-ray structure and numerous binding studies (24), the crescent-shaped distamycin tripeptide binds at AT-rich regions of DNA with a binding constant of about 106 M-1.…”

Section: Resultsmentioning

confidence: 99%

“…It has been estimated that the half-life for the hydrolysis of a simple dialkyl phosphate ester at pH 7.0 is about 200 million years (1). It is apparent then why phosphodiester bonds link the letters of the genetic code. Chemists have yet to design and prepare worthwhile catalysts for the hydrolysis of dialkyl phosphate esters.…”

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confidence: 99%

Rational design of substituted tripyrrole peptides that complex with DNA by both selective minor-groove binding and electrostatic interaction with the phosphate backbone.

Bruice

Mei

et al. 1992

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

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The structures of the compounds we call 3a, 3b, and 3c-compounds that incorporate (i) the tripyrrole peptide of the minor-groove-binding distamycin class of compounds and (ii) polyamine ligands that extend from the minor groove and can interact with phosphodiester bonds-were arrived at by computer-graphics designing by using the x-ray structure of distamycin A complexed in the minor groove of d(CGCAAATTTGCG)2. Compounds 3a, 3b, and 3c are elaborations ofdistamycin analog 2, designed for improved stability in solution and easier synthesis and purification, which itself binds weakly to DNA. Compounds 3a, 3b, and 3c have been synthesized, and the interaction of distamycin A, 2, 3a, 3b, and 3c with calf thymus DNA, poly(dA-dT), poly(dG-dC), poly(dIdC), pBR322 superhelical plasmid DNA, and, in the case of 3b, T4 coliphage DNA have been studied. The following pertinent conclusions can be drawn. Binding of 3a, 3b, and 3c occurs in the minor groove of DNA and, because of favorable electrostatic interaction of diprotonated polyamine side chains and DNA phosphodiester linkages, the tenacity ofDNA binding and site specificity of3a, 3b, and 3c are comparable to that ofnative distamycin A. 3b has been found to induce changes in the superhelical density of pBR322 plasmid DNA. The study establishes that the central pyrrole N-CH3 substituent of 2 can be replaced by bulky polyamine metal ligands to create any number of compounds that bind into the minor groove at A+T-rich sites and are putative catalysts for the hydrolysis of DNA.It has been estimated that the half-life for the hydrolysis of a simple dialkyl phosphate ester at pH 7.0 is about 200 million years (1). It is apparent then why phosphodiester bonds link the letters of the genetic code. Chemists have yet to design and prepare worthwhile catalysts for the hydrolysis of dialkyl phosphate esters. This remains a desirable goal. Having small molecules that catalyze the hydrolysis of DNA at given sequences could be of great advantage in the study of DNA structure and function.The desired characteristics of a small molecule capable of hydrolyzing DNA would include: (i) its binding to a specific base sequence of DNA, and (ii) a catalytic site holding metal ions or protons and a nucleophile juxtaposed to the phosphodiester bond. The hydrolysis of DNA phosphodiester linkages is catalyzed by nuclease enzymes, which require metal ions for their activity. Both Mg2" and Zn2+ are directly involved in the 3'-to-5' exonuclease activity of the Klenow fragment of DNA polymerase I from Escherichia coli. Evidence for the catalytic role of the metal ions comes from the x-ray crystallographic data of a cocrystal of DNA and the Klenow fragment (2, 3). It has been proposed that the established (4) in-line displacement of the 5' oxygen is by HO-ligated to the Zn2+ and that the incipient 5' oxyanion leaving group is coordinated by Mg2'. A combination of two metals has also been reported as essential to phosphodiester hydrolysis by E. coli alkaline phosphatase (5) and phospholipase C from...

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“…Bis-p-nitrophenyl phosphate (BNPP) is a phosphodiester compound that can be used as a model to study the hydrolysis of P-O bonds by catalytic interaction with metal nanoparticles. The stability of this molecule is relatively high; its t 1/2 is 2000 years in water at 20 °C and 53 years in water at 50 °C [5]. The hydrolytic cleavage of this molecule assisted by transition metal complexes is well-known [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Degradation of bis-p-nitrophenyl phosphate using zero-valent iron nanoparticles

Valle‐Orta

Díaz

Zumeta-Dubé

et al. 2017

J. Phys.: Conf. Ser.

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Abstract. Phosphate esters are employed in some agrochemical formulations and have long life time in the Environment. They are neurotoxic to mammals and it is very difficult to hydrolyze them. It is easy to find papers in the literature dealing with transition metal complexes used in the hydrolysis processes of organophosphorous compounds. However, there are few reports related with degradation of phosphate esters with inorganic nanoparticles. In this work bis-4-nitrophenyl phosphate (BNPP) was used as an agrochemical agent model. The BNPP interaction with zero-valent iron nanoparticles (ZVI NPs), in aqueous media, was searched. The concentration of BNPP was 1000 times higher than the ZVI NPs concentration. The average size of the used iron nanoparticles was 10.2 ± 3.2 nm. The BNPP degradation process was monitored by means of UV-visible method. Initially, the BNPP hydrolysis happens through the P-O bonds breaking-off under the action of the ZVI NPs. Subsequently, the nitro groups were reduced to amine groups. The overall process takes place in 10 minutes. The reaction products were identified employing standard substances in adequate concentrations. The iron by-products were isolated and characterized by X-RD. These iron derivatives were identified as magnetite (Fe 3 O 4 ) and/or maghemite (-Fe 2 O 3 ) and lepidocrocite (γ-FeOOH). A suggested BNPP degradation mechanism will be discussed. IntroductionHydrolysis of phosphoester bonds is involved in many biological processes. They have close relation to information store and conduction, energy transfer and protein phosphoacylation [1]. Phosphoesters have also been the most widely used as pesticides for many decades. They are a large source of potential hazard to humans [2,3]. These compounds are extremely stable and are highly resistant toward hydrolytic processes [4]. Bis-p-nitrophenyl phosphate (BNPP) is a phosphodiester compound that can be used as a model to study the hydrolysis of P-O bonds by catalytic interaction with metal nanoparticles. The stability of this molecule is relatively high; its t 1/2 is 2000 years in water at 20 °C and 53 years in water at 50 °C [5]. The hydrolytic cleavage of this molecule assisted by transition metal complexes is well-known [6][7][8][9]. However, there are few reports related with degradation of phosphate esters with inorganic nanoparticles.

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Cobalt(III) complex-promoted hydrolysis of phosphate diesters: comparison in reactivity of rigid cis-diaquo(tetraaza)cobalt(III) complexes

Cited by 265 publications

References 1 publication

Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases

Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases

Rational design of substituted tripyrrole peptides that complex with DNA by both selective minor-groove binding and electrostatic interaction with the phosphate backbone.

Degradation of bis-p-nitrophenyl phosphate using zero-valent iron nanoparticles

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