Metal ions that promote the hydrolysis of nucleoside phosphoesters do not enhance intramolecular phosphate migration

Kuusela, Satu; Lönnberg, Harri

doi:10.1002/poc.610060606

Cited by 59 publications

(82 citation statements)

References 22 publications

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“…Metal ions alone accelerate phosphate transfer reactions by up to 2 orders of magnitude (k cat ∕k uncat ) (28), and in enzyme models one metal ion can provide up to 6 orders of magnitude in secondorder rate acceleration [ðk cat ∕K M Þ∕k uncat ] (29,30). The larger accelerations observed here for PMH suggest that the active site provides the potential for additional effects that synergize with the reactivity of the metal ion.…”

Section: Discussionmentioning

confidence: 50%

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

Loo

Jonas

Babtie

et al. 2010

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

164

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We report a catalytically promiscuous enzyme able to efficiently promote the hydrolysis of six different substrate classes. Originally assigned as a phosphonate monoester hydrolase (PMH) this enzyme exhibits substantial second-order rate accelerations (ðk cat ∕K M Þ∕ k w ), ranging from 10 7 to as high as 10 19 , for the hydrolyses of phosphate mono-, di-, and triesters, phosphonate monoesters, sulfate monoesters, and sulfonate monoesters. This substrate collection encompasses a range of substrate charges between 0 and −2, transition states of a different nature, and involves attack at two different reaction centers (P and S). Intrinsic reactivities (half-lives) range from 200 days to 10 5 years under near neutrality. The substantial rate accelerations for a set of relatively difficult reactions suggest that efficient catalysis is not necessarily limited to efficient stabilization of just one transition state. The crystal structure of PMH identifies it as a member of the alkaline phosphatase superfamily. PMH encompasses four of the native activities previously observed in this superfamily and extends its repertoire by two further activities, one of which, sulfonate monoesterase, has not been observed previously for a natural enzyme. PMH is thus one of the most promiscuous hydrolases described to date. The functional links between superfamily activities can be presumed to have played a role in functional evolution by gene duplication.catalytic promiscuity | evolution | mechanism | sulfatase | superfamily E nzymes are usually seen as highly specific catalysts following the classical rule "one enzyme, one activity." This view is challenged by an increasing number of enzymes with broad substrate specificities or side activities indicating that enzymes are catalytically more flexible than originally assumed. Some of these promiscuous enzymes can turn over substrates with different structures while catalyzing the same chemical reaction involving the same transition state (substrate promiscuity). Catalytic promiscuity, by contrast, is the ability of an enzyme to catalyze chemically distinct reactions by stabilization of different transition states (TSs) (1). Catalytic efficiencies (k cat ∕K M ) for the promiscuous substrates are often substantially lower (2 to 9 orders of magnitude) than for the native conversions (1-3). The growing number of examples of this phenomenon (1-4) has engendered excitement on a number of fronts. Catalytic promiscuity provides a functional basis for enzyme evolution by gene duplication. The initial head-start activity of the duplicated gene copy could support an immediate selective advantage (1, 2, 5, 6), to be followed by improvement of the initially weak activity (7). Even low k cat ∕K M values for a promiscuous function can support a significant selective advantage (8). Mimicking this evolutionary shortcut could also provide a more efficient route to changing the function of proteins by directed evolution (5).We describe multiple and efficient catalytic promiscuity in an enzyme from Burkh...

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Section: Discussionmentioning

confidence: 50%

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

Loo

Jonas

Babtie

et al. 2010

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

164

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“…; Scheme 1). By contrast, the isomerization of UpU (3a) to its 2',5'-isomer is not accelerated by metal ions [19] [20]. Fig.…”

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confidence: 79%

“…The rate-accelerating effect of the mononuclear 2 complex is equal to that of the Zn 2 complex of 1,5,9-triazacyclododecane [20] [21]. In all likelihood, the metal ion in 2 is bound to only one of the azacrown moieties, the other one having no effect on the course of the reaction.…”

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confidence: 97%

Bimetallic Complexes of Spiro‐Azacrown Ligands as Catalysts of Phosphoester and Phosphoric Anhydride Cleavage

