A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium leguminosarum

Jonas, Steven; Loo, Bert van; Hyvönen, Marko; Hollfelder, Florian

doi:10.1016/j.jmb.2008.08.072

Cited by 64 publications

(157 citation statements)

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“…The x-ray structure of BcPMH confirms that it is structurally and mechanistically closely related to arylsulfatases and also, albeit more distantly, to AP and nucleotide phosphodiesterase (11,13). These three enzymes catalyze at least two reactions besides their native activity that are the native reactions of another family member (14)(15)(16)(17)(18)(19).…”

Section: Discussionmentioning

confidence: 60%

“…The fGly residue that results from the oxidation of Cys57 (Fig. 3D) is likely to contribute to catalysis in its deprotonated state (11), represented by pK E 1. The protonated forms of residues His218 and Lys337 ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…However, the presence of other metal ions with occupancies <10% cannot be excluded. Furthermore, Mn 2þ ions are known to increase enzyme activity (9), and in RlPMH, Mn 2þ has been suggested as the native metal ion (11). Indeed, when BcPMH was coexpressed with MtbFGE to increase the fGly-modification efficiency, 0.19 eq Mn, 0.29 eq Ca, 0.40 eq Fe, and 0.36 eq Zn were detected by microPIXE.…”

Section: Resultsmentioning

confidence: 99%

“…By contrast, imperfect catalysts perform only one turnover: If the covalent intermediate is not broken down, substrates become in effect suicide inhibitors. We hypothesize that the fGly nucleophile provides a solution to this problem: The breakdown of all intermediates is expected to occur by cleavage of the C-O bond in the second step (11,12) (Fig. 3D, shown in red).…”

Section: Discussionmentioning

confidence: 99%

“…In a closely related ortholog (RlPMH from Rhizobium leguminosarum; 86% amino acid identity), the unusual formylglycine (fGly) residue, first discovered in type I sulfatases (10), was shown to act as a nucleophile. fGly results from enzymatic posttranslational oxidation of a cysteine embedded in a recognition sequence (CxPxR) to an aldehyde (11). On the basis of structural, mutational, and kinetic studies and in analogy to the structurally related arylsulfatases (12), a double displacement mechanism involving a covalent fGly-substrate intermediate was proposed for RlPMH.…”

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confidence: 99%

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An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

Loo

Jonas

Babtie

et al. 2010

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

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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: 60%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

Loo

Jonas

Babtie

et al. 2010

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

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164

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Promiscuous Enzymes

Olguín¹

2013

Proteins in Solution and at Interfaces

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Structural Basis for Copper–Oxygen Mediated C−H Bond Activation by the Formylglycine‐Generating Enzyme

2017

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The formylglycine-generating enzyme (FGE) is aunique copper protein that catalyzes oxygen-dependent C À H activation. We describe 1.66 -a nd 1.28 -resolution crystal structures of FGE from Thermomonospora curvata in complex with either Ag I or Cd II providing definitive evidence for ahigh-affinity metal-binding site in this enzyme.The structures reveal ab is-cysteine linear coordination of the monovalent metal, and tetrahedral coordination of the bivalent metal. Similar coordination changes may occur in the active enzyme as ar esult of Cu I/II redoxc ycling. Complexation of copper atoms by two cysteine residues is common among coppertrafficking proteins,b ut is unprecedented for redox-active copper enzymes or synthetic copper catalysts. Figure 3. Left:Model of FGE curvata as the Cu II superoxo-complex in complex with the peptidyl-cysteine substrate. Right:Proposed catalytic mechanism of FGE (see text for details).T he Cu II superoxo-complex is highlighted in yellow. Angewandte Chemie Communications 8117

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A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium leguminosarum

Cited by 64 publications

References 66 publications

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

Promiscuous Enzymes

Structural Basis for Copper–Oxygen Mediated C−H Bond Activation by the Formylglycine‐Generating Enzyme

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