Wang

Mikkola²,

Lönnberg³

2004

Chemistry & Biodiversity

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The ability of bimetallic homo- and heteronuclear complexes of two spiro-linked ligands, viz. a biazacrown (i.e., 2,6,10,14,18,22-hexaazaspiro[11.11]tricosane (1)) and an azacrown-crown ether (i.e., 14,17,20,23,26-pentaoxa-2,6,10-triaza-spiro[11.15]heptacosane (2)), to promote the cleavage of the phosphoester linkage of dinucleoside 3',5'-phosphates and the phosphoric anhydride bridge of dinucleoside 5',5'-triphosphates was studied. In both reactions, the bimetallic homonuclear Cu2+ and Zn2+ complexes were better catalysts than their monometallic counterparts. The acceleration was two- to five-fold with the phosphoester cleavage and 3- to 20-fold with the phosphoric anhydride cleavage. Interestingly, the most-efficient catalyst of the phosphoester cleavage was the heterodinuclear Ni2+,Zn2+ complex of 1, the catalytic activity of which was up to 5- and 100-fold that of the homodinuclear Zn2+ and Ni2+ complexes, respectively. Moreover, this cooperative acceleration was observed to depend on the identity of the 5'-linked nucleoside: 3',5'-UpU and 3',5'-ApU were cleaved much faster than 3',5'-UpA, and no cooperative acceleration was observed with 3',5'-ApA. The reaction was second-order in hydroxide ion concentration, suggesting that a double deprotonation took place on going from the initial to the transition state. Evidently, in addition to deprotonation of the attacking 2'-OH group, N(3)H of the 5'-linked uridine was displaced by one of the metal ions of the cleaving agent. With the phosphoric anhydride cleavage, no similar cooperativity of two different metal ions was observed, but the greatest rate-acceleration was achieved with the homodinuclear Cu2+ complexes.

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“…First, a 2-aminoethyl sidearm was 25 attached to the free secondary amino function of N 4 ,N 7 ,N 10 -tritert-butoxycarbonylcyclen (3) 8 by ring-opening of N-4-nitrobenzenesulfonylaziridine (4), prepared from ethanolamine as previously described for several other aminoalcohols. 9 Subsequent removal of the 4-nitrobenzenesulfonyl group afforded 30 Boc-protected aminoethyl-functionalized cyclen (6) which was used to displace two of the chloro substituents of cyanuric chloride, giving the protected non-substituted scaffold (7). Finally, the last chloride was displaced by histamine, methylamine or methanol, the Boc protections were removed and 35 the products were converted to free amines (2i, 2n and 2o, respectively) by passing them through an OH --form strong cation exchange resin.…”

Section: Preparation Of the Cleaving Agentsmentioning

confidence: 99%

“…6 It should be noted that the Zn II chelate of cyclen is a poorer catalyst for phosphodiester cleavage than the Zn II chelate of the previously used 1,5,9-triazacyclododecane. 7 It is, hence, expected that the cyclen moieties are only engaged in binding with the uracil bases and are catalytically inactive (Fig. 15 1).…”

Section: Introductionmentioning

confidence: 99%

Mimics of small ribozymes utilizing a supramolecular scaffold

et al. 2012

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For elucidating the mechanism of the general acid/base catalysis of the hydrolysis of RNA phosphodiester 5 bonds, a number of cleaving agents having two cyclen moieties tethered to a 1,3,5-triazine core have been prepared and their ability to bind and cleave UpU studied over a wide pH range. Around neutral pH, the cleaving agents form a highly stable ternary complex with UpU and Zn II through coordination of the uracil N3 and the cyclen nitrogen atoms to the Zn II ions. Under conditions where the triazine core exists in the deprotonated neutral form, hydrolysis of UpU, but not of ApA, is accelerated by approximately two 10 orders of magnitude in the presence of the cleaving agents, suggesting general base rather than metal ion catalysis. The probable mechanism of the observed catalysis and implications to understanding the general acid/base-catalyzed phosphodiester hydrolysis by ribozymes are discussed.

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Metal ions that promote the hydrolysis of nucleoside phosphoesters do not enhance intramolecular phosphate migration

Cited by 59 publications

References 22 publications

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

Bimetallic Complexes of Spiro‐Azacrown Ligands as Catalysts of Phosphoester and Phosphoric Anhydride Cleavage

Mimics of small ribozymes utilizing a supramolecular scaffold

